Bio-Rad GS-900 Calibrated Densitometer User Manual

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Sample Prep + 2-D Electrophoresis + Imaging

2-D

2-D Electrophoresis Workﬂow

How-To Guide

Fourth Edition

2-D Electrophoresis Guide

Table of Contents

About This Guide

This guide describes the experimental methods and tools used in 2-D electrophoresis and proteomics research. It provides background information about technologies common to all proteomics studies as well as protocols and advice you can use as a starting point for your studies. This guide also explains how experimental conditions can be varied and interpreted to optimize your results and provides an extensive set of references that you can consult for more information. Since each sample, experimental approach, and objective is different, this guide offers ideas for developing customized protocols suitable for the analysis of your samples.

Part I: Theory and Product Selection 5

Chapter 1 Overview of Two-Dimensional Electrophoresis

The Context of Proteomics 6

Overview of Experimental Design 6

Sample Preparation 8 First-Dimension Separation: IEF 8 Second-Dimension Separation: SDS-PAGE 8 Detection 9 Image Acquisition, Analysis, and Spot Cutting 9 Protein Digestion and Identiﬁcation by Mass Spectrometry 9

Chapter 2 Sample Preparation 11

The Importance of Sample Preparation 12

General Considerations 12

Cell Lysis 12

Protein Solubilization 15

Chaotropic Agents 15 Detergents 15 Reducing Agents 16 Ampholytes, Buffers, and Other Additives 17

Removal of Interfering Substances 19

General Considerations 19 Nucleic acids (DNA and RNA) 19 Polysaccharides 20 Phenolic Compounds 20 Lipids 20 Salts and Other Small Ionic Compounds 20 Prevention of Keratin Contamination 21

Prefractionation 22

Fractionation by Subcellular Location 22 Fractionation by Solubility/Hydrophobicity 24 Fractionation by Protein Charge 24 Fractionation by pI 25 Fractionation by Size (MW) 26

Depletion and Dynamic Range Reduction 27

Depletion 27 Dynamic Range Reduction 28

ProteoMiner Technology 29

Sample Quantitation (Protein Assays) 30

Chapter 3 The First Dimension: Isoelectric Focusing (IEF)

Protein Separation by Isoelectric Point (pI) 34

IEF Media: IPG Strips vs. Carrier Ampholytes 35

Selection of IPG Strips 36

Choice of pH Gradient 36 Choice of IPG Strip Length 36

Estimation of pl 37

Sample Application 38

Sample Application during Rehydration 38 Sample Application by Cup Loading 39

Setup for IEF 39

Power Conditions for IEF 40

Chapter 4 The Second Dimension: SDS-PAGE

Protein Separation by Size 44

Selection of Polyacrylamide Gels 44

Choice of Gel Percentage (Composition) 45 Choice of Gel Size 47 Choice of Buffer System 47

Transition from First to Second Dimension 52

Power Conditions and Reagents for SDS-PAGE 52

Molecular Weight Estimation 53

Chapter 5 Detection 55

Detection of Proteins in Gels 56

Coomassie Stains 56 Silver Stains 57 Fluorescent Stains 57 Negative Stains 57 Stain-Free Technology 57

Detection of Proteins on Western Blots 61

Bio-Rad’s Proteomics Program

From sample preparation to protein analysis, Bio-Rad’s tools provide you with choices in methodology, protocols, and products. Our informative 2-D Electrophoresis and Analysis Applications and Technologies web pages are a valuable resource with video tutorials, protocols, troubleshooting tips, and much more. To learn more, visit www.bio-rad.com/2DElectroAnalysis.

2-D Electrophoresis Guide Table of Contents

Chapter 6 Image Acquisition, Analysis, and Spot Cutting

Finding Protein Spots of Interest 64

Image Acquisition 64

Image Analysis 65

Image Optimization, Spot Detection, and Quantitation 66 Gel Comparison 66 Data Normalization 66 Data Analysis and Reporting 67

Spot Cutting from 2-D Gels 67

Chapter 7 Identiﬁcation and Characterization of 2-D Protein Spots

Beyond Excision 70

Proteolytic Digestion 70

Washing 70 Reduction and Alkylation 70 In-Gel Proteolytic Digestion 70

Identiﬁcation by Mass Spectrometry 71

Peptide Mass Fingerprinting 72 Tandem Mass Spectrometry (MS/MS) 73

Establishment of 2-D Databases 73

Part II: Methods 75

Chapter 8 Sample Preparation 75

Tips for Sample Preparation 76

Lysis (Cell Disruption) 76 Protein Solubilization 76

Buffers and Solutions 77

Cell Lysis and Protein Extraction Procedures 78

Suspension Cultured Human Cells 78 Monolayer Cultured Human Cells 78 Mammalian Tissue 79 Microbial Cultures 79 Plant Leaves 80

Sample Cleanup 81

Buffer Exchange (Desalting) 81

Chapter 9 First-Dimension IEF with IPG Strips

Tips for IEF 86

IPG Strip Rehydration and Sample Loading 86

Performing IEF 87

IPG Strip Rehydration in Rehydration/Equilibration Trays Followed by IEF 87

IEF with Gel-Side Up 87 IEF with Gel-Side Down 88 Cup Loading (IEF with Gel-Side Up) 88 IPG Strip Rehydration in the Focusing Tray Followed by IEF 89

IEF Programming Recommendations 90

Chapter 10 Second-Dimension SDS-PAGE 95

Tips for SDS-PAGE 96

IPG Strip Equilibration 97

Sealing IPG Strips onto SDS-PAGE Gels 98

SDS-PAG E 99

Chapter 11 Protein Detection 101

Tips for Total Protein Staining 102

Long-Term Storage of Stained Gels 10 2

Total Protein Staining 10 3

Bio-Safe Coomassie Stain 103 Flamingo Fluorescent Gel Stain 103 Oriole Fluorescent Gel Stain 104 SYPRO Ruby Protein Gel Stain 104 Silver Stain Plus Kit 105

Chapter 12 In-Gel Trypsin Digestion 107

Tryptic Digestion Protocol 108

Reagents and Solutions 108 Destaining Gel Plugs from Silver-Stained Gels 108 (Pre-Treatment) General Destaining Protocol 109 Reduction and Alkylation Protocol 109 Digestion Protocol 109 Extraction Protocol 109

Part III: Troubleshooting 111

Isoelectric Focusing 112

SDS-PAG E 113

Total Protein Staining 114

2-D Gel Evaluation 115

Part IV: Appendices 125

Appendix A 126

Glossary 126

Appendix B 130

References 130 Related Bio-Rad Literature 132

Appendix C 133

Ordering Information 133

Sample Quantitation (RC DC Protein Assay) 82

Microfuge Tube Assay Protocol (1.5 ml) 82

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2-D Electrophoresis Guide

Theor y and Product Selection

PART I

Theory and Product Selection

CHAPTER 1

Overview of Two-Dimensional Electrophoresis

4 5

2-D Electrophoresis Guide

Chapter 1: Overview of Two-Dimensional Electrophoresis

Theor y and Product Selection

The Context of Proteomics

Proteome analysis (proteomics) is the comprehensive analysis of proteins present in a sample and representing a particular physiological state at a particular point in time. The aim of proteomics is to determine the presence, relative abundance, and posttranslational modiﬁcation state of a large fraction of the proteins in a sample (Wilkins et al. 1996). Since proteins are directly involved in cellular structure, regulation, and metabolism, proteomics can often yield a more informative and accurate picture of the state of a living cell than can analysis of the genome or mRNA.

One of the greatest challenges of proteome analysis is the reproducible separation of complex protein mixtures while retaining both qualitative and quantitative relationships. Many combinations of techniques can be used to separate and analyze proteins, but two-dimensional (2-D) electrophoresis is uniquely powerful in its ability to separate hundreds to thousands of products simultaneously (Choe and Lee 2000). This technique uses two different electrophoretic separations, isoelectric focusing (IEF) and SDS-PAGE, to separate proteins according to their isoelectric point (pI) and molecular weight. The identities of individual protein spots from the gel can then be identiﬁed by mass spectrometry (MS) of their tryptic peptides. Together with computerassisted image evaluation systems for comprehensive qualitative and quantitative examination of proteomes, proteome analysis also allows cataloguing and comparison of data among groups of researchers.

Other common methods of proteome analysis involve the proteolytic digestion of sample proteins and the chromatographic separation of the resulting peptides coupled directly to mass spectrometric analysis. Peptides are identiﬁed by referencing a database, and their proteins of origin are inferred. While these methods are largely automatable and provide an impressive depth of proteome coverage, some information is lost when analyzing protein fragments instead of intact proteins. The 2-D electrophoresis approach maintains proteins in their intact states and enables the study of isoform distribution, which is not possible if the sample is proteolytically digested prior to separation. Since proteins can be selected through image analysis, mass spectrometry need be applied only to the proteins of interest. This is an important consideration when access to instrumentation or the expense of mass spectrometric analysis is a limitation.

The suitability of 2-D electrophoresis to proteome analysis is clear, but its applications also extend to biomarker detection, development of drug and other therapies, and optimization and development of protein puriﬁcation strategies.

Overview of Experimental Design

The general workﬂow in a 2-D electrophoresis experiment (Figure 1.1) and some of the factors affecting the way the experiment is performed are outlined next.

2-D Electrophoresis Workflow

Sample Preparation

Prepare the protein at a concentration and in a solution suitable

for IEF. Choose a method that maintains the native charge,

solubility, and relative abundance of proteins of interest.

First-Dimension Separation: IEF

Separate proteins according to pI by IEF. Select the appropriate IPG

strip length and pH gradient for the desired resolution and sample

load. Select appropriate sample loading and separation conditions.

Second-Dimension Separation: SDS-PAGE

Separate proteins according to size by SDS-PAGE.

Select the appropriate gel size and composition

and separation conditions.

Detection

Visualize proteins using either a total protein stain or ﬂuorescent

protein tags. Select a staining technique that matches

sensitivity requirements and available imaging equipment.

Image Acquisition and Analysis

Capture digital images of the 2-D protein patterns

using appropriate imaging equipment and software.

Then analyze the patterns using 2-D analysis software.

Protein Excision, Digestion, and Identiﬁcation

Excise protein spots of interest from the gel,

digest the proteins, and analyze the digests by MS.

Fig. 1.1. General workﬂow for a 2-D experiment.

6 7

Low MW

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 1: Overview of Two-Dimensional Electrophoresis

Sample Preparation

Effective sample preparation is key for the success of the experiment. The sample dictates the type of extraction technique used, and the solubility, charge, and pI of the proteins of interest affect the method of solubilization. The protein fraction used for 2-D electrophoresis must be solubilized in a denaturing solution of low ionic strength; this solution cannot contain components that alter protein size or charge. Sample preparation also involves optional steps to deplete abundant proteins, reduce the complexity of the protein mixture, or select a subproteome of interest. Details and recommendations for sample preparation can be found in Chapter 2.

First-Dimension Separation: IEF

In 2-D electrophoresis, the ﬁrst-dimension separation step is IEF. Proteins are separated electrophoretically on the basis of their pI, the pH at which a protein carries no net charge. For general proteome analysis,

(IPG) strip and under conditions aimed at completely denaturing and solubilizing all the proteins in the sample (as opposed to native IEF, which aims to preserve native structures and activities). Chapter 3 discusses IEF.

Second-Dimension Separation: SDS-PAGE

The second-dimension separation step is SDS-PAGE, where the proteins already separated by IEF are further separated by their size. Prior to second-dimension separation, an equilibration step is applied to the IPG strip containing the separated proteins. This process reduces any disulﬁde bonds that may have re-formed during the ﬁrst dimension and alkylates the resultant sulfhydryl groups. Concurrently, the proteins are complexed with SDS for separation on the basis of size. Following electrophoretic separation on a slab gel, the result is a two-dimensional array of separated protein “spots” (Figure 1.2). Seconddimension SDS-PAGE is discussed in Chapter 4.

IEF is best performed in an immobilized pH gradient

Sample Preparation

First Dimension

Isoelectric focusing (IEF), separation by pl

Low pH High pH

Second Dimension

SDS-PAGE, separation by MW

High MW

Detection

Proteins separated in gels are usually not visible to the naked eye and must, therefore, be either stained or labeled for visualization. Several factors determine the best choice of staining method, including desired sensitivity, linear range, ease of use, expense, and the type of imaging equipment available. There is no ideal universal stain. Sometimes proteins are detected after transfer to a membrane support by western blotting. These topics are discussed in Chapters 5 and 6.

Image Acquisition, Analysis, and Spot Cutting

The ability to collect data in digital form is one of the major factors that make 2-D gels a practical means of collecting proteome information. It allows the unbiased comparison of samples and gels, transfer of information among research groups, and cataloguing of data. Many types of imaging devices interface with software designed speciﬁcally to collect, interpret, and compare proteomics data.

Once interesting proteins are selected by differential analysis or other criteria, the proteins can be excised from gels and identiﬁed by mass spectrometry. The ExQuest independently or programmed to run from PDQuest

™

spot cutter, which can be operated

™

software, automatically cuts selected protein spots from gels with precision and deposits them into the wells of microplates.

Imaging equipment, software, and the ExQuest spot cutter are discussed in Chapter 6.

Protein Digestion and Identiﬁcation by Mass Spectrometry

The excised gel plugs are destained and enzymatically digested (usually with trypsin) in preparation for identiﬁcation by mass spectrometry. The use of mass spectrometry for precise mass and partial sequence determination, coupled with the availability of protein sequence databases, has made high-throughput protein identiﬁcation possible. An overview of this process is provided in Chapter 7.

Fig. 1.2. 2-D electrophoresis. Protein spots result from two separations: ﬁrst by pI (IEF) and then by size (SDS-PAGE).

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2-D Electrophoresis Guide Theor y and Product Selection

CHAPTER 2

Sample Preparation

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2-D Electrophoresis Guide Theor y and Product Selection

Chapter 2: Sample Preparation

The Importance of Sample Preparation

Sample preparation contributes signiﬁcantly to the overall reproducibility and accuracy of protein expression analysis (Link 1999, Rabilloud 1999, Molloy 2000). Without proper sample preparation, proteins may not separate from one another or may not be represented in the 2-D pattern.

A successful sample preparation strategy enhances separation quality by:



Effectively and reproducibly solubilizing proteins of interest



Preventing protein aggregation and loss of solubility during IEF



Preventing proteolysis or other chemical or enzymatic protein modiﬁcations



Removing or minimizing the effect of contaminants such as salts, detergents, nucleic acids, and other interfering molecules



Yielding proteins of interest at detectable levels, which may require fractionation to reduce protein sample complexity or removal of interfering abundant or irrelevant proteins

This chapter provides an overview of the principles and recent developments in sample preparation strategies prior to ﬁrst-dimension IEF.

General Considerations

Since protein types and sample origins show great diversity, there is no universal sample preparation method. In addition, some proteins simply cannot be solubilized under conditions compatible with IEF. Sample preparation procedures must be optimized empirically and tailored to each sample type and experimental goal. The following general sample preparation guidelines should be kept in mind:



Keep the sample preparation workﬂow as simple as possible; increasing the number of sample handling steps may increase variability and the risk of sample loss



With cell or tissue lysates, include protease inhibitors to minimize artifacts generated by proteolysis; protease inhibitors are generally not required for samples like serum or plasma



Solubilize proteins in a solution that is compatible with IEF. Incubate proteins in 2-D lysis solution for at least 30 min at room temperature (denaturation, solubilization, and disaggregation are timedependent processes)



Determine the amount of total protein in each sample using a protein assay that is compatible with chemicals in your samples



Avoid freeze-thaw cycles; use protein extracts immediately or aliquot them into appropriately sized batches and store them at –70°C

Cell Lysis

The effectiveness of a cell lysis method determines the accessibility of intracellular proteins for extraction and solubilization. Different biological materials require different lysis strategies, which can be divided into two main categories: gentle methods and harsher methods (Table 2.1).



Use gentle cell disruption protocols with cells that lyse easily, such as blood cells and tissue culture cells



Use harsher methods, which are based mainly on mechanical rupture (Goldberg 2008), with biological materials that have tough cell walls (for example, plant cells and tissues, and some microbes)



When working with a new sample, compare at least two different cell disruption protocols with respect to yield (by protein assay) and qualitative protein content (by one-dimensional SDS-PAGE)



Optimize the power settings of mechanical rupture systems and the incubation times of lysis approaches



Mechanical cell lysis usually generates heat; use cooling where required to avoid overheating the sample

A number of other components are often added to disruption protocols. Sand, resin, or glass beads facilitate the disruption of tissues and of plant and yeast cell walls when added to manual grinding procedures. Hypotonic buffers cause cells to burst more readily under physical shearing, and enzymes such as cellulase, pectinase, lyticase, and lysozyme are added to break down plant, yeast, and bacterial cell walls. Nucleases can be added to remove nucleic acids, which can increase sample viscosity and interfere with subsequent separation (see the Removal of Interfering Substances section).

Table 2.1. Suitabilit y of ce ll disruption methods for various sample ty pes.

Yeast, Green Mammalian Algae, Plant Soft Cell Technique Description Bacteria Fungi Seeds Material Tissues Culture

Gentle Methods

Osmotic lysis Suspension of cells in hypotonic solution; — — — — — •

cells swe ll and burst, releasing cellular contents

Freeze-thaw lysis Freezing of cells in liquid nitrogen — — — — — •

and subsequent thawing

Detergent lysis Suspension of cells in detergent-containing — — — — — • solution to solubilize the cell membrane; this method is usually followed by another disruption method, such as sonication

Enzymatic lysis Suspension of cells in iso-osmotic solutions • • — • — — containing enzymes that digest the cell wall (for example, cellulase and pectinase for plant cells, lyticase for yeast cells, and lysozyme for bacterial cells); this method is usually followed by another disruption method, such as sonication

Harsher Methods

Sonication Disruption of a cell suspension, cooled on ice • • — — — •

to avoid heating and subjected to shor t bursts

of ultrasonic waves

French pre ss Application of shear forces by forcing a cell • • — • — •

suspension through a small oriﬁce at high pressure

Grinding Breaking cells of solid tissues and microorganisms • • • • • —

with a mortar and pestle; usually, the mortar is

chilled with liquid nitrogen and the tissue or cells

are ground to a ﬁne powder

Mechanical Homogenization with either a handheld device — — — • • —

homogenization (for example, Dounce and Potter-Elvehjem

homogenizers), blenders, or other motorized

devices; this approach is best suited for soft,

solid tissues

Glass-bead Application of gentle abrasion by vortexing • • — — — •

homogenization cells with glass beads

All but the most gentle cell disruption methods destroy the compartmentalization of a cell, causing the release of hydrolases (phosphatases, glycosidases, and proteases). These enzymes modify proteins in the lysate, which complicates differential analysis. The data generated by 2-D electrophoresis are only meaningful when the integrity of the sample proteins reﬂects the state in which they are found in the living organism. Avoid enzymatic degradation by using one or a combination of the following techniques:



Disrupt the sample or place freshly lysed samples in solutions containing strong denaturing agents such as 7–9 M urea, 2 M thiourea, or 2% SDS. In this environment, enzymatic activity is often negligible



Perform cell lysis at low temperatures to diminish enzymatic activity



Lyse samples at pH >9 by adding a base such as sodium carbonate or Tris(hydroxymethyl)aminomethane (Tris) to the lysis solution (proteases are often least active at basic pH)



Add protease inhibitors to the lysis solution. Examples include either small molecules, such as phenylmethylsulfonyl ﬂuoride (PMSF), aminoethyl-benzene sulphonyl ﬂuoride (AEBSF), tosyl lysine chloromethyl ketone (TLCK), tosyl phenyl chloromethyl ketone (TPCK), ethylenediaminetetraacetic acid (EDTA), and benzamidine, or peptide protease inhibitors such as leupeptin, pepstatin, aprotinin, and bestatin. For best results, use a combination of inhibitors in a protease inhibitor cocktail



If protein phosphorylation is to be studied, include phosphatase inhibitors such as ﬂuoride or vanadate

Following cell disruption:



Check the efﬁcacy of cell disruption by light microscopy (if the sample is a cell suspension)



Centrifuge all extracts extensively (20,000 × g for 15 min at 15°C) to remove any insoluble material; solid particles may block the pores of the IPG strip

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2-D Electrophoresis Guide Theor y and Product Selection

Chapter 2: Sample Preparation

Products for Cell Lysis and Protein Extraction

ReadyPrep™ mini grinders contain a grinding tube, grinding resin, and ﬁtted pestle and offer an easy, efﬁcient mechanism for manually grinding small biological samples. The grinding resin is a neutral abrasive material made of a high-tensile microparticle that does not bind protein or nucleic acids. The combination of the pestle and resin effectively disrupts animal or plant tissues and cells. ReadyPrep mini grinders are available for purchase separately or as components of the MicroRotofor

™

cell lysis kits.

Bio-Rad also offers a range of kits for cell disruption and protein extraction:



MicroRotofor lysis kits

provide convenient, effective methods optimized for the preparation of protein samples from mammalian, plant, yeast, and bacterial sources. Depending on the sample type, these kits employ tissue maceration using ReadyPrep mini grinders and/or solubilization into a chaotropic extraction buffer



The ReadyPrep protein extraction kit (total protein) uses the powerful zwitterionic detergent ASB-14 in a strongly chaotropic solubilization buffer to prepare total cellular protein extracts suitable for 2-D electrophoresis (depending on sample type, additional cell lysis protocols may be needed when using this kit)



Other ReadyPrep protein extraction kits facilitate extraction of speciﬁc classes of proteins and are discussed later in this chapter

Such standardized lysis and extraction protocols are often useful for initial proteomic analyses and

Products for cell lysis and protein ex traction. A number of other ReadyPrep protein extraction kits facilitate disruption and extraction of speciﬁc classes of proteins.

for consistent sample preparation.

For added convenience, the extraction buffer included with these kits can also be used as the sample solution for IEF with the

MicroRotofor cell or with IPG strips.

ReadyPrep Mini Grinder

MicroRotofor Lysis Kit

ReadyPrep Protein Extraction Kit

Protein Solubilization

Proteins in a biological sample are often associated with other proteins, integrated into membranes, or parts of large complexes. Protein solubilization is the process of breaking interactions involved in protein aggregation (Rabilloud 1996), which include disulﬁde and hydrogen bonds, van der Waals forces, and ionic and hydrophobic interactions. If these interactions are not disrupted, proteins can aggregate or precipitate, resulting in artifacts or sample loss. For successful 2-D electrophoresis, proteins must be well solubilized.

Sample lysis solutions typically contain a number of compounds that meet the requirements, both electrically and chemically, for compatibility with IEF. To allow high voltages to be applied during IEF without producing high currents, the compounds must not increase the ionic strength of the solution. In some cases, it may be necessary to prepare samples using additives that facilitate protein solubilization but that have limited compatibility with IEF (for example, salts and SDS). In these cases, the potentially interfering substance must be removed prior to sample application, or actions must be taken to mitigate its effect (see the Removal of Interfering Substances section). See Chapter 9 for sample preparation procedures and solutions; for a thorough discussion of solubilization methods, refer to Rabilloud (2000).

Chaotropic Agents

These compounds disrupt hydrogen bonds and hydrophobic interactions both between and within proteins. When used at high concentrations, chaotropic agents disrupt secondary protein structure and bring into solution proteins that are otherwise insoluble. The neutral chaotropic agent urea is used at 5–9 M, often with up to 2 M thiourea, which can dramatically increase the number of proteins solubilized (Rabilloud et al. 1997). Thiourea is weakly soluble in water but more soluble in high concentrations of urea; therefore, a mixture of 2 M thiourea and 5–8 M urea is used when strongly chaotropic conditions are required. Charged chaotropic agents such as guanidine hydrochloride are incompatible with IEF.

If using thiourea during sample preparation, also add it to the ﬁrst-dimension rehydration solution; otherwise, the proteins that require thiourea for solubility will come out of solution during IEF.

Urea and thiourea can hydrolyze to cyanate and thiocyanate, respectively; these products modify amino groups on proteins (carbamylation) and give rise to artifactual charge heterogeneity. Since heat promotes this hydrolytic reaction, never heat ureaor thiourea-containing solutions above 37°C in the presence of protein (McCarthy et al. 2003).

Detergents

Detergents disrupt hydrophobic interactions between and within proteins and are classiﬁed as neutral, zwitterionic, anionic, and cationic (Luche et al. 2003). Some proteins, especially membrane proteins, require detergents for solubilization during isolation and for maintaining solubility during IEF.

Sample preparation for 2-D electrophoresis commonly uses neutral or zwitterionic (having both positive and negative charges resulting in a neutral net charge) detergents at concentrations of 1–4%, since these detergents do not introduce a net charge and therefore allow proteins to migrate at their own charges during IEF. Examples of neutral detergents include Tween, octylglucoside, dodecyl maltoside, Triton X-100, and Triton X-114. Examples of zwitterionic detergents include CHAPS, CHAPSO, ASB-14, and SB 3-10. In practice, only a few detergents are used in IEF (Table 2.2). With few exceptions, only a single detergent should be used because the effects of detergents are not additive and can be unpredictable in combination. Anionic and cationic detergents are generally not suitable for IEF.

SDS is unparalleled in its ability to efﬁciently and rapidly solubilize proteins. Although SDS is incompatible with IEF as an anionic detergent, it can be used in the initial preparation of concentrated protein samples. In these cases, another IEFcompatible detergent must be used in excess to disrupt the binding of SDS to protein (Ames and Nikaido 1976). Also to be considered is how the detergent interacts with high concentrations of urea. When using SB 3-10, for example, the urea concentration is limited to 5 M, but ASB-14 can be used with 9 M urea (Chevallet et al. 1998).

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2-D Electrophoresis Guide Theor y and Product Selection

Chapter 2: Sample Preparation

Reducing Agents

Reducing agents cleave disulﬁde bond crosslinks within and between protein subunits, thereby promoting protein unfolding and maintaining proteins in their fully reduced states. The compounds used for 2-D sample preparation are either sulfhydryl or phosphine reducing agents. Examples of sulfhydryl reductants include dithiothreitol (DTT), dithioerythritol (DTE), and b-mercaptoethanol (BME). DTT and DTE can be used at lower concentrations than b-mercaptoethanol and are more commonly used, but high concentrations of DTT can affect the pH gradient since its pKa is around 8. Examples of phosphine reductants include tributylphosphine (TBP) and Triscarboxyethylphosphine (TCEP). These reducing agents can be used at lower concentrations and over a wider pH range than the sulfhydryl reductants; however, their use is limited by low solubility and instability (TBP) or a highly charged characteristic (TCEP).

–S– S–

Reducing agents added during protein extraction help to solubilize proteins; during IEF, however, reducing agents such as DTT become depleted from the basic end of pH gradients extending above pH 8, which can cause proteins to aggregate and precipitate (Hoving et al. 2002). The result is streaking and other random spot patterns, particularly in the alkaline regions of the IPG strip (Herbert et al. 2001). To address this problem, proteins can be reduced with TBP and then irreversibly alkylated with iodoacetamide (Figure 2.1). This treatment blocks protein sulfhydryls and prevents proteins from aggregating and precipitating due to oxidative cross-linking, ensuring that proteins remain soluble throughout electrophoresis (Figure 2.2).

pH 3 pH 10

Fig. 2.2. Effect of treatment with the ReadyPrep reduction-alkylation kit. Human HeLa cell extract (100 µg) separated by 2-D electrophoresis (ﬁrst dimension on 11 cm ReadyStrip

™

Flamingo than the untreated sample (left), especially in the basic range of the gel.

protein gel stain. The sample treated with the ReadyPrep reduction alkylation kit (right) and shows much better spot resolution

Untreated

™

IPG strips pH 3–10, second dimension using 12% Criterion™ gels) and stained with

pH 3 pH 10

ReadyPrep reduction-alkylation kit

ReadyPrep Reduction-Alkylation Kit

Bio-Rad’s ReadyPrep reduction-alkylation kit provides the reagents for reduction and alkylation of sample proteins prior to IEF. Its use produces a 2-D pattern with more spots, fewer streaks, and greater reproducibility.

Protein with disulﬁde bridges

S R

Disulﬁde Tributylphosphine Thiols

+ +

Reduction cleaves disulﬁde bridges

and allows unfolding

H2O

Reduction

R—SH

Thiol Iodoacetamide Alkylated thiol

+ + HI

Alkylation with iodoacetamide prevents

disulﬁde bridges from reforming

—SH + R2—HS +

Tributylphosphine oxide

Ampholytes, Buffers, and Other Additives

Sample solution components that modify pH or impart ionic strength affect the solubilization of proteins during sample preparation and strongly inﬂuence 2-D electrophoresis.

Carrier ampholyte mixtures increase both buffering power and ionic strength. Unlike non-ampholytic ions, they do not interfere with IEF and can, in fact, improve protein solubility by “salting in” proteins that are otherwise insoluble under IEF conditions. In addition, carrier ampholytes can diminish proteinmatrix interactions, which tend to occur at the basic end of an IPG strip and lead to streaking caused by precipitation (Righetti and Gianazza 1987). Carrier ampholytes are routinely added to solutions used during IEF with IPG strips and can be of value

during protein extraction as well.

ReadyPrep Reduction-Alkylation Kit

Since proteins are often more soluble and proteases are less active at higher pH, a base such as Tris may be included in a lysis solution to elevate pH.

Many proteins also require ions in solution for optimum solubility. Normally, this is achieved by adding salt to the sample solution; however, adding salt prior to IEF increases conductivity and consequently limits the voltage at which IEF can be performed until the salt is eventually removed from the system. Ions also leave the IPG strip during IEF, causing any protein requiring ions for solubility to precipitate. Proteins also become less soluble as they approach their pI; they may precipitate at their pI in a phenomenon known as isoelectric precipitation or pI fallout.

Alkylation

Fig. 2.1. Reduction and alkylation.

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2-D Electrophoresis Guide Theor y and Product Selection

Chapter 2: Sample Preparation

Table 2. 2. S ummary of compoun ds used in 2-D elec tro phoresi s sample so lutions . Refer to Ordering Information (Appendix C) for c atalog numbers and details of options available for purchase.

Role in Concentration Compound or product Solution Range Comments

Urea Chaotrope 5–9.5 M Present during ﬁrst-dimension IEF

Thiourea Chaotrope 2 M Used with urea, usually in the combination 7 M urea, 2 M thiourea;

CHAPS Detergent 1–4% (w/v) Zwitterionic detergent that may enhance protein solubility with minimal

CHAPSO Detergent 1– 4% (w/v) Zwitterionic detergent similar to CHAPS

NP-40 Detergent 0.5–1% (w/v) Neutral detergent originally used in 2-D electrophoresis (O’Farrell 1975,

Triton X-100 Detergent 0.5–1% (w/v) Neutral detergent similar to NP-40 also used for 2-D sample

SB 3 -10 Deter ge nt 1–2% (w/v) Zwitterionic detergent shown in some cases to give better solubilization

ASB-14 Detergent 1–2% (w/v) Zwitterionic detergent developed for solubilization of membrane

ASB-C8Ø Detergent 1–2% (w/v) Zwitterionic detergent developed for solubilization of membrane

Sodium dodecy l sulfate Detergent Up to 2% (w/v) Anionic detergent widely used in sample preparation for (SDS) during sample electrophoresis and unparalleled in its ability to solubilize protein; preparation, no more also effective at inactivating proteases and other undesirable than 0.2% (w/v) enz ymatic activities. It is, however, incompatible with IEF unless during IEF diluted to 0.2% or less and used with at least an eightfold excess of

Dithiothreitol (DTT) Reductant 20–60 mM Most commonly used sulfhydryl reductant for 2-D electrophoresis

b-Mercaptoethanol Reductant 1–5% (v/v) Sulfhydryl reductant originally used for 2-D electrophoresis (O’Farrell

Tributylphosphine (TBP) Reductant 2 mM Phosphine reductant effective at low concentrations and repor ted

Tris-carboxyethylphosphine Reductant 2–40 mM Phosphine reductant that may be useful during sample preparation; (TCEP) it is highly charged and so is not recommended as the sole reductant

Tris Base 10–40 mM (Unbuf fered) free base often added to sample preparation solutions to

Bio-Lyte

ampholytes Carrier 0.2–1.0% (w/v) Carrier ampholytes may be used during sample preparation to

ampholy te enhance protein solubility. Although IEF with IPG strips does not

more effective than urea alone for solubilizing hydrophobic or high molecular weight proteins

disruptive effect on 2-D electrophoresis (Perdew et al. 1983)

Görg et al. 1988); its use has been largely superseded by CHAPS (Görg et al. 20 04)

preparation (Kawaguchi and Kuramitsu 1995)

than CHAPS; insoluble in higher concentrations of urea and generally used with 5 M urea, 2 M thiourea (Rabilloud et al. 1997)

proteins to be analy zed by 2-D electrophoresis (Chevallet et al. 1998)

proteins to be analyzed by 2-D electrophoresis (Chevallet et al. 1998)

an IEF-compatible detergent such as CHAPS

1975); must be used at a relatively high concentration and can cause disturbances to IEF, so is rarely used

to enhance solubilization of recalcitrant samples (Herbert et al.

1998). It has low water solubility and is unstable and therefore not recommended as the sole reductant for ﬁrst-dimension IEF

present during ﬁrst-dimension IEF

raise the pH to a range where proteolysis is minimal and proteins are optimally soluble. Other bases (for example, potassium carbonate or spermine) are occasionally used as well (Rabilloud 1999). If Tris is used during sample preparation, it should be diluted to 20 mM or less for ﬁrst-dimension IEF, as it may cause disturbances in the basic pH range

require carrier ampholytes for pH gradient generation, the presence of a relatively low (0.2% [w/v]) conce ntration of carr ier ampholy te is essential for optimum resolution. Use pH 3–10 ampholy tes or ampholytes appropriate to the IPG strip pH range

Removal of Interfering Substances

Impurities such as ionic detergents, lipids, nucleic acids, salts and other ionic compounds, and even high-abundance proteins can impact a 2-D electrophoresis experiment by interfering with protein separation or by obscuring proteins of interest. These interfering substances can be endogenous (for example, phenolics, lipids, and nucleic acids) or exogenous (added during sample preparation; for example, salts and detergents). Either way, removing these impurities prior to analysis or mitigating their effect is often essential for good results.

General Considerations

Though removal or mitigation of interfering substances often yields clearer 2-D patterns and improves resolution of protein spots, any treatment of the sample can reduce yield and alter the relative abundance of sample proteins. Procedures for the removal of interfering substances represent a compromise between removal of non-protein contaminants and minimal interference with the integrity and relative abundance of the sample proteins. Since proteomics aims to study the relationship among proteins in their natural state, it is important to remove an interfering substance only when necessary and by using techniques appropriate for the sample.

Protein precipitation is a common general method for contaminant removal. Conditions are chosen under which sample proteins are selectively precipitated while leaving soluble the major nonprotein contaminants. Following centrifugation, the precipitated proteins are resuspended in a solution suitable for IEF. Methods used in sample preparation for 2-D electrophoresis include precipitation with TCA and acetone (Damerval et al. 1986, Görg et al.

1988) and precipitation with methanol and chloroform (Wessel and Flügge 1984). Precipitation procedures also have the beneﬁt of concentrating sample protein, which is often necessary for effective sample application.

Individual types of interfering contaminants cause speciﬁc problems and can be removed or mitigated in different ways. The most prevalent interfering contaminants and their removal methods are discussed next.

Nucleic Acids (DNA and RNA)

Nucleic acids, particularly DNA, can interfere with IEF (for example by clogging gel pores) and increase sample viscosity, thus limiting the effectiveness of cell lysis and sample application. Because smaller nucleic acids are generally tolerated better, strategies to reduce nucleic acid interference involve either shearing or enzymatic digestion: sonication shears DNA and renders the sample less viscous, and addition of nuclease digests nucleic acids to oligo- or mononucleotides.

Nucleases are often employed during sample preparation, particularly with bacterial lysates in which nucleic acid:protein ratios are high. Successful application of nuclease treatment requires attention to three factors:



Nucleases may be inactive under the strongly denaturing conditions often used to prepare protein samples for 2-D electrophoresis



DNase requires magnesium ions for activity



Nucleases are proteins and can appear in the 2-D pattern as extra spots

Benzonase is a nuclease with properties that make it particularly useful in sample preparation for 2-D electrophoresis (Chan et al. 2002). It is active in the presence of urea, and the amount required for treatment is usually not visible in a 2-D gel. It is applied in the presence of 1 mM MgSO

or MgCl2.

The magnesium ions are subsequently sequestered with EDTA in order to inhibit proteases that may require metal ions for activity.

18 19

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 2: Sample Preparation

Polysaccharides

Polysaccharides can interfere with electrophoresis by clogging gel pores and by forming complexes with proteins. Like nucleic acids, they can also cause a sample to be viscous, making it difﬁcult to work with. Polysaccharides are a particularly prominent problem with plant-derived samples.

Centrifugation may be used to remove high molecular weight polysaccharides. Phenol extraction, followed by precipitation with ammonium acetate in methanol, is a commonly used method that is very effective at removing polysaccharides in plant samples (Hurkman and Tanaka 1986, Wang et al. 2008).

Phenolic Compounds

Phenolic compounds are found in all plants and in some microorganisms and they can modify proteins in an enzyme-catalyzed oxidative reaction. The modiﬁcation can cross-link proteins together or render them insoluble. The reaction can be prevented with reductants such as DTT, b-mercaptoethanol, or ascorbic acid, and the enzyme is inactivated by thiourea. Phenolic compounds may also be removed from the extract using the ReadyPrep 2-D cleanup kit (see the Products for Contaminant Removal sidebar) or by including polyvinylpyrrolidone (PVP) or polyvinylpolypyrrolidone (PVPP) in the extraction solution. These compounds bind phenolic compounds, and the precipitated complex can be removed from the extract by centrifugation (Toth and Pavia 2001). The phenol extraction

Lipids

Lipids can form insoluble complexes with proteins, but lipids can also complex with detergents, thereby reducing the detergents’ effectiveness at solublilizing protein. The effect of lipids can be minimized by using excess detergent (for example, 4% CHAPS in the lysis solution when preparing lipid-rich tissues such as brain). Precipitation methods that employ organic solvents (Damerval et al. 1986, Görg et al. 1988, Wessel and Flügge 1984) or the ReadyPrep 2-D cleanup kit can also be used to remove lipids.

Salts and Other Small Ionic Compounds

IEF requires samples that are free of salts and other small ionic compounds that may interfere with pH gradient formation. Salts formed from strong acids and strong bases (for example, NaCl) dissociate into their component base and acid, which is eventually drawn to either end of the IPG strip. Until this occurs, the conductivity of the IPG strip remains high and the voltage attained is low. The ﬂow of ions from the IPG strip is accompanied by water ﬂow, and one end of the strip may dry out, breaking electrical contact. Weak acids and weak bases (for example, acetate, Tris, or ammonium ions) may not completely leave the IPG strip during focusing. These compounds interfere with the pH gradient, resulting in streaking and loss of resolution at one end of the pH range or the other (Figure 2.3). Amphoteric buffers such as HEPES can focus within the pH gradient, resulting in a portion of the pH gradient where proteins focus poorly.

procedure described above (see Polysaccharides) is also effective at removing phenolic contaminants (Hurkman and Tanaka 1986, Wang et al. 2008).

Before

Fig. 2.3. Effect of salt removal. E. coli extracts containing 1 M NaCl were separated by 2-D ele ctrophoresis before and after treatment with

the ReadyPrep 2-D cleanup kit. The sample s were focused using 11 cm ReadyStrip pH 3 –10 IPG strips and then separated on Criterion 8–16% Tris-HCl precast gels.

After

Samples of low ionic strength are desired, yet many samples contain salts and small ionic compounds that are either intrinsic to the sample type or have been introduced during sample preparation. Precipitation and dialysis methods are very effective at removing ionic contaminants, as is treatment with a desalting column (Chan et al. 2002).

Prevention of Keratin Contamination

Skin keratin is a common contaminant of 2-D gels and mass spectra. It may appear in silver-stained and ﬂuorescently stained 2-D gels as an artifact focusing near pH 5 in the 50 –70 kD region, or as an irregular but distinctive vertical streaking parallel to the SDS-PAGE direction of migration. The best remedy for this keratin artifact is to avoid introducing it into the sample in the ﬁrst place. Filter all monomer solutions, stock sample buffers, gel buffers, and electrode buffers through nitrocellulose and store them in sealed containers; then, clean the electrophoresis cell thoroughly with detergent. Above all, careful sample handling is important when sensitive detection methods are used, and gloves should be worn while handling samples, solution, or equipment.

Products for Contaminant Removal

For quick and effective contaminant removal, Bio-Rad offers:



ReadyPrep 2-D cleanup kit, which uses an optimized version of a TCA-sodium deoxycholate coprecipitation procedure (Arnold and UlbrichHoffmann 1999) to quantitatively precipitate proteins while removing most interfering substances. The protein precipitation process also enables concentration of proteins from samples that are too dilute, allowing for higher protein loads that can improve spot detection



Bio-Spin® 6 and Micro Bio-Spin™ 6 columns are ready to use and are ﬁlled with Bio-Gel P-6 support for the quick desalting and buffer exchange of protein samples

ReadyPrep 2-D Cleanup Kit

5 cm

Bio- Spin Column

End cap

Reservoir

3.7 cm working bed height

1.2 ml bed volu me

Porous 30 µm polyethylene bed support retains fine particles

Luer end fitting with snap-off tip

3 cm

2 cm working bed height

Micro Bio-Spin Column

End cap

Reservoir

0.8 ml bed volume

Luer end fitting with snap-off tip

20 21

2-D Electrophoresis Guide Theor y and Product Selection



Prefractionation

Proteomic analysis is often applied to samples that have undergone prior fractionation (prefractionation), and the reasons for this are varied. In cases where only a deﬁned subset of the proteome is under study, prefractionation can increase the chances of meaningful discovery by removing proteins not likely to be of interest from the sample. For example, in studies of mitochondrial processes, it is sensible to perform the proteomic analysis on a subcellular fraction enriched in mitochondria. In other cases, speciﬁc proteins of interest may be enriched through fractionation and analyzed by 2-D electrophoresis in the absence of potentially interfering proteins. Prefractionation can also be used to separate a sample into multiple fractions of lower complexity that can then be analyzed separately; this can enable identiﬁcation of lower-abundance proteins that might otherwise be undetectable in the unfractionated sample.

Prefractionation increases the depth of proteome analysis, but it does so at the expense of a greater workload and reduced throughput. Try to use a fractionation method that generates minimal protein overlap between fractions.

Proteins can be fractionated by a number of different techniques. The choice of method depends on the sample, experimental goals, and available instrumentation:



Chemical and centrifugal methods — use of selective precipitation or selective extraction or centrifugation steps to separate proteins or partition different subcellular compartments. In many instances, protein extraction protocols can incorporate fractionation steps through the selective use of certain chemical reagents



Electrophoretic methods — application of liquid-phase IEF or preparative SDS-PAGE with the goal of protein enrichment. Though neither of these techniques is orthogonal to either of the two dimensions employed in 2-D electrophoresis and neither offers additional resolving power to the analysis, electrophoresis has proven useful in allowing the enrichment of low-abundance proteins.

Chromatographic methods — use of chromatographic separation principles to enrich low-abundance proteins or generate fractions of reduced complexity (Fountoulakis et al. 1997, Badock et al. 2001, Butt et al. 2001, Smith et al. 2004, Qin et al. 2005, Yuan and Desiderio 2005). Virtually any chromatographic procedure can be used as a prefractionation step; examples include size exclusion, afﬁnity, ion exchange, and reversephase resins

Using these methods alone or in combination, proteins can be separated upstream of 2-D electrophoresis (prefractionated) by their physical or chemical properties, as described below. Some of these methods, however, may introduce ionic or other contaminants that must be removed before IEF. Also, increasing the number of sample handling steps may increase variability and the risk of sample loss.

Fractionation by Subcellular Location

There are many techniques for preparing fractions enriched in subcellular organelles or membrane types, and there are several examples in which these techniques have been used to prepare samples for 2-D electrophoresis and other proteomic analyses (Huber et al. 2003). Methods for organellar fractionation generally involve differential and density gradient centrifugation (Stasyk et al. 2007, Fialka et al. 1997). However, fractionation schemes involving aqueous polymer phase separation (Tang et al.

2008) and free-ﬂow electrophoresis (Zischka et al. 2003, Eubel et al. 2008) have been described for this purpose as well. These methods are usually speciﬁc for the source material (cells or tissue). In some cases, fractions representing different subcellular sites can be generated on the basis of solubility under different conditions (see the Fractionation by Solubility/ Hydrophobicity section). These methods are more general in application.

Bio-Rad offers several ReadyPrep protein extraction kits for the isolation of fractions enriched in integral membrane and transmembrane proteins (Figure 2.4), as well as nuclear and cytoplasmic proteins (see the Products for Fractionation by Subcellular Location sidebar).

Products for Fractionation by Subcellular Location

Each of the following kits produces a fraction with a distinct protein composition:



ReadyPrep protein extraction kit (signal) takes advantage of the limited solubility of plasma membrane microdomain structures (for example, lipid rafts and caveolae) in nonionic detergents at 4°C to yield a protein pellet that is enriched in membrane-associated signalling proteins, including glycophosphatidylinositol (GPI)-anchored proteins, caveolin and associated proteins, acetylated tyrosine kinases, and G proteins (Simons and Ikonen 1997)



ReadyPrep protein extraction kits (membrane I and membrane II) use different techniques to isolate integral membrane and membrane-associated proteins without the need for density gradients. The membrane I kit is based on temperaturedependent partitioning of hydrophobic proteins into the detergent-rich phase of a Triton X-114/ water two-phase system (Bordier 1981, Prime et al. 2000, Santoni et al. 2000). It is a quick and effective protocol for enriching membrane proteins without the need for ultracentrifugation. More complex membrane proteins (those with

Fig. 2.4. Differences in 2-D patterns obtained using ReadyPrep protein extraction kits: signal (A), membrane I (B), and membrane II (C) kits. Mouse liver samples were extracted using each kit, and puriﬁed proteins we re separated using 17 cm ReadyStrip pH 3 –10 NL IPG strips

and 8–16% gels. Overall spot patterns dif fer for A, B, and C even though all three kits isolate membrane proteins, indicating that e ach kit isolates different sets of proteins.

Chapter 2: Sample Preparation

larger numbers of transmembrane domains) are better isolated using the membrane II kit, which enriches integral membrane proteins by treating a membrane preparation with sodium carbonate (Fujiki et al. 1982, Molloy et al. 2000); this protocol requires ultracentrifugation



ReadyPrep protein extraction kit (cytoplasmic/ nuclear) uses a proprietary buffer and differential centrifugation to isolate intact nuclei and a strongly chaotropic extraction buffer to quickly prepare highly enriched fractions of cytoplasmic and nuclear proteins from eukaryotic samples

ReadyPrep Protein Extraction Kit

A protein in a size- or pI-enriched fraction can be subjected to 2-D electrophoresis at a higher amount relative to the unfractionated sample, allowing the analysis of proteins present below detection levels (Zuo and Speicher 2000, Fountoulakis and Juranville 2003)

22 23

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 2: Sample Preparation

Products for Fractionation by Solubility/Hydrophobicity



ReadyPrep sequential extraction kit is based on a published method (Molloy et al. 1998) that uses sequentially more highly solubilizing chaotrope and detergent mixtures. Applying each extracted fraction to a separate gel allows the resolution of more protein spots



ReadyPrep protein extraction kit (soluble/insoluble) uses a different set of detergents to fractionate proteins on the basis of their solubility in detergents

The ReadyPrep sequential extraction kit and the ReadyPrep protein extraction kit (soluble/insoluble) can be used either independently or sequentially for even greater depth of coverage.

Protein sample

ReadyPrep reagent 1

Collect supernatant 1

Reagent 2

Step 1

Insoluble pellet from reagent 1

ReadyPrep reagent 2

Step 2

Insoluble pellet from reagent 2

Collect supernatant 2

Products for Fractionation by Protein Charge

For prefractionation in a convenient kit format,

™

Aurum exchange) mini kits and columns employ ion exchange chromatography in an easy-to-use spin column format for fractionating and concentrating acidic and basic proteins from small sample volumes (<1 ml). Micro Bio-Spin 6 columns are included for salt removal from the fractionated samples. Requiring only 15–20 min operating time, Aurum ion exchange mini spin columns provide a quick, convenient, and reproducible sample preparation

ReadyPrep Sequential Extraction Kit Aurum I on Exch ange K it

tool for 2-D electrophoresis, and their use can improve detection of low-abundance proteins (Liu and Paulus 2008).

ReadyPrep reagent 3

Collect supernatant 3

Step 3

Insoluble pellet from reagent 3

pH 3 pH 10

AEX (anion exchange) and CEX (cation

Total Protein

pH 3 pH 10

AEX bound fraction

pH 3 pH 10

AEX unbound fraction

Fig. 2.5. Distribution of proteins based on differential solubility using the ReadyPrep sequential extraction kit. The gene ration of three

fractions provides increased resolution of proteins on 2-D gels.

Fractionation by Solubility/Hydrophobicity

Proteins can be separated according to their solubility in different reagents using either chemical or chromatographic methods. Sequential extraction under different solvent conditions can be used to fractionate a protein sample based on solubility, and this strategy has also been used to prepare discrete fractions for analysis by 2-D electrophoresis (Lenstra and Bloemendal 1983, Weiss et al. 1992). Extraction using different detergents can also yield different protein fractions (Figure 2.5), and chromatographic methods that can be used include reverse-phase (Van den bergh and Arckens 2008) and hydrophobic interaction chromatography (McNulty and Annan 2009).

Fractionation by Protein Charge

Ion exchange chromatography has been used to reduce proteome complexity, enrich low-abundance proteins, and improve peptide mass ﬁngerprints (Butt et al. 2001). This technique separates proteins according to their charge at various pHs. It is based on the reversible adsorption of proteins to a solid phase containing charged chemical groups. Cationic (+) or anionic (-) resins (Figure 2.6) attract molecules of opposite charge in the solvent. A variety of systems and media are available for ion exchange chromatography, but because elution involves gradient elution by washing the column with buffers of gradually increasing ionic strength or pH, a subsequent cleanup step must be included.

Fig. 2.6. Fractionation of rat brain tissue using Aurum ion exchange mini columns. Rat brain total protein ex tracts (3 ml) were loaded onto an Aurum AEX column and eluted. The unfractionated and fractionated samples were then treated with the ReadyPrep reduction alk ylation and 2-D cleanup kits and separated by 2-D electrophoresis. Red circles indicate a group of protein spots with increased intensities after fractionation. Blue arrows show t wo repre sentative spots detected only in the gels of the AEX bound fraction.

Fractionation by pI

Fractionation by pI, for example by liquid-phase IEF, may seem counterintuitive as a fractionation technique upstream of the ﬁrst-dimension IEF separation. It can, however, improve downstream sample loading and separation on narrow- and micro-range IPG strips by eliminating proteins outside the pH region of interest (Figure 2.7). This unique separation method can also be coupled to analytical or preparative SDS-PAGE for a powerful, complementary ﬁrst-dimension separation and enrichment strategy for high molecular weight, membrane, hydrophobic, or other proteins that are often underrepresented in IPG-based 2-D gels (Davidsson 2002, Hansson et al. 2004, Brobey and Soong 2007)

Liquid IEF introduces ampholy tes that must be removed, for example

with the ReadyPrep 2-D cleanup kit, before IEF in IPG strips.

24 25

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 2: Sample Preparation

Products for Fractionation by pI

The Rotofor®, Mini Rotofor, and MicroRotofor cells separate and concentrate proteins into discrete fractions by liquid-phase IEF. Following ampholyte removal and sample concentration with the ReadyPrep 2-D cleanup kit, each of the resulting liquid fractions can then be separated on narrow- or micro-range IPG strips.

Rotofor Family o f Liqui d-Ph ase IEF Cells

Unfractionated

pH 3 10

Fraction 3, pH 6 .04

pH 3 10

Fractionation by Size (MW)

Size-dependent separation is a powerful fractionation strategy in studies focused on a particular protein or protein family and their posttranslational modiﬁcations because these proteins tend to be of similar size (Fountoulakis and Juranville 2003). Proteins can be separated into size-dependent fractions by polyacrylamide gel electrophoresis (PAGE), particularly continuous-elution electrophoresis.

Products for Fractionation by Size (MW)

The Model 491 prep cell and mini prep cell perform size-dependent high-resolution fractionation of proteins by continuous-elution gel electrophoresis (using native PAGE or SDS-PAGE). The large sample capacity (50 µl–15 ml, and

0.5–500 mg protein) of these cells makes them particularly effective tools for the enrichment of low-abundance proteins (Zerefos et al. 2006, Xixi et al. 2006, Fountoulakis et al. 2004).

Depletion and Dynamic Range Reduction

One of the major difﬁculties facing proteomics is the issue of dynamic range, or the variation in abundance among sample proteins that typically spans several orders of magnitude. This range typically exceeds that over which proteins can be effectively detected and quantiﬁed. Various strategies have been developed for the reduction of sample dynamic range, and they have proven beneﬁcial for the study of lowabundance proteins.

Depletion

Samples may be dominated by a few abundant proteins whose presence can obscure less abundant proteins and limit the capacity and resolution of the separation technique employed. This is particularly apparent for serum and plasma; the study of lowerabundance proteins from serum or plasma is often complicated by the presence of albumin and immunoglobulin G (IgG), which together contribute up to 90% of the total protein in a serum sample. These proteins obscure comigrating proteins and limit the amount of total serum protein that can be loaded on 2-D gels. To obtain meaningful results from serum samples, these proteins must be removed (Figure 2.8).

A strategy for speciﬁc depletion of abundant proteins by immunoafﬁnity chromatography has been widely used (Pieper et al. 2003, Roche et al. 2009, Tu et al. 2010, Ichibangase et al. 2008). Though this method is effective, the need for antibodies renders it expensive and limits its applicability to the speciﬁc sample type for which the antibodies were developed.

Before

Albumin

After

Albumin

Fig. 2.8. Albumin and IgG removal from serum using the Aur um serum protein mini kit. Serum proteins were separated by 2-D

electrophore sis before and af ter treatment with an Aurum serum protein mini column. Albumin and IgG are removed following treatment with the column, improving resolution of other protein species. Samples (100 µg) were focused on 11 cm ReadyStrip pH 5–8 IPG strips, then run on 8–16% gels.

Heavy-chain IgG

Light-chain IgG

pH 4.7 5.9

Fraction 3, pH 6 .04

Fig. 2.7. Clean fractionation by pI. Mouse liver extract was

fractionated using the MicroRotofor cell. 2-D separations of the unfractionated sample (120 µg) and fractions (30 µg) are shown. Prior to 2-D separation, samples were treated with the ReadyPrep 2-D cleanup kit to remove extra ampholytes. Note the cle an pH bounda ries of f raction 3 and the enrichment of proteins in the pH region it covers.

Model 4 91 Prep C ell and Mini Pr ep Cell

Products for Depletion

Bio-Rad’s Aurum Afﬁ-Gel protein mini kits represent a simple, low-cost alternative to immunodepletion. These kits use afﬁnity chromatography to easily and effectively remove albumin (Afﬁ-Gel Blue) or albumin and IgG (serum protein kit) in a single spin column.

Blue and Aurum serum

Aurum I on Exch ange K it

26 27

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 2: Sample Preparation

Dynamic Range Reduction

ProteoMiner™ protein enrichment technology uses a bead-based library of combinatorial peptide ligands that act as unique binders for proteins (Thalusiraman et al. 2005, Guerrier et al. 2006). When a complex sample is applied to the beads, abundant proteins saturate their speciﬁc ligands while the remaining proteins can be washed away. Low-abundance proteins are concentrated on their speciﬁc ligands and will be enriched relative to the abundant proteins following elution. In contrast to immunodepletion, ProteoMiner has no intrinsic speciﬁcity for any particular sample type and can be used to decrease high-abundance proteins in any sample that could beneﬁt from such a treatment. The technology has been most widely applied to serum and plasma (Sennels et al. 2007); however, several examples of successful application of ProteoMiner to other samples have also been reported (Castagna et al. 2005, Guerrier et al. 2007, D’Ambrosio et al. 2008, Bandhakavi et al. 2009).

ProteoMiner protein enrichment kits:



Decrease the amount of high-abundance proteins without immunodepletion, preventing the loss of proteins bound to high-abundance proteins



Enrich medium- and low-abundance proteins that cannot be detected through traditional methods (Figure 2.9)



Do not rely on a predeﬁned set of antibodies, unlike immunodepletion products



Are compatible with a variety of sample types



Offer a convenient, easy-to-use format



Can be used for differential expression analysis

Untreated

Tre ate d

Fig. 2.9. The ProteoMiner protein enrichment kit improves resolution and spot counts in 2-D gels. In an untreated sample,

albumin and other high-abundance proteins dominate the gel and obscure signals from less abundant proteins. On a gel generated using an equal amount of total protein from a treated serum sample, however, resolution is dramatically improved and a greater number of protein spots is visualized.

ProteoMiner Technology

ProteoMiner technology employs a combinatorial library of hexapeptides bound to a chromatographic support. Combinatorial synthesis creates a large library of unique hexapeptides, with each hexapeptide bound to a stationary support, or bead. Each bead, featuring a unique ligand, is expected to bind speciﬁcally to one or a small number of different proteins in a mixture, and the library of all possible sequences binds proteins up to the capacity of available beads.

Biological sample

(large dynamic range)

Bind mixture

to library

Ligand library

When a complex biological sample is applied to the beads, high-abundance proteins saturate their ligands and excess proteins are washed away. In contrast, low-abundance proteins do not saturate their binding sites. Therefore, different samples retain relative expression levels similar to the original samples. Moreover, low-abundance proteins are enriched if the beads are eluted in a volume smaller than the original sample. The overall effect of ProteoMiner technology results in the bound and eluted material consisting of a signiﬁcantly lower amount of total protein, thus allowing resolution of a greater diversity of species.

Wash away

unbound protein

Elute bound

sample for analysis

Depletion of plasma and serum samples by ProteoMiner technology. Each bead features a different hexapeptide ligand with affinity for specific proteins in a sample. Samples are applied to the beads, allowing proteins to bind to their specific ligands. Proteins in excess are washed away, and those proteins bound to the beads are eventually eluted, allowing further downstream analysis.

28 29

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 2: Sample Preparation

Additional Resources

Samples can be prepared for 2-D electrophoresis using many other techniques. Consult Posch (2008) for more information on:



Sample preparation basics (cell disruption, sample solubilization, protein assays, contaminant removal)



Protein labeling techniques



Fractionation using chemical reagents and chromatography



Fractionation using electrophoresis methods



Enrichment strategies for organelles, multiprotein complexes, and speciﬁc protein classes



Application of sample preparation tools and fractionation strategies to study different biological systems

Sample Quantitation (Protein Assays)

Determine the concentration of protein in a sample (Berkelman 2008) by protein assay to:



Ensure that the amount of protein to be separated is appropriate for the IPG strip length and visualization method



Facilitate comparison among similar samples; image-based analysis is simpliﬁed when equivalent quantities of proteins have been separated

The most commonly used protein assays are visible assays, assays in which the presence of protein causes a visible color change that can be measured with a spectrophotometer (Sapan et al. 1999; Noble and Bailey 2009; see the Protein Assay Products and SmartSpec sidebar). All protein assays utilize a dilution series of a known protein (usually bovine serum albumin or bovine g-globulin) to create a standard curve from which the concentration of the sample is derived (for a protocol describing protein quantitation, refer to Part II of this guide).

™

Plus Spectrophotometer

The chemical components of the sample buffer and the amount of protein available for assay dictate the type of assay that may be used.



Bradford assays (Bradford 1976) — based on an absorbance shift of Coomassie (Brilliant) Blue G-250 dye under acid conditions, when a redder form of the dye is converted into a bluer form upon binding to protein. The increase of absorbance at 595 nm is proportional to the amount of bound dye and, therefore, to the amount (concentration) of protein present in the sample. In comparison to other protein assays, the Bradford protein assay is less susceptible to interference by various chemicals that may be present in protein samples, with the exception of elevated concentrations of detergents like SDS. The response of the Bradford protein assay is only slightly affected by urea, thiourea, and CHAPS in concentrations up to 1.75 M, 0.5 M, and 1% (w/v), respectively



Lowry (Lowry et al. 1951) — combines the reactions of cupric ions with the peptide bonds under alkaline conditions with the oxidation of aromatic protein residues. The Lowry method is based on the reaction of Cu peptide-mediated reduction of Cu

, produced by the

, with FolinCiocalteu reagent (a mixture of phosphotungstic acid and phosphomolybdic acid in the Folin-Ciocalteu reaction). The Lowry assay is intolerant of thiourea, reductants such as DTT, and chelating agents such as EDTA



BCA (bicinchoninic acid, Smith et al. 1985) — BCA reacts directly with Cu mediated reduction of Cu

(generated by peptide-

) to produce a purple end product. The reagent is fairly stable under alkaline conditions and can be included in the copper solution to allow a one-step procedure. Like the Lowry assay, the BCA assay is intolerant of thiourea, reductants such as DTT, and chelating agents such as EDTA

2-D sample solutions typically contain reagents that interfere with all of the assays described above. The Bradford assay may be used on samples that are concentrated enough to be diluted with water so that urea, thiourea, and CHAPS are no longer present at interfering levels (typically at least fourfold). Otherwise, modiﬁed assay procedures may need to be employed (see the Protein Assay Products sidebar).

Protein Assay Products

Protein concentration in 2-D sample solutions is best measured using the RC DC

™

protein assay, a modiﬁcation of the Lowry assay that incorporates a precipitation step that removes

Table 2. 3. Bio-Rad protein assay selection gui de.

Quick Start

Method

Bradford • • — — Lowry — — • •

Description One-step determination; Standard Bradford Detergent compatible Reducing agent not for use with assay, not to be (DC); Lowry assay and detergent SDS-containing samples used with elevated modiﬁed to save time compatible (RC DC) levels of detergents and to be more (>0.1% SDS) accurate

Standard-concentration Assay Sample volume 100 µl 100 µl 100 µl 100 µl Linear range 0.125–1.5 mg/ml 0.125 –1.5 mg/ml 0.125–1.5 mg/ml 0.2–1.5 mg/ml

Low-concentration Assay Sample volume 1 ml 800 µl 200 µl 200 µl Linear range 1.25–25 µg/ml 1.25–25 µg/ml 5 –250 µg/ml 5–250 µg/ml Microplate assay volume 5 µl 10 µl 5 µl ** Minimum incubation 5 min 5 min 15 min 15 min Assay wavelength 595 nm 595 nm 650–750 nm 650 –750 nm

™

Bradford Bio-Rad DC™ RC DC

reducing agents and detergents. For more information on protein quantitation using visible assays, refer to Bio-Rad bulletin 1069.

SmartSpec Plus Spectrophotometer

The color change observed in protein assays is measured using a spectrophotometer. Bio-Rad’s SmartSpec Plus spectrophotometer has preprogrammed methods for protein quantitation and a working wavelength range of 200–800 nm. It can be used for routine applications such as:



Quantitation of proteins via the Bradford, Lowry, and BCA assay methods



Quantitation of DNA, RNA, and oligonucleotides



Monitoring bacterial culture growth



Simple kinetic assays



Wavelength scans with peak detection

Features built into the SmartSpec assay methods facilitate data collection and present a complete analysis of assay results. Bio-Rad also offers compatible quartz and UV-transparent plastic cuvettes.

SmartSpec Plus Spectrophotometer

30 31

2-D Electrophoresis Guide Theor y and Product Selection

CHAPTER 3

The First Dimension: Isoelectric Focusing (IEF)

32 33

COOH

pH = pl

COO

pH > pl

COO



2-D Electrophoresis Guide Theor y and Product Selection

Chapter 3: The First Dimension: Isoelectric Focusing (IEF)

Protein Separation by Isoelectric point (pI)

The ﬁrst-dimension separation of 2-D electrophoresis is IEF, where proteins are separated on the basis of differences in their pI. The pI of a protein is the pH at which it carries no net charge, and it is a characteristic that is determined by the number and types of charged groups the protein carries.

Proteins are amphoteric molecules, which carry a positive, negative, or zero net charge depending on the pH of their environment. For every protein, there is a speciﬁc pH at which its net charge is zero (its pI). Proteins show considerable variation in pI, though pI values usually fall in the range of pH 3–12, with the majority falling between pH 4 and pH 8. A protein is positively charged at pH values below its pI and negatively charged at pH values above its pI (Figure 3.1).

For IEF, a protein is placed in a medium with a pH gradient and subjected to an electric ﬁeld. In response to the ﬁeld, the protein moves toward the electrode with the opposite charge. Along the way, it either picks up or loses protons. Its net charge and mobility decrease until the protein eventually arrives at the point in the pH gradient equal to its pI. There, the protein is

uncharged and stops migrating (Figure 3.2). If, by diffusion, it drifts away from the point in the gradient corresponding to its pI, it acquires charge and is pulled back. In this way, proteins condense, or are focused, into sharp bands in the pH gradient at their characteristic pI values.

IEF proceeds until a steady state is reached. Proteins approach their pI values at different rates but remain relatively ﬁxed at those pH values for extended periods. This is in contrast to conventional electrophoresis (for example, polyacrylamide gel electrophoresis, or PAGE), where proteins continue to move through the medium until the electric ﬁeld is removed. Moreover, in IEF, proteins migrate to their steady-state positions from anywhere in the system. IEF for 2-D electrophoresis is performed under denaturing conditions so that proteins are completely disaggregated and all charged groups are exposed to the bulk solution. Consequently, resolution is best under denaturing conditions. Complete denaturation and solubilization are required to minimize aggregation and intermolecular interactions, thus ensuring that each protein is present in only one conﬁguration.

IEF Media: IPG Strips vs. Carrier Ampholytes

IEF for 2-D electrophoresis is most commonly performed using immobilized pH gradient (IPG) strips. As their name implies, IPG strips contain buffering groups covalently bound to a polyacrylamide gel strip to generate an immobilized pH gradient. The pH gradients are created with sets of acrylamido buffers, which are derivatives of acrylamide containing both reactive double bonds and buffering groups. The general structure is CH R contains either a carboxyl [–COOH] or a tertiary amino group (for example, –N(CH derivatives are covalently incorporated into polyacrylamide gels at the time of casting and can form almost any pH gradient (Righetti 1990).

IPG strips are:



Supplied commercially and ready to use



Prepared on a plastic backing to simplify handling



Highly reproducible and stable over even extended IEF runs (Bjellqvist et al. 1982)



Available in a wide variety of pH gradients and lengths (see the ReadyStrip

=CH–CO–NH–R, where

). These acrylamide

3)2

™

IPG Strips sidebar)

Historically, ﬁrst-dimension IEF was performed using carrier ampholyte–generated pH gradients and tube gels. This type of ﬁrst dimension has been largely superseded by the use of IPG strips for the following reasons:



Carrier ampholyte tube gels must be cast by the user



Carrier ampholyte–generated pH gradients drift over time and are, therefore, not as reproducible as immobilized pH gradients



Carrier ampholytes are complex chemical mixtures, and batch-to-batch variations affect the characteristics of the pH gradient



Narrow pH gradients and gradients encompassing the extremes of the pH range (below pH 4 and above pH 9) cannot be accommodated



Tube gels can be difﬁcult to handle

COOH



COOH



pH < pl

Fig. 3.1. Dependence of protein net charge on the pH of its environment. The pH at which the net charge is 0 is the isoelectric point (pI).

pH = pl

COO



pH > pl

COO

Net Charge

+ 3

+ 2

+ 1

3 4 5 6 7 8 9 10 11 pH

– 1

– 2

– 3

Isoelectric point (pl)

ReadyStrip IPG Strips

IPG strips simplify ﬁrst-dimension separations by immobilizing the pH gradient on an easy-to-handle support strip. ReadyStrip IPG strips are available in a wide selection of pH gradients and strip lengths (from 7 to 24 cm) to ﬁt Bio-Rad vertical electrophoresis cells and gels. Premade ReadyStrip IEF buffers are also available for convenience and maximum reproducibility.

Relative separation. Relative focusing power

is arbitrarily assigned a baseline focusing power of

1.0 to calculate the relative focusing powers of the other strips.

expresses the enhanced resolution expected in the

Anode

Fig. 3.2. Principle of IEF. A mixture of proteins is separated in a pH gradient and within an electric ﬁeld according to each protein’s pI and independently of its size. The proteins migrate until they reach their pI.

3 4 5 6 7 8 9 10

Focusing

Cathode

–

Cathode

–

ﬁrst dimension when using IPG strips of different lengths or pH ranges. The 7 cm pH 3–10 IPG strip

ReadyStrip IPG strip pH ranges.

pH Relative Focusing Power ReadyStrip IEF Buffer

Strip Range* 3 4 5 6 7 8 9 10 7 cm 11 cm 17 cm 18 cm 24 cm 3–10 7–10 3.9–5.1 4.7–5.9 5.5–6.7 6.3–8.3

Broad Range

3–10 1× 1.6× 2.4× 2.6× 3.4× • 3–10 nonlinear (NL) 1× 1.6× 2.4× 2.6× 3.4× •

Narrow range

3–6 2.3× 3.7× 5.7× 6.0× 8.0× • 5–8 2.3× 3.7× 5.7× 6.0× 8.0× • 7–10 2.3× 3.7× 5.7× 6.0× 8.0× • 4–7 2.3× 3.7× 5.7× 6.0× 8.0× •

Micro range

3.9– 5.1 5.8× 9.2× 14.2× 15.0× 20.0× •

4.7–5.9 5.8× 9.2× 14.2× 15.0× 20.0× •

5.5– 6.7 5.8× 9.2× 14.2× 15.0× 20.0× •

6.3–8.3 3.5× 5.5× 8.5× 9.0× 12.0× •

* Strips are designed with sufﬁcient overlap to allow spot matching while limiting the extent of redundant data.

Ready Stri p IPG str ips ar e prep rinte d to indi cate an ode (+) and p H rang e; in addition, a bar code i s prin ted on th e 24 cm str ip.

34 35

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 3: The First Dimension: Isoelectric Focusing (IEF)

Selection of IPG Strips

When selecting the IPG strip, consider both the pH gradient and strip length, as both determine the resolution in the ﬁnal 2-D gel (see the ReadyStrip IPG strips sidebar).

Choice of pH Gradient

IPG strips are available in various pH gradients (see the table in the ReadyStrip IPG Strips sidebar). The pH gradients are linear (pH varies in a linear manner with respect to length of the strip) except in the case of nonlinear pH 3–10 gradients (NL, see the Estimation of pI sidebar).



Use broad-range strips (for example, pH 3–10) for an overview of the spot distribution along the pH gradient and for comparing different sample

in the middle of the pH range 3–10, using NL gradients can improve resolution of proteins in the middle of that range and compress the width of the extreme pH ranges at the ends of the gradients



Use narrow- and micro-range gradients for greater resolution (there is a larger separation distance, more cm of gel, per pH unit). With the exclusion of proteins outside the pH range of the strip, more total protein mass can be loaded per strip to also allow detection of more proteins



Use overlapping pH ranges to increase resolution by expanding a small pH range across the entire width of a gel (Figure 3.3). This also allows the creation of composite gels by matching spots from the overlapping regions using imaging software

preparation strategies. Since many proteins focus

pH 3 –10

pH 3– 6 p H 5– 8 pH 7–10

Fig. 3.3. A mouse liver sample was extr acted in a urea-thiourea-CHAPS solution. T he extract was run in a single PROTEAN® i12™ IEF cell

run on twelve 11 cm ReadyStrip IPG strips simultaneously at each of the following pH ranges: 3–10, 3–6, 5–8, and 7–10. Each pH gradient was run in triplicate. The second dimension for each IPG strip was run in 8 –16% gradient Cr iterion Coomassie stain. The above ﬁgure shows a representative gel image for each pH range.

Choice of IPG Strip Length

IPG strips are available in a variety of lengths that match the size of most commercial second-dimension vertical electrophoresis systems. Shorter strips match mini-format systems, and longer strips match largeformat systems. Deciding which strips to use depends on the requirements for speed, sample volume, resolution, and throughput (see Chapter 4 for more details on selecting size format for 2-D electrophoresis):



Use shorter strips and mini-format gels for fast, convenient sample screening or method development



Use longer strips for the best separation with higher protein loads and for maximum resolution. The longest IPG strips and large-format gels have a large area to resolve protein spots; however, they take a long time to run



Combine different size formats for various beneﬁts. For example, use a mini-format system for rapid optimization of sample preparation methods, then switch to a large format for thorough assessment of a complex sample and identiﬁcation of proteins of interest. In many cases, a mini system and narrowrange IPG strips can then be used to focus in on proteins of interest



Use overlapping narrow- and micro-range IPG strips to increase the effective length of pI resolution. When three narrow-range overlapping ReadyStrip IPG strips (pH 3–6, 5–8, 7–10) are used with the Criterion system, for example, the resolution in the ﬁrst dimension (11 cm strip, pH 3–10 NL) is increased from 11 to 26 cm. When four micro-range strips are used, the resolution in the ﬁrst dimension is expanded from 11 to 44 cm

™

precast gels that were stained with Bio-Safe™

Estimation of pI

The pI of a protein is a useful parameter for protein characterization. With puriﬁed proteins, pI can be determined by IEF using IPG strips, usually under denaturing conditions. Using linear IPG strips, the pH gradient can be assumed to extend linearly between the pH extremes. Knowing the length and pH range of the IPG strip implies that experimental pI values can be assigned with a high level of accuracy (see ﬁgure). Protein pI estimations can also be made using NL IPG strips, assuming the pH proﬁle of the IPG strip is available from the manufacturer; without the exact pH proﬁle of the strip, the pI estimate will be less accurate.

For pI estimation, stain the IPG strips after IEF, for example with Bio-Safe Coomassie blue stain, and then plot the migration distance along the length of the IPG strips of each of the protein standards. Graph A shows the pH gradient along the length of a linear pH 4–7 IPG strip. To determine the pI of an unknown, simply determine the band position (as a percentage of gel length) and read the pI from the graph. In the example, a band positioned at 50% of the gel length will have an estimated pI of 5.5.

The same strategy can be applied for protein spots on 2-D gels, but with less accuracy due to swelling or shrinkage of the 2-D gel. It may also be difﬁcult to deﬁne the start and end positions of the IPG strip on stained 2-D gels.

With knowledge of experimental pI and molecular weight values (see Chapter 4 for details about molecular weight estimation), it is possible to make comparisons with the calculated values derived after protein spot identiﬁcation using mass spectrometry. The calculation of theoretical pI values is possible with software tools available on the Internet, for example at http://web.expasy.org/compute_pi. If the values differ signiﬁcantly from each other, this may indicate a false identiﬁcation or the identiﬁcation of a fragment of the respective protein. However, differences in pI or molecular weight can also suggest posttranslational modiﬁcations, such as phosphorylation or glycosylation. The detection of posttranslational modiﬁcations is a unique strength of gel-based proteomics. These modiﬁcations offer information about the function, regulation, and cellular location of proteins.

A. Linear pH 4 –7 ReadyStrip IPG strip

0 25 50 75 100

B. Nonlinear pH 3–10 ReadyStrip IPG strip

pH pH

0 25 50 75 100

Estimating the pI of a protein fr om its position along an IPG strip. A, By plot ting the pH of an IPG strip as a function of its

length, the pI of a protein may be derived from its focused position on that strip. In the example shown, the pI of a protein that migrates across 50% of the strip length is 5.5. B, pH proﬁle of Bio-Rad ReadyStrip nonlinear pH 3–10 IPG strips.

% Total IPG stri p lengt h

36 37

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 3: The First Dimension: Isoelectric Focusing (IEF)

Sample Application

Commercial IPG strips are dehydrated and must be rehydrated to their original gel thickness (0.5 mm) before use. The protein sample can be applied to the IPG strip either during or after rehydration, and rehydration can be done in either disposable rehydration/equilibration trays or directly in the focusing tray. Sample application during rehydration is the easiest and, in most cases, most efﬁcient way to apply sample. In some instances, however, it is best to rehydrate the IPG strips and then apply sample through sample cups while current is applied (cup loading) (Table 3.1). Each method is discussed in the following sections.

The rehydration solution generally contains the following components to maintain protein solubility and allow tracking of the separation (see Part II, Methods for recipes):



Chaotrope — urea (8 M or up to 9.8 M if necessary for sample solubility), with or without 2 M thiourea



Detergent — nonionic or zwitterionic detergent such as CHAPS, Triton X-100, or NP-40 at 0.5–4% (w/v)



Reducing agent — 20–100 mM DTT



Ampholytes — 0.2% (w/v), usually pH 3–10; concentrations up to 1% (w/v) may be used, though this reduces the voltage and results in correspondingly longer runs



Tracking dye — a trace of bromophenol blue to render the IPG strip more visible for simpliﬁed handling

The composition of the rehydration solution should also resemble the composition of the sample solution in terms of the additives present to aid solubility. If the sample was prepared using thiourea, the rehydration solution should also contain thiourea. Likewise, the same detergent should be used. Otherwise, transition from one solution to the other can cause precipitation of proteins that are soluble in the sample solution but not in the rehydration solution

Sample Application during Rehydration

In this option, the sample is prepared in, or diluted into, rehydration solution and introduced to the IPG strip at the time of rehydration. As the strips hydrate for at least 12 hr, proteins in the sample are absorbed and distributed over the entire length of the strip (Rabilloud et al. 1994, Sanchez et al. 1997).

Sample application can be in either the absence (passive) or presence (active) of applied voltage:



Active rehydration is performed in the IEF cell. A low voltage (30–100 V) is applied, and proteins enter the gel matrix under current as well as by absorption. Active rehydration with the sample is believed to promote the entry of large proteins into the strip by applying an electrical “pull”



In passive rehydration, proteins enter the gel by absorption only. This allows efﬁcient use of equipment, since strips can be rehydrated in sample rehydration trays while other samples are focused in the IEF cell

and act as a tracking dye for conﬁrmation of focusing

Table 3.1. Advantages and disadvantages of sample loading methods.

Method Advantages Disadvantages

In-gel rehydration Simple sample application Poor resolution of basic proteins

No precipitation at the point of sample application

Accommodates dilute samples and larger protein loads

Passive Focusing can follow rehydration without manual Not all proteins, particularly large or hydrophobic intervention if pe rformed within the IEF instrument proteins, will be taken up

Active More effe ctive with cer tain proteins, particularly those Rehydration must occur within the IEF instrument of high molecular weight

Cup loading More effective for basic proteins Setup more complicated; the cup must form a seal

Can improve resolution at ex tremes of the pH gradient High protein loads are difﬁcult to accommodate; (the end opposite the point of application) concentrated samples are required.

Sample precipitation may occur at the point

with the IPG strip

of application

Whether IPG strips are rehydrated actively or passively, they must be incubated with sample for at least 12 hr prior to IEF. This gives high molecular weight proteins time to enter the gel after the gel has become fully hydrated and the pores have attained full size.

Sample application during rehydration works because IEF is a steady-state technique; therefore, proteins migrate to their pI independently of their initial positions. The advantages of these approaches over cup loading are:



Simplicity



Reduced risk of sample precipitation, which can occur with cup loading at the sample application point if sample concentration is too high (Rabilloud 1999)



Shorter focusing times can be used because the sample proteins are in the IPG strip prior to IEF



Large amounts of protein can be loaded

Sample Application by Cup Loading

To apply samples after IPG strip rehydration, the sample is loaded into sample cups positioned on the rehydrated strip. This technique can be more challenging than in-gel sample loading from a technical standpoint, but it can be beneﬁcial in the following cases (Cordwell et al. 1997, Görg et al. 2000):



When samples contain high levels of DNA, RNA, or other large molecules, such as cellulose



When running acidic and basic IPG strips; for example, pH 7–10



When running micro-range IPG strips spanning ~1 pH unit



For samples that contain large amounts of glycoproteins

Setup for IEF

For IEF, the rehydrated IPG strips are placed into the focusing tray. The orientation (gel-side up or gel-side down) of the IPG strip in the focusing tray is largely determined by the sample loading method employed:



Cup loading requires gel-side up strip placement so that the sample cup may be placed in contact with the gel surface



In-gel sample loading is conducted gel-side down. If the IEF cell is programmed for an unattended start following rehydration, IEF must be conducted gelside down as well



If in-gel sample loading is performed in the rehydration/equilibration tray, IEF may be performed either gel-side up or gel-side down. This is largely a matter of user preference, though improved resolution may be observed with the gel-side up conﬁguration, particularly with higher protein loads

In addition, electrode wicks may be placed between the electrode in the focusing tray and the IPG strip in either running conﬁguration. Electrode wicks serve as a sink for ionic sample contaminants and proteins with pIs outside the pH range of the IPG strip used. They also prevent drying of the ends of the IPG strips during IEF. In some cases, however, the use of electrode wicks has little effect on separation quality, and they may be omitted for convenience in either running conﬁguration if satisfactory results are obtained in their absence.

38 39

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 3: The First Dimension: Isoelectric Focusing (IEF)

Power Conditions for IEF

The pH gradient and the electric ﬁeld strength both inﬂuence the time required to reach steady state and the resolution of the separation. The electric ﬁeld strength is determined by the length of the IPG strip and the applied electrical ﬁeld. In general, narrow pH ranges yield higher resolution and require higher voltages and more time to reach a steady state.

Longer IPG strips can withstand higher programmed voltages and require an increased number of volthours (Vh) for proper focusing. Vh are the product of voltage and time. Because the actual voltage reached is current dependent and the maximum programmed voltage may not be reached, programming the IEF cell with Vh can better ensure that samples receive a consistent number of volts.

The electrical conductivity of the system changes during an IEF run. At the beginning, the current is relatively high because of the large number of charge carriers present. As the proteins and ampholytes move toward their pIs, and as ionic contaminants move to the ends of the IPG strip, the current gradually decreases. When the proteins reach their ﬁnal positions in the pH gradient, there is little ionic movement in the system; the voltage reaches a maximum, and the current reaches a minimum.

Focusing should occur with a gradual increase in voltage followed by a prolonged focusing phase at the maximum voltage advisable for the IPG strip length used and until a set number of Vh have accumulated. The optimum duration depends on the length of the IPG strip and the pH gradient. Current is generally limited to 50 µA per IPG strip, and a streamlined onestep protocol is adequate in most circumstances, as the voltage will rise gradually without the need for a phased focusing protocol with programmed voltage ramping. A more gradual focusing protocol may be advisable in circumstances of heavy protein load, for some narrow- and micro-range IPG strips, or when there are high levels of charged contaminants present. Since the duration of the prolonged focusing phase is speciﬁed in Vh, the actual duration may vary depending on the average voltage during focusing. Focusing may conclude at different times for IPG strips run at the same time with the same protocol. It is important, therefore, to include a hold step during which the IPG strip is held at a relatively low voltage to maintain focusing until the IPG strip can be removed from the instrument.

Electrical current generates heat, which limits the magnitude of the electric ﬁeld that can be applied and the ionic strength of the solutions that can be used. Thin gels dissipate heat better than thick gels and thus better withstand the high voltage that offers higher resolution. Also, as mentioned above, the current drops to a constant low value as focusing reaches a steady state.

PROTEAN i12 IEF System

The PROTEAN i12 IEF system allows multistep runs at durations set by either time or Vh. Recommended starting electrical conditions and voltage ramping options are provided in Part II of this guide; however, sometimes the number of Vh required to complete a run must be determined empirically in a time course experiment. The optimum Vh depends on the sample and the composition of the sample solution as well as the pH gradient of the IPG strip. A more complex sample or different sample buffer might change the Vh required. The time needed to achieve the programmed Vh depends on the pH range of the IPG strip as well as sample and buffer characteristics.

Other IEF cells only support running identical pH gradients and similar samples in batches because the programmed current and voltage are spread across all lanes. If different pH ranges or samples with varying conductivity are run at the same time,

the electrical conditions experienced by individual IPG strips are different. This may expose some strips to more or less current than desired, since the total current limit is averaged over the tray. The individual lane control provided by the PROTEAN i12 IEF cell, however, ensures that the current limit is not exceeded in any IPG strip, even in situations where conductivity differs signiﬁcantly among samples run at the same time.

The PROTEAN i12 IEF cell also allows each lane to be programmed individually, making it possible to run different protocols in different lanes. The ﬂexibility of this system allows running different experiments at once or varying conditions within an experiment to allow optimization in fewer runs. The system also results in better reproducibility because focusing conditions are not inﬂuenced by other samples in the run.

PROTEA N i12 IEF Cell and Acc esso ries

40 41

2-D Electrophoresis Guide Theor y and Product Selection

CHAPTER 4

The Second Dimension: SDS-PAGE

42 43

Mini-PROTEAN TGX

Any kD4–20%4–15%12%10%7.5%

Precision Plus Protein Unstained

250 150

100

250

150

100

250

150

100

250

150

100

250

150

100

250

150

100

Mini-PROTEAN TGX

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 4: The Second Dimension: SDS-PAGE

Protein Separation by Size

The second-dimension separation is by protein size (mass) using SDS-PAGE. The proteins separated in IPG strips by IEF in the ﬁrst dimension are applied to polyacrylamide gels and separated a second time by SDS-PAGE (Figure 4.1).

A two-step equilibration process prepares the proteins for SDS-PAGE. The proteins are complexed with SDS, reduced with DTT, and then alkylated with iodoacetamide. Treatment of the proteins with SDS yields protein-SDS complexes with a consistent charge-to-mass ratio. When electrophoresed through a polyacrylamide gel, these complexes migrate with a mobility that is related logarithmically to mass. As the proteins migrate through the gel, the pores of the gel sieve proteins according to size.

Selection of Polyacrylamide Gels

Polyacrylamide gels are prepared by free radical polymerization of acylamide and a comonomer crosslinker such as bis-acrylamide. By convention, gels are characterized by two parameters that determine pore size: total monomer concentration (%T, in g/100 ml) and weight percentage of crosslinker (%C). SDS-PAGE gels typically have a %C of 2.7%, and the %T is varied to give separation characteristics appropriate to the experimental needs. %T determines the relative pore size of the resulting polyacrylamide gel, with higher %T resulting in smaller pores and separation characteristics more appropriate for smaller proteins.

Gels are either purchased as commercial precast gels or cast in the laboratory using unpolymerized monomer and buffer components. Precast gels are available in smaller formats to ﬁt commercially available electrophoresis cells. These are appropriate for the second dimension when the ﬁrst dimension is run on 7 cm or 11 cm IPG strips. Larger second dimensions are generally run on lab-cast gels.

First Dimension Isoelectric focusing (IEF), separation by pl

Second Dimension

SDS-PAGE, separation by MW

Low pH High pH

High MW

Choice of Gel Percentage (Composition)

Gels for SDS-PAGE are made with either a single, continuous %T throughout the gel (single-percentage gels) or a gradient of %T (gradient gels). Gradient gels are cast with acrylamide concentrations that increase from top to bottom so that the pore size decreases as proteins migrate into the gels. Single percentage gels are cast in the laboratory by simply pouring the appropriate percentage of acrylamide, along with bis-acrylamide, buffer, initiator, and catalyst, into a gel cassette prepared using glass plates and spacers clamped together. The mixture is poured into the cassette and allowed to polymerize. A stacking layer is not necessary for second-dimension gels. Gradient gels may also be cast in the laboratory using solutions of differing acrylamide percentage and a gradient maker. Typical gel compositions are 7.5–20% for single-percentage gels, and 4–15% to 10–20% for gradient gels.

Use protein migration charts and tables to select the gel type that offers optimum separation of your sample (Figure 4.2):



Use single-percentage gels to separate bands of similar size. Since optimum separation occurs in the lower half of the gel, choose a percentage in which the protein of interest migrates to the lower half of the gel



Use gradient gels to separate a broad range of protein sizes. Gradient gels allow resolution of both high- and low-molecular weight bands on the same gel. The larger pore size towards the top of the gel permits resolution of larger molecules, and decreasing pore sizes toward the bottom of the gel restrict excessive separation of small molecules. Gradient gels are often the most appropriate choice for 2-D electrophoresis, which is most often applied to complex samples with proteins spanning a large size range



For new or unknown samples, use a broad gradient gel (for example, 4–20 %T or 8–16 %T or Bio-Rad’s

™ 3

Any kD

formulation) for a global evaluation of the

sample, and then move to an appropriate single-

Precision Plus Protein Unstained

Any kD4–20%4–15%12%10%7.5%

200

116

250

150

100

97.4

21.5

14.4

6.5

250

150

100

200

116

97.4

Fig. 4.2. Examples of migration charts. The protein standards were run on Mini-PROTEAN

250

150

100

Broad Range Unstained

200

116

97.4

21.5

97.4

21.5

14.4

200

116

250

150

100

97.4

21.5

14.4

TGX™ gels.

200

116

250 150

100

Any kD4–20%4–15%12%10%7.5%

200

116

97.4

6.5

21.5

14.4

6.5

percentage gel for more detailed investigation of a particular size range of interest

Low MW

Fig. 4.1. Separation of proteins by SDS -PAGE after separation by IEF. The IPG strip containing proteins already separated by pI is applied to the top of a polyacrylamide gel. The proteins are then separated according to size (MW) by SDS-PAGE.

Bio-Rad’s Any kD formulation provides separation of 10–250 kD

proteins, with the best resolution in to the 20–100 kD range. These gels are useful for screening samples or for 2-D applications aimed at rapid protein analysis.

44 45

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 4: The Second Dimension: SDS-PAGE

Vertical Electrophoresis Systems for SDS-PAGE

The electrophoresis systems offered by Bio-Rad for second-dimension electrophoresis are detailed in the table.



The Mini-PROTEAN system includes the Mini-PROTEAN Tetra cell (with a capacity of up to four gels) and the high-throughput Mini-PROTEAN

3 Dodeca™ cell (for running up to 12 gels). These systems accommodate 7 cm IPG strips and are compatible with handcast or precast Mini-PROTEAN gels (8.6 × 6.7 cm)

Bio-Rad’s vertical electrophoresis systems.

Mini-PROTE AN System Criterion System PROTEAN II System PROTE AN Plus System

Cells Mini-PROTEAN Tetra Cell Criterion Cell PROTEAN II XL Cell PROTE AN Plus Dodeca Cell

Mini-PROTEAN Dodeca Cell Criterion Dodeca Cell PROTEAN II XL Multi Cell

Number of gels 1–4 1–2 1–4* 1–12

1–12 1–12 1–6

Gel formats Mini-PROTEAN precast Criterion precast PROTE AN II ha ndcast PROTEAN Plus handcast

Mini-PROTEAN handcast Criterion empty cassettes

IPG strip length 7 cm 11 cm 17 cm 18 and 24 cm

* For 2-D applications running a maximum of 2 gels at a time is recommended.



The Criterion™ system includes the Criterion cell (for 1–2 gels) and the high-throughput Criterion Dodeca cell (for 1–12 gels); both cells accommodate Criterion precast gels (13.3 × 8.7 cm) and 11 cm IPG strips



The PROTEAN II and PROTEAN Plus Dodeca systems accommodate 17, 18, or 24 cm IPG strips. The PROTEAN II system provides the ability to choose the glass plates, spacer, and sandwich clamps to cast two gel lengths: 16 or 20 cm. The PROTEAN Plus Dodeca cell allows maximum throughput for 2-D electrophoresis, with the capability to run up to 12 2-D gels at a time

PowerPac™ Power Supplies

Power supplies are required to meet the power requirements of numerous applications. The choice of power supply for second-dimension PAGE usually depends on the size and number of gels being run:



Use the PowerPac Basic or PowerPac HC highcurrent power supply for mini-format vertical PAGE applications



Use the PowerPac HV high-voltage or PowerPac Universal power supply for large-format vertical PAGE applications



Use the PowerPac HC power supply for applications that require high currents, such as PAGE with the high-throughput Dodeca cells

PowerPa c HC High -Cu rren t

Power Supply

PowerPac Univer sal

Power Supply

PowerPac Basic

Power Supply

PowerPac HV High-Voltage

Power Supply

Choice of Gel Size

The choice of gel size depends on the same factors determining the length of IPG strip used, namely speed, resolution, and throughput (see the Choice of IPG Strip Length section):



Mini-format systems accommodate short IPG strips (7 cm) and mini-format gels. The short separation distance of the gels maximizes the electrical ﬁeld strength (V/cm) to yield rapid separations with moderate resolution. Use mini gels and systems for rapid analysis and method development



Midi gels and midi-format systems accommodate 11 cm IPG strips and are slightly larger (both in width and length) gels. They still offer rapid runs, but because of the longer separation distance, they provide better coverage than mini-format gels



Large-format systems accommodate 17–24 cm IPG strips and large gels and offer the maximum resolution possible; however, large gel sizes require longer run times

Choice of Buffer System

The pH and ionic composition of the buffer systems used to prepare the gels and samples and to ﬁll the electrode reservoirs determine the power requirements and heavily inﬂuence the separation characteristics of a polyacrylamide gel. Different buffer systems also vary widely in their stability.

Precast Gels for Second-Dimension SDS-PAG E

Bio-Rad offers precast gels in two size formats and in a variety of formulations, some of which feature IPG wells to hold two lengths of ReadyStrip strips (7 cm and 11 cm).

Bio-Rad’s TGX

™

(Tris-Glycine eXtended shelf life) precast gels are Laemmli gels with a proprietary modiﬁcation that extends shelf life to 12 months and allows gels to be run at higher voltages without producing excess heat. The TGX formulation does not require special, expensive buffers. Like Tris-HCl gels, TGX gels use a discontinuous buffer system, with glycinate as the trailing ion, and are, therefore,

™

IPG

The most common buffer system for seconddimension SDS-PAGE is the Tris-HCl system described by Laemmli (Laemmli 1970). The reagents are inexpensive and readily available, and the precast gels are also readily available in a wide variety of gel percentages. The system is robust and highly tolerant of high sample loads. However, Tris-HCl resolving gels are prepared at pH 8.6–8.8; at this basic pH, polyacrylamide slowly hydrolyzes to polyacrylic acid, which can compromise separation. For this reason, Tris-HCl gels have a relatively short shelf life. In addition, the gel pH can rise to pH 9.5 during a run, causing proteins to undergo deamination and alkylation, thereby diminishing resolution and complicating post-electrophoresis analysis.

To alleviate these shortcomings, a number of alternative buffer systems have been developed. For example, bis-Tris, Tris-acetate, and other proprietary buffer systems (see the Precast Gels for Second-Dimension SDS-PAGE sidebar) offer extended shelf life as well as other separation characteristics unique to their formulations.

High-quality precast gels are preferred for highthroughput applications. They provide savings in time and labor, and the precision-poured gradients result in reproducibility among runs.

compatible with conventional Laemmli and Tris/glycine/SDS buffers. These are the best choice when long shelf life is needed and traditional Laemmli separation patterns are desired. TGX Stain-Free

™

gels are Laemmli-like extended shelf life gels that allow rapid ﬂuorescent detection of proteins with the stain-free enabled imagers Gel Doc

™

EZ and ChemiDoc™ MP, eliminating staining and destaining steps. Other precast gel formulations have also been developed to circumvent the shelf life issues of Tris-HCl systems.

46 47

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 4: The Second Dimension: SDS-PAGE

Precast Gels for Second-Dimension SDS-PAGE (contd.)

Gel For mat and For mulation Selection Cr iteria Compos ition Migration (%T)

Mini-PROTEAN* (for 7 cm IPG Strips)

Mini-PROTEAN TGX Laemmli-like extended Any kD Stain-Free shelf life gels 7.5%

7.5% 10% 12%Any kD

10%

Best choice when 12% long shelf life is needed and traditional Laemmli separation patterns are desired

Stain-Free formulation includes an additive for rapid ﬂuorescence detection without staining

Mini-PROTEAN TGX Laemmli-like extended Any kD shelf life gels 7. 5%

250

150

100

150

100

7.5% 10% 12% 4-15% 4-20%Any kD

10%

Best choice when 12% long shelf life is 4 –15% needed and traditional 4–20% Laemmli separation patterns are desired

250

150

100

150

100

Gel For mat and For mulation Selection Cr iteria Compos ition Migration (%T)

Criterion* (for 11 cm IPG Strips)

Criterion TGX Laemmli-like ex tended Any kD shelf life gels 7.5%

4– 20%4–15%18%7. 5% 10% 12% 10– 20%Any kD 8–16%

10% Best choice when 12% long shelf life is 18%

250

150

100

needed and traditional 4 –15% Laemmli separation 4–20% patterns are desired 8 –16 %

10 – 2 0%

250 150

100

250

150

100

150

100

Criterion TGX Laemmli-like ex tended Any kD Stain-Free shelf life gels 7.5%

250

150

100

250

150

100

250

150

100

4– 20%4–15%18%7. 5% 10% 12% 10– 20%Any kD 8–16%

10% Best choice when 12% long shelf life is 18%

250

150

100

250

150

100

25 20

needed and traditional 4 –15% Laemmli separation 4– 20% patterns are desired 8 –16% 10 – 2 0% Stain-Free formulation includes an additive for rapid ﬂuorescence detection without staining

250 150

100

250

150

100

150

100

250

150

100

250

150

100

250

150

100

Mini-PROTEAN Best choice for 16.5% Tris-Tricine separation of low 10–20% MW proteins

10–20%16.5%

Criterion Tris-HCl Reagents are easy to 5% prepare, inexpensive, 7. 5% and readily available 10%

12 . 5%

Best choice when 15% switching between 18% precast and handcast 4–15% gels and need to 4–20% compare results 8–16% 10 – 20% 10 . 5 –14%

18%15%12.5%5% 7.5% 10% 4 –20% 8 –16% 10–20% 10.5–14%4–15%

250 150

250

100

150

250

150

250

100

150

100

250 150 100

250

150 100

250

150

100

25 20

250 150

100

250

150

100

20 25 20

250

150

100

* All gel percentages listed in bold are available in IPG and /or prep-well comb format.

48 49

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 4: The Second Dimension: SDS-PAGE

Precast gels for Second-Dimension SDS-PAGE (contd.)

Gel For mat and For mulation Selection Cr iteria Compos ition Migration (%T)

Criterion* (for 11 cm IPG Strips)

Criterion Stain Free Reagents are easy to 10% Tris-HCl prepare, inexpensive 4–20%

10% 4–20% 8–16%

and readily available 8 –16 %

Best choice when

switching between precast and handcast gels and when comparing results

Stain-Free formulation

includes an additive for rapid ﬂuorescence detection without staining

250 150

250

100

150

100

Criterion XT Bis-Tris Offer long shelf life, 10% but require dedicated 12% sample and r unning 4–12 % buffers

250 150

100

4–12%12%10% 4–12%12%10%

Gel For mat and For mulation Selection Cr iteria Compos ition Migration (%T)

Criterion* (for 11 cm IPG Strips)

Criterion Tris-Tricine Best choice for 16.5% separation of 10–20%

10–20%16.5%

low MW proteins

26.6

17.0

14.0

17.0

14.0

6.5

3.5

1.4

Size, kD

(XT MOPS running buffer)

Criterion XT Offer best resolution of 7% Tris-Acetate high molecular weight 3–8%

Size, kD

(XT MES running buffer)

3–8%7%

proteins, but require dedicated sample and running buffers

Size, kD

(XT Tricine running buffer)

* All gel percentages listed in bold are available in IPG and /or prep-well comb format.

50 51

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 4: The Second Dimension: SDS-PAGE

Casting SDS-PAGE Gels Using Multi-Casting Chambers

In general, proteomics work requires running several IPG strips and second-dimension gels per experiment. It is important that gels have a very similar composition. The best way to ensure that handcast gels have the same composition is to cast them at the same time in a multi-casting chamber. This is especially important when casting gradient gels. Details of the assembly and use of multi-casting chambers are available in their accompanying instruction manuals. Tips that generally apply to all multi-casting systems are:



Before assembling the casting chamber, glass plates should be carefully cleaned with Bio-Rad cleaning concentrate and thoroughly rinsed with deionized water

Apparatus for casting multiple gels. Multi-casting chambers for 12 PROTEAN Plus™ gels or fo r 12 Mini-PROT EAN gels allow unifo rm cast ing of gradi ent gel s. Gradient ma kers are availab le for both size for mats.

Transition from First to Second Dimension

The transition from ﬁrst- to second-dimension gel electrophoresis involves the following:



Equilibration, which involves two steps that treat the focused IPG strips with an SDS-containing buffer to prepare the proteins for SDS-PAGE. The ﬁrst equilibration solution contains buffer, urea, glycerol, reductant, SDS, and dye (optional). The second equilibration step replaces the reductant with iodoacetamide to alkylate the thiol groups. Equilibration ensures the proteins are coated with dodecyl sulfate and all cysteines are reduced and alkylated



Embedding of the strip on the top of the seconddimension gel. The equilibrated IPG strips are placed on top of the gel and sealed in place with molten agarose solution to ensure good contact between the gel and the IPG strip

Methods for equilibrating and embedding IPG strips onto second-dimension gels are available in Part II of this guide.



Each pair of glass plates (two per gel) should be separated from the next by a spacer sheet; the spacer sheet allows easier separation of the cassettes after gel polymerization



The volume of gel solution should be determined by measuring the volume of water needed to ﬁll the assembled glass plates to the desired level in the multi-casting stand



Allow overnight polymerization to compensate for the low concentrations of catalysts (recommended to ensure that polymerization does not start while the gradient gels are being cast)

Power Conditions and Reagents for SDS-PAGE

For SDS-PAGE, use running conditions that provide optimum separation across the size range of interest and that maintain the temperature of the system during operation. For a complete discussion of running conditions and the parameters that affect them, please refer to A Guide to Polyacrylamide Gel Electrophoresis and Detection, Bio-Rad bulletin 6040. For seconddimension SDS-PAGE, include a short, low voltage (50 V) step at the beginning of the run to ensure that all of the proteins are removed from the IPG strip before ﬁnal voltages are applied.

Molecular Weight (MW) Estimation

SDS-PAGE is a reliable method for estimating the MW of an unknown protein. The migration rate of a protein–SDS complex is inversely proportional to the logarithm of its MW: the larger the polypeptide, the more slowly it migrates in a gel. The key to accurate MW determination is selecting separation conditions that produce a linear relationship between log (MW) and migration within the likely MW range of the unknown protein. These parameters are discussed more thoroughly in Molecular Weight Determination by SDS-PAGE (bulletin 3133), and a protocol for MW estimation is provided in Part II of this guide.

For best results, separate the protein sample on the same gel with a set of protein standards. See The Little Book of Standards (bulletin 2414) and the Protein Standards Application Guide (bulletin 2998) for more information regarding selection of protein standards. Mixtures of standard proteins with known MW can be unstained, prestained, or include tags for development with various secondary reagents (useful when blotting). Standards can be run in a reference well or attached to the end of a focused IPG strip by ﬁlter paper onto the second-dimension gel. For convenience, Bio-Rad’s Precision Plus Protein standard plugs (catalog #161-0378), which are embedded in agarose plugs, can also be used.

After separation, determine the relative migration distance (R unknown protein. R a protein divided by the mobility of the ion front (Figure 1). Because the ion front can be difﬁcult to locate, mobilities are normalized to the tracking dye that migrates only slightly behind the ion front:

= (distance to band)/(distance to dye front)

Using the values obtained for the protein standards, plot a graph of log (MW) vs. R should be linear for most proteins, provided they are fully denatured and that the gel percentage is appropriate for the MW range of the sample. The standard curve is sigmoid at extreme MW values, because the sieving affect of the matrix is so large at high MW that molecules are unable to penetrate the gel; but at low MW, the sieving effect is negligible and proteins migrate almost freely. To determine the MW of the unknown protein band, interpolate the value from this graph (Figure 2).

) of the protein standards and of the

is deﬁned as the mobility of

(see below). The plot

Gradient SDS-PAGE gels can also be used to estimate MW. In this case, log (MW) is proportional to log (%T). With linear gradients, %T is proportional to the distance migrated, so the data can be plotted as log (MW) vs. log (migration distance). Standard curves are actually sigmoid. The apparent linearity of a standard curve may not cover the full MW range for a given protein mixture in a particular gel. However, log (MW) varies sufﬁciently slowly to allow fairly accurate MW estimates to be made by interpolation, and even extrapolation, over relatively wide ranges.

1 2 3 4 5 6 7 8

MW, kD

250

150

100

25 20

Fig. 1. Example showing MW determination of an unknown protein. Lane 1, 10 μl of Precision Plus Protein unstained standards;

lanes 2– 8, a dilution series of an E. coli lysate containing a hypothetical unknown protein (GFP). Proteins were separated by SDS-PAGE in a Criterion 4–20% Tris-HCI gel and stained with Bio-Safe Coomassie stain.

3.0

2.0

log MW

y = –1.9944x + 2 .7824

1.0

= 0.997

0 0.2 0.4 0.6 0.8 1.0

Fig. 2. Determining the MW of an unknown protein by SDS-PAGE.

A standard curve of the log (MW) versus R Precision Plus Protein standards from Figure 1. The strong linear relationship (r distance demonstrates exceptional reliability in predicting MW.

> 0.99) between the proteins’ MW and migration

Top of resolving ge l

Migration dista nce of unknown band (45 mm)

was generated using the

Migration

distance

of dye fro nt

(67 mm)

Unknown band

Dye front

Standards Unknown

52 53

2-D Electrophoresis Guide Theor y and Product Selection

CHAPTER 5

Detection

54 55

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 5: Detection

Detection of Proteins in Gels

In 2-D electrophoresis, proteins in gels are most commonly visualized using total protein stains. Selection of the most appropriate stain involves consideration of the stain characteristics, limitations with regard to the sensitivity of detection and the types of proteins it stains best, downstream applications, and the type of imaging equipment available (see Chapter 6). For use in proteomics applications, stains should be compatible with high-throughput protocols and downstream analysis, including digestion and mass spectrometry (Patton 2000).

It is also possible to label protein samples after sample preparation and prior to IEF with ﬂuorescent dyes such as the CyDye DIGE ﬂuors (Westermeier and Scheibe

2008). At the time of writing, three dyes with spectrally different excitation and emission wavelengths were available, allowing labeling of up to three different samples and their separation in a single 2-D gel. The dyes are matched for size and charge to obtain migration of differently labeled identical proteins to the same spot positions. The labeled samples are mixed together before they are applied on the gel of the ﬁrst dimension. After separation, the gels are scanned with ﬂuorescence imagers at the different wavelengths.

The following are general tips for staining 2-D gels:



2-D gels are clearer, sharper, and more reproducible when less protein is loaded. When sample preparation and IEF conditions are not optimized, it is often beneﬁcial to load relatively little protein and to use a relatively sensitive staining technique



To identify low-abundance proteins, apply a high protein load and use a high-sensitivity stain (for example, silver or a ﬂuorescent stain) (Corthals et al. 2000)



To obtain enough protein for mass spectrometry, apply a high protein load and use a compatible staining procedure



For quantitative comparisons, use stains with broad linear ranges of quantitation (for example, Flamingo

™

Oriole

, and SYPRO Ruby)



Since no stain is capable of staining all proteins,

™

consider staining replicate gels with two or more different stains. Coomassie (Brilliant) Blue appears to stain the broadest spectrum of proteins. Therefore, it is instructive, especially with 2-D gels, to stain a Coomassie Blue–stained gel with silver, or to stain a ﬂuorescently stained gel with colloidal Coomassie Blue or silver. Often, this double staining procedure reveals a few differences between the protein patterns. It is possible to stain gels ﬁrst with Coomassie Blue or a ﬂuorescent stain, then again with silver

The sensitivity achievable in staining is determined by:



The amount of stain that binds to the proteins



The intensity of the coloration



The difference in color intensity between stained proteins and the residual background in the body of the gel (the signal-to-noise ratio); unbound stain molecules can be washed out of the gels without removing much stain from the proteins

No stain interacts with all proteins in a gel in precise proportion to their mass, and all stains interact differently with different proteins (Carroll et al. 2000). The only observation that seems to apply for most stains is that they interact best with proteins with a high basic amino acid content.

Coomassie Stains

Coomassie (Brilliant) Blue is the most common stain for protein detection in polyacrylamide gels. Coomassie R-250 and G-250 are fabric dyes that have been adapted to stain proteins in gels. The “R” and “G” designations indicate red and green hues, respectively. These stains generate visible protein patterns that can be analyzed using densitometric methods.

Silver Stains

Silver stains offer high sensitivity but with a low linear dynamic range (Merril et al. 1981). Often, these protocols are time-consuming and complex. Silver staining protocols have multiple steps with critical timing; for this reason, they can be insufﬁciently reproducible for quantitative analysis. In addition, their compatibility with mass spectrometric protein identiﬁcation techniques is lower than Coomassie stains and ﬂuorescent dyes. There are many different silver staining techniques with differing chemistries and sensitivities.

Fluorescent Stains

Fluorescent stains fulﬁll almost all the requirements for an ideal protein stain by offering high sensitivity, a wide linear dynamic range (up to four orders of magnitude), a simple and robust protocol, and compatibility with mass spectrometry. These sensitive stains generate little background and are easy to use.

Because ﬂuorescent stains require specialized instrumentation for imaging, the choice of stain may be dictated by the instrumentation available. Fluorescent dyes absorb light at one wavelength and re-emit the light at another longer wavelength. Imaging instruments differ in both the type of light delivered for absorbance and the capabilities for detecting the emitted light. The simplest and least expensive systems use UV transillumination and a camera for image capture; however, not all ﬂuorescent stains are optimally excited by UV light. Other imaging systems use laser light to scan the gel. Laser light is monochromatic, and the laser must be selected according to the absorbance properties of the dye.

Fluorescent stains can be at least as sensitive as silver stains and are, therefore, subject to some of the same potential problems stemming from high sensitivity. Clean technique is essential, as any dust or dirt transferred to the surface of the gel may appear in the ﬂuorescence image as smudges or speckles. Contaminant proteins such as keratin will also appear in the gel image if care is not taken to minimize such contamination.

All ﬂuorescent reagents are subject to photobleaching to varying degrees. The ﬂuorescent stains discussed in the Protein Stains sidebar are reasonably photostable and do not degrade noticeably through routine exposure to room light during a staining procedure. However, avoid exposure of the gel or staining solution to intense light and cover the staining tray with an opaque lid or foil.

Negative Stains

These rapid stains require only ~15 min for highsensitivity staining and generate protein bands that appear as clear areas in a white background. Zinc and copper stains do not require gel ﬁxation and proteins are thus not altered or denatured. Negative stains can be used as a quality check before transferring to a western blot or analysis by mass spectrometry, though they are not the best choice when quantitative information is desired.

Stain-Free™ Technology

This proprietary Bio-Rad technology allows protein detection in a gel both before and after transfer, as well as total protein detection on a blot when using wet PVDF membranes, without the need for application of a stain (see sidebar).

Not all ﬂuorescent gel stains absorb visible light at wavelengths supplied by imaging lasers.

56 57

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 5: Detection

Protein Stains

Bio-Rad total protein stain selection guide.

Detection Sensitivity MS Total Protein Stain Method (Lower Limit) Time Comments Compatible?

Coomassie Stains Visible

Coomassie (Brilliant) Blue 36–47 ng 2.5 hr Simple and consistent; requires destaining Yes R-250 with methanol

™

Bio-Safe G-250 solution; premixed

Silver Stains Visible

Silver stain 0.6 –1.2 ng 2 hr Stains glycoproteins, lipoproteins, No (Merril et al. 1981) lipopolysaccharides, nucleic acids

Silver Stain Plus (Gottlieb and Chavko 1987)

Dodeca with Dodeca stainers (Sinha et al. 2001)

Fluorescent Stains Fluorescence

Oriole ﬂuorescent 0.5–1 ng 1.5 hr Rapid protocol requires no ﬁxing or Yes gel stain destaining; requires UV excitation

Flamingo ﬂuorescent 0.25–0.5 ng 5 hr Simple protocol requires no destaining; Yes gel stain high sensitivity, broad dynamic range; excellent for laser-based scanners

SYPRO Ruby protein 1–10 ng Overnight Simple, robust protocol; Ye s gel stain broad dynamic range

Negative Stains Visible

Zinc stain 6–12 ng 15 min High-contrast results; simple, fast, and Yes reversible; compatible with elution or blotting as well (Fernandez-Patron et al. 1992)

Copper stain 6 –12 ng 10 min Single reagent; simple, fast protocol and Yes reversible stain; compatible with elution or blotting as well (Lee et al. 1987)

Stain-Free Technology Stain-Free 8–28 ng 5 min No separate staining steps Yes, but ﬂuorescence tryptophan

Coomassie 8–28 ng 1–2.5 hr Nonhazardous staining in aqueous Yes

™

kit 0.6–1.2 ng 1.5 hr Simple, robust protocol Limited

™

silver stain kit 0.25–0.5 ng 3 hr Simple, robust protocol; ideal for use Yes

Coomassie Brilliant Blue R-250 Silver St ain Kit Si lver St ain Plus Kit

residues are modiﬁed

(contd.)

Coomassie Stains

Coomassie R-250 staining solution is prepared for a traditional staining procedure in which gels are stained in a methanol-water-acetic acid solution of Coomassie R-250 dye. It requires ~40 ng protein per spot for detection, though absolute sensitivity and staining linearity depend on the proteins being stained.

Bio-Safe Coomassie stain is a ready-to-use, singlereagent protein stain made with Coomassie (Brilliant) Blue G-250. It offers sensitivity similar to colloidal Coomassie stains (down to 8 ng) and a rapid staining protocol. No additional reagents besides water are required.

Fluorescent Stains

Flamingo ﬂuorescent gel stain is prepared from a dye that binds denatured protein. Normally non-ﬂuorescent in solution, it becomes strongly ﬂuorescent when bound to protein. There is, therefore, no need for destaining, since unbound dye in the gel is only minimally ﬂuorescent. A prolonged ﬁxing step is necessary to wash buffers and SDS out of the gel prior to staining, as these substances can prevent dye binding. Flamingo ﬂuorescent gel stain is the most sensitive of the listed ﬂuorescent stains, with sensitivity to

0.25–0.5 ng, and it can be linear over three orders of magnitude. The simple two-step staining procedure can be completed in as little as ﬁve hours.

With a primary ﬂuorescence excitation maximum at 512 nm and a considerably weaker excitation peak at 271 nm, Flamingo ﬂuorescent gel stain gives the most sensitive results when imaged with laser ﬂuorescence scanning instruments equipped with green or blue laser light sources. UV transilluminatorbased systems may also be used, but extended exposure times may be required and sensitivity will not be as high.

Oriole ﬂuorescent gel stain is sensitive and, of the stains listed, it is the easiest and most rapid to use. The one-step staining process does not require ﬁxation or destaining, allowing protein samples to be accurately visualized and quantitated in less than two hours. Since SDS is required for optimal staining, prior ﬁxing or washing of the gel can impair staining sensitivity.

The dye in Oriole stain is excited only weakly by wavelengths longer than 400 nm and can, therefore, only be imaged using UV-based imaging systems. Oriole’s limit of detection is 1 ng or less in a typical protein spot.

SYPRO Ruby was one of the original ﬂuorescent protein gel stains, and it has a combination of high sensitivity and wide dynamic range that cannot be achieved with traditional Coomassie blue or silver stains. SYPRO Ruby has two prominent absorbance peaks, one at ~270 nm in the UV range and the other at ~460 nm in the visible range. This allows imaging with both UV transilluminator and laserscanning systems. Detection sensitivity in SYPRO Ruby–stained gels can be as low as 1 ng. SYPRO Ruby stains most classes of proteins with little protein-to-protein variability.

The principle advantage of SYPRO Ruby is its versatility with respect to imaging requirements. It is, however, time-consuming to use and does not produce the high-quality mass spectrometric data generated with other ﬂuorescent stains (Berkelman et al. 2009).

Oriole Fluorescent

Gel Stain

Flamingo Fluorescent

Gel Stain

Zinc St ain an d

Destain Kit

Copper Stain

58 59

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 5: Detection

(contd.)

Silver Stains

Three silver staining methods are recommended for use with 2-D gels. Though they are based on slightly different chemistries, they have similar protein sensitivities.

The Bio-Rad silver stain kit, based on the method of Merril et al. (1981), can be up to 100 times more sensitive than Coomassie Blue R-250 dye staining and allows visualization of heavily glycosylated proteins in gels. Protein spots containing 10–100 ng of protein can be easily seen. Proteins in gels are ﬁxed with alcohol and acetic acid, then oxidized in a solution of potassium dichromate in dilute nitric acid, washed with water, and treated with silver nitrate solution. Silver ions bind to the oxidized proteins and are subsequently reduced to metallic silver by treatment with alkaline formaldehyde. Color development is stopped with acetic acid when the desired staining intensity has been achieved. This method is not compatible with mass spectroscopic analysis since the oxidative step affects protein mass.

Silver Stain Plus stain from Bio-Rad, based on the method developed by Gottlieb and Chavko (1987), requires only one simultaneous staining and development step. Proteins are ﬁxed with a solution containing methanol, acetic acid, and glycerol and then washed extensively with water. The gels are then soaked in a solution containing a silver-amine complex bound to colloidal tungstosilicic acid. Silver ions transfer from the tungstosilicic acid to the proteins in the gel by means of an ion exchange or electrophilic process. Formaldehyde in the alkaline solution reduces the silver ions to metallic silver to produce the images of protein spots. The reaction is stopped with acetic acid when the desired intensity

has been achieved. Silver ions do not accumulate within the gel, so background staining is light. Since this method lacks an oxidizing step, visualization of heavily glycosylated proteins and lipoproteins can be less sensitive than with the Merril stain.

Dodeca silver stain is based on the method described by Sinha et al. (2001), in which proteinbound silver ions are chemically reduced to form visible metallic silver. This stain was developed for use with the high-throughput Dodeca stainers and can be used with mass spectrometry.

Stain-Free Technology

A special additive in Bio-Rad’s Criterion Stain Free™, Criterion TGX Stain-Free residues when activated with UV light. This enhances the proteins’ intrinsic ﬂuorescence and shifts the emission into the visible range (>400 nm), allowing protein detection (with a stain-free compatible imager, such as the Gel Doc ChemiDoc after transfer, as well as total protein detection on a blot when using wet PVDF membranes.

This system is ideal for quick sample assessment during puriﬁcation procedures and as a precursor to blotting and proﬁling workﬂows in which Coomassie (Brilliant) Blue staining is ordinarily used. The sensitivity of the Stain-Free system is comparable to that of staining with Coomassie Blue for proteins with a tryptophan content >1.5%; sensitivity superior to Coomassie staining is possible for proteins with a tryptophan content >3%. Proteins that do not contain tryptophan residues are not detected.

™

TGX Stain-Free™, and Mini-PROTEAN®

™

gels covalently modiﬁes tryptophan

™

MP systems) in a gel both before and

EZ or

Dodeca High-Throughput Stainers

Dodeca stainers are high-throughput gel staining devices available in two sizes: the small size accommodates up to 24 Criterion gels while the large size can accommodate up to 12 large-format gels. The stainers feature a shaking rack designed to hold staining trays at an angle to allow air bubbles to escape and ensure uniform gel staining to protect gels from breaking. Use of the stainers ensures high-quality, consistent results and eliminates gel breakage from excess handling. They are compatible with the following stains:



Bio-Safe Coomassie (Brilliant) Blue G-250 stain



Coomassie (Brilliant) Blue R-250 stain



SYPRO Ruby protein gel stain



Flamingo ﬂuorescent protein gel stain



Oriole ﬂuorescent gel stain



Dodeca silver stain kits

Detection of Proteins on Western Blots

Certain synthetic membranes bind proteins tightly and can be used as supports for solid-phase immunoassays, staining, or other analysis. These membranes, known as western blots, are useful for the identiﬁcation of speciﬁc proteins and protein modiﬁcations.

2-D electrophoresis can be combined with western blotting for monitoring the posttranslational modiﬁcation of trace proteins in complex mixtures and evaluating the speciﬁcity of antibodies and antisera. Numerous techniques are available for the transfer of proteins to membranes and for the probing of western blots with antibodies, stains, and other reagents. These techniques are described in more detail in the Protein Blotting Guide (bulletin 2895).

High-Throughput Dodeca Stainers

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2-D Electrophoresis Guide Theor y and Product Selection

CHAPTER 6

Image Acquisition, Analysis, and Spot Cutting

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2-D Electrophoresis Guide Theor y and Product Selection



Finding Protein Spots of Interest

After 2-D gels are stained, the protein patterns can be digitized and analyzed with an image evaluation system comprising an imaging device and analysis software. Following analysis, spots of interest can be excised from gels for further analysis, by mass spectrometry for example (see Chapter 7).

Charge-coupled device (CCD) camera systems can feature different light sources for greater application ﬂexibility. They can be used for visualization of visible and ﬂuorescent stains and of chemiluminescence in some cases. Systems offer transillumination (visible or UV light source underneath the gel or blot) or epi-illumination

Imaging Systems

System Type and Application

Chapter 6: Image Acquisition, Analysis, and Spot Cutting

(colored or white light positioned above the sample).

Image Acquisition

In proteomic applications, selecting the image acquisition device depends on the staining technique used. A number of imaging systems are capable of multiple detection modes and can be used with a variety of applications.



Densitometers enable the visualization of gels stained with visible light–absorbing stains such as Coomassie, negative, or silver stains

Heat in the camera system can manifest as noise, and this noise can prevent detection of faint chemiluminescent signals above the background. Supercooled CCD cameras reduce image noise, allowing detection of faint signals



Laser-based scanners offer the highest sensitivity, resolution, and linear dynamic range. They are powerful image acquisition tools for electrophoresis gels and blots stained with ﬂuorescent dyes. Lasers can be matched to the excitation wavelengths of a multitude of ﬂuorophores

™

GS-900 Densitometer ChemiDoc

Type of imager Densitometer CCD camera-based CCD camera-based Laser-based

Light source options Epi- and Transillumination of UV Transillumination of UV 488 nm external laser

transillumination of and white light* and white light 532 nm internal laser white light 635 nm external laser Epi-illumination by LEDs (red, green, blue, and white)

Optimized applications

Visible stains • • • —

UV light– excited — • • —

ﬂuorescent stains

Visible light– excited — • — • ﬂuorescent stains and labels

Fluorescent multiplexing — • — •

Chemilumine scence — • — —

Stain-Free

* White light conversion screen is required.

™

— • • —

PharosFX™ and

™

MP Gel Doc™ EZ PharosFX Plus

Bio-Rad’s GS-900 calibrated imaging densitometer has transmittance and true reﬂectance capabilities that allow accurate scans of samples that are either transparent (gels and ﬁlm) or opaque (blots). It provides high-quality imaging to resolve close spots and a variable resolution feature to preview and crop images.

Bio-Rad’s ChemiDoc MP supercooled CCD system provides maximum ﬂexibility. It offers transillumination of both UV light (for imaging UV ﬂuorescent stains) and white light (for imaging visible stains). It also offers optional LED epi-illumination in red, green, and blue for single ﬂuorescent stains or ﬂuorescent multiplexing. In addition, it can also image stain-free gels, which require no staining or destaining and are ready for imaging in a matter of

minutes after completing the SDS-PAGE run.

Image Analysis

Following image acquisition, a robust software package is required to analyze and present the data and to draw conclusions from 2-D gel images. The software should provide a variety of tools to enhance the user’s ability to evaluate the acquired data. For example, the software should be able to adjust contrast and brightness and magnify, rotate, resize, and crop gel images. It should measure total and average quantities and determine relative amounts of protein. It should also be capable of determining

The PharosFX systems use multiple lasers, which enhance application ﬂexibility and allow optimum excitation of single- or multicolor ﬂuorescent samples to enable detection of most ﬂuorescent dyes and labels. Computer-controlled, useraccessible ﬁlter wheels have eight ﬁlter slots, supporting multiplex or multicolor ﬂuorescence imaging applications in gels and blots, such as Qdot multiplex blotting, DIGE, and gel staining with Pro-Q stains. The Molecular Imager

PharosFX system has all the features of the PharosFX Plus imager for ﬂuorescence and visible detection, but it lacks the storage phosphor option for imaging radioisotopes.

the presence/absence and up- or downregulation of proteins, their molecular weight, pI, and other values.

Following this initial analysis, computer-assisted image analysis software should allow:



Storage and structuring of large amounts of collected experimental image data



Rapid and sophisticated analysis of experimental information



Supplementation and distribution of data among labs



Establishment of 2-D-protein data banks

64 65

2-D Electrophoresis Guide Theor y and Product Selection

Data Analysis and Reporting

PDQuest™ 2-D Analysis Software EXQuest Spot Cutter

Bio-Rad’s PDQuest 2-D analysis software is used for analyzing and creating databases for 2-D electrophoresis gels. It provides a series of “wizards” for the analysis of digitized gel images and for spot detection and quantitation, gel comparison, and statistical analysis. The Experiment Wizard guides selection of gels for analysis, detection of spots of interest, creation of an experiment, and matching of gels. The Spot Detection Wizard then guides the identiﬁcation and quantitation of the spots in gel images.

After detection, gels in the same series are placed in an experiment for comparison, statistical analysis, and databasing. Histograms allow quick comparisons of the quantities of the same spot in all the gels in an experiment. Spots can also be compared qualitatively, organized into userdeﬁned sets for further analysis, and annotated and databased for easy identiﬁcation. Spots from

Image Optimization, Spot Detection, and Quantitation

Before any software can detect the protein spots of a 2-D gel, raw image data must be optimized and the gel background subtracted.

PDQuest software models protein spots mathematically as 3-D Gaussian distributions and uses the models to determine protein maxima. A 3-D Gaussian spot is a precise representation of an original scanned spot. Gaussian curves are ﬁtted to the scanned spot in the X and Y dimensions, and then additional modeling is performed to create the ﬁnal Gaussian spot. Using Gaussian modeling, it is possible to accurately quantitate overlapping spots, spots in gel streaks, and multiple spots in dense clusters.

The accuracy of automatic spot detection depends on the quality of the 2-D gels and their images. Correction capabilities of PDQuest software can be used to add undetected spots to the list of spots or to delete spots that arise from gel artifacts.

Gel Comparison

The next step in 2-D gel evaluation is identiﬁcation of proteins that are present in all gels of a series. Since inherent problems with gel-to-gel reproducibility affect the positions of spots within a gel series, gel analysis software must be able to detect minor shifts in individual spot position within the gel series.

different experimental series can be organized and compared in higher-level experiments. PDQuest can be used to simultaneously analyze thousands of spots on hundreds of gels. Data can be exported to other applications, such as spreadsheets, for further analysis.

PDQuest software has the further advantage of integration with Bio-Rad’s EXQuest

™

spot cut t e r, which accurately locates and excises protein spots from 2-D gels or blots at high speed (up to 600 spots per hour) and then loads them into 96- or 384-well microplates or 96-tube racks for downstream processing and analysis.

PDQuest has no imaging functions besides driving the camera system in the ExQuest spot cutter, but it can read and import multiple ﬁle formats from other gel imaging software packages like Quantity One

Many software packages for automatic gel comparison are created with the assumption that the relative positions of spots are altered only slightly relative to each other, and they allocate the spots on this basis. Prior to automatic gel comparison, PDQuest software selects the best 2-D gel of a gel series as a reference, or standard gel, and compares all other 2-D gels to this gel. Proteins in a gel series that are not present in the reference gel can be added automatically so that the reference gel includes all proteins of a gel series.

PDQuest includes the ability to match spots with no manual assistance, and it is possible to display up to 100 enlarged details of 2-D gels on the screen simultaneously, enabling rapid and error-free determination of the matching quality.

Data Normalization

When comparing gels in an experiment, there is often some variation in spot size and intensity among gels that is not due to differential protein expression. Multiple normalization methods can be used to compensate for gel-to-gel variations in spot intensity caused by inconsistencies in sample loading, gel staining, and imaging. To accurately compare spot quantities among gels, compensation for these variations in spot intensity, which are not related to expression levels, is required.

With PDQuest software, all gels in a single experiment are viewed as a unit. To compare gels from different experiments, the reference images are compared. In such comparisons, each spot is automatically assigned a number such that identical spots have identical numbers. In an experiment, the molecular weight and pI values for known protein spots can also be entered. With these data, PDQuest can estimate molecular weight and pI values for all the spots in the experiment.

Analysis sets allow the study of sets of proteins that are statistically and scientiﬁcally signiﬁcant and to identify spots to cut using the ExQuest spot cutter. There are six different kinds of analysis sets:



Qualitative analysis sets — spots that are present in one gel but not in another



Quantitative analysis sets — spots whose intensity (amount) has increased or decreased by a certain degree, or whose intensity has changed above, below, or within the fold change factor that you specify



Statistical analysis sets — spots that are signiﬁcant according to the statistical test that you apply



Arbitrary analysis sets — manually selected spots



Boolean analysis sets — created by comparing two or more analysis sets (for example, set C could be made up of those spots present in both sets A and B)



Matching analysis sets — spots that are either unique to one member or present in all members

Once proteins of interest are determined, the corresponding analysis sets are uploaded to the spot cutter. The spots of interest are then excised from the gels and digested to release peptides for analysis by various mass spectrometry methods.

Spot Cutting from 2-D Gels

Spots of interest can be excised from gels either manually (for example, with a scalpel, razor blade, or modiﬁed pipet tip) or with an automated spot cutting system. The advantages of automated systems are numerous and include improved precision and reproducibility, tracking of gel spots, and decreased risk of contamination. The excised gel plugs are then transferred to microplates or other vessels for digestion and further analysis.

Chapter 6: Image Acquisition, Analysis, and Spot Cutting

Bio-Rad’s EXQuest spot cutter accurately locates and excises protein bands or spots from gels or blots and loads them into 96- or 384-well microplates or 96-tube racks for downstream processing and analysis. Its camera works with PDQuest 2-D analysis software to visualize gels and blots that are either visibly or ﬂuorescently stained. In 2-D electrophoresis applications, PDQuest software tracks the protein bands or spots through spot cutting and protein identiﬁcation, which is usually accomplished using mass spectrometry.

The EXQuest spot cutter allows use of any common proteome separation and staining methods:



Freestanding or plastic- or glass-backed 2-D and 1-D SDS-PAGE gels



PVDF and nitrocellulose membrane blots



Gels or membranes stained for proteins with visible stains (such as silver and Coomassie blue stains) or ﬂuorescent stains (such as Flamingo

™

Oriole

, and SYPRO Ruby protein stains)

ExQuest Spot Cutter

™

66 67

2-D Electrophoresis Guide Theor y and Product Selection

CHAPTER 7

Identiﬁcation and Characterization of 2-D Protein Spots

68 69

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 7: Identication and Characterization of 2-D Protein Spots

Beyond Excision

2-D electrophoresis has the unique capability of simultaneously displaying several hundred proteins. When coupled with the ability of mass spectrometry to identify and characterize small quantities of protein, 2-D electrophoresis is a very powerful and effective analytical method.

Several mass spectrometric techniques can be used for protein identiﬁcation at the end of a 2-D electrophoresis workﬂow. Most of these methods ﬁrst require proteolytic digestion of the protein into discrete fragments that can be eluted from the excised gel plug. The most basic mass spectrometric method, peptide mass ﬁngerprinting, simply determines accurate masses of the peptides generated. These masses are then compared to a database, and the protein of origin can often be uniquely identiﬁed. Another technique, tandem mass spectrometry (MS/MS) further fragments selected peptides along the peptide backbone, allowing the generation of limited sequence information that can be used to reﬁne the protein identiﬁcation step.

Proteolytic Digestion

In-gel digestion (Rosenfeld 1992) of selected proteins is part of the sample preparation process for mass spectrometry, and it comprises four basic steps: destaining (washing) the gel pieces, reduction and alkylation, proteolytic cleavage of the protein, and extraction of the resultant peptides.

Washing

After excision of the protein spot of interest from the gel, most protocols require destaining of the proteins before proceeding. The destaining or wash protocol depends on the stain used for visualization. Commonly used protocols for various stains are described in Part II of this guide.

Reduction and Alkylation

Reduction and alkylation together reduce and irreversibly block the formation of inter- and intramolecular disulﬁde bridges, which can signiﬁcantly improve the efﬁcacy of proteolytic cleavage and subsequent mass spectrometry.

Proteins excised from 2-D gels have usually been reduced and alkylated either during sample preparation or equilibration prior to the second dimension and may not require this step. This step is mandatory if upstream processing did not incorporate reduction and alkylation. Any reduction or reduction plus alkylation step must be followed by a cleanup step prior to mass spectrometry.

In-Gel Proteolytic Digestion

Proteolytic digestion can be performed directly on processed gel pieces. Because proteases are also subject to autolysis, always include a blank piece as a control. Proteases used for this purpose are selected for their efﬁciency in in-gel digestion and for their deﬁned cleavage speciﬁcity, which allows prediction of the generated peptide masses. The most commonly used protease is trypsin, but other proteases used include LysC, GluC, ArgC, AspN, and LysN, which cleave to either the C- or N-terminal side of a single amino acid, as signiﬁed by their nomenclature. These enzymes are all commercially available as preparations that have been speciﬁcally modiﬁed for use prior to mass spectrometry. Enzymes speciﬁcally recommended for mass spectrometry should always be used for in-gel digestion.



Use trypsin (modiﬁed porcine pancreatic trypsin, mass spectrometry grade) for initial protein digestion. Trypsin is one of the most speciﬁc proteases and cleaves at the C-terminal side of Arg and Lys



Use GluC, AspN, or LysC with proteins of smaller mass. These enzymes generate fewer peptides of larger mass than trypsin, which may generate fragments too small for deﬁnitive identiﬁcation



Use acid hydrolysis, cyanogen bromide cleavage, or other chemical methods if alternatives to enzymatic digestion are required



Some proteins are processed forms of larger proteins; therefore, once the protein is identiﬁed based on a trypsin digestion, other methods can be used to deﬁne the N- and C-termini of the fragment

The resulting peptides can be extracted with acetonitrile, dried under vacuum, and dissolved in a small amount of water. Prior to mass spectrometry, the samples should be further puriﬁed by solid phase extraction, for example using ZipTip pipet tips. A protocol is provided in Part II of this guide.

Identiﬁcation by Mass Spectrometry

Identiﬁcation of the peptides derived from digestion can be achieved using several mass spectrometry techniques. Only a brief overview of mass spectrometry theory and techniques is presented here. Refer to the literature from mass spectrometer vendors for more information about systems and methods.

Mass spectrometry systems contain the following components (Figure 7.1):



Ionization source — converts the sample into gas-phase ions, which are then injected into a mass analyzer. The two ionization sources most commonly used for peptide mass spectrometry are matrixassisted laser desorption ionization (MALDI) and electrospray ionization (ESI)

– MALDI — the protein is mixed with an organic

molecule (the “matrix”), deposited onto a planar substrate, allowed to dry, and illuminated with a pulsed UV laser. The matrix compound absorbs the laser energy and promotes peptide ionization, typically generating singly-charged molecular ions. MALDI is useful for high-throughput applications but is limited by ion suppression (particularly in complex peptide mixtures) and chemical noise from the matrix in the low mass range

Sample

Introduction

Ionization

Source

Fig. 7.1. Components of a mass spectrometer.

Mass

Analyzer

– ESI — a ﬂowing liquid is passed through a

charged oriﬁce to produce charged droplets, which are then desolvated to yield gas-phase peptide ions. ESI can be coupled directly to liquidphase separations such as chromatography (LC-MS) and generates multiply-charged molecular ions that bring mass-to-charge ratio (m/z) values within the mass range of mass spectrometry instruments most commonly used with ESI



Mass analyzer — sorts the ions according the m/z. A number of different types of mass analyzers are available, including time-of-ﬂight (TOF), quadrupole, and ion trap systems as well as combinations of these (hydrid mass spectrometers)



Ion detector — records the ion current, ampliﬁes it, and sends it to the data analysis system where it is presented in the form of a mass spectrum. The m/z values of the ions are plotted against their intensities to show the number of components in the sample, the molecular mass of each component, and the relative abundance of the various components in the sample

The data from the mass analyzer(s) are used for protein identiﬁcation, and two options are most common in the 2-D electrophoresis workﬂow: peptide mass ﬁngerprinting and tandem mass spectrometry.

Detector

Data

Handling

70 71

2-D Electrophoresis Guide Theor y and Product Selection

Chapter 7: Identication and Characterization of 2-D Protein Spots

Peptide Mass Fingerprinting

In this method, the peptides resulting from digestion of the protein of interest are analyzed by mass spectrometry and compared to a database of calculated peptide masses generated by “in silico” cleavage of protein sequences using the same speciﬁcity as the enzyme that was employed in the experiment. Identiﬁcations (“hits”) are scored in terms of conﬁdence of match (Figure 7.2).

This approach requires simple mixtures of proteins or pure proteins and is, therefore, suitable for analysis of proteins isolated from 2-D electrophoresis. Limitations

of peptide mass ﬁngerprinting, however, include the following: (i) the protein sequence has to be present in the database of interest, and (ii) several peptides are required to uniquely identify a protein. Additionally, most algorithms assume that the peptides come from a single protein, which is why resolution in the 2-D separation is so critical. If this information does not allow unequivocal identiﬁcation of the protein, peptides can then be analyzed by tandem mass spectrometry.

Digestion

Tandem Mass Spectrometry (MS/MS)

In MS/MS, a peptide ion is isolated in the mass analyzer and subjected to dissociation to product ion fragments. Peptides dissociate according to certain rules. For example, fragmentation typically occurs along the peptide backbone; each residue of the peptide chain is successively cut off, both in the N->C (a-, b-, c- ions) and C->N (x-, y-, z- ions) directions. The product ions resulting from the fragmentation are analyzed in a second stage of mass analysis, which enables sequence derivation (Figure 7.3). Tandem MS can allow identiﬁcation of proteins from a single peptide (Lovric 2011).

Establishment of 2-D Databases

After the spots are cut, analyzed, and identiﬁed, by MS for example, the information can be imported back into the experiment as annotations. Annotations are organized in categories, for example by protein name, protein family amino acid composition, protein function, cellular location, binding properties, and translational regulation. A single spot may be annotated in multiple categories, depending on the amount and type of information available about it. Most categories contain simple text annotations. Specialized categories can be used to link spots to Internet protein databases or to open ﬁles in other applications.

Fig. 7.2. Peptide mass ﬁngerprinting. Peptides resulting from digestion are analyzed by mass spe ctrometry, and the resulting m/z values and mass spectrum are compared to theoretical values derived from “in silico” digestion of known proteins in a database.

Abundance

Analysis

m/z

Ion currentIon current

VQVSR

AWGI

SPVR

Fig. 7.3. MS/MS analysis. The ﬁrst mass analyzer selects ions of a particular m/z for fragmentation. The second mass analyzer produces the mass spectrum for those fragments.

AWGISPVR

AWGIS

ISPVR

m/ z

AWGISP

QGLWIVDMSSGAVK

NQNEYQVSWDTEK

AWGISPV

WGISPVR

ENIYPEDQQESPSIGLK

MS/MS

72 73

2-D Electrophoresis Guide Methods

2-D Electrophoresis Guide

TABLE OF CONTENTS

PART II

Methods

CHAPTER 8

Sample Preparation

74 75

2-D Electrophoresis Guide MethodsChapter 8: Sample Preparation

Tips for Sample Preparation

Keep the sample preparation workﬂow simple (increasing the number of sample handling steps may increase variability).

Lysis (Cell Disruption)



For each 10 mg (fresh weight) pelleted cells or animal tissue, use about 1 ml of 2-D sample solution for a protein concentration of 1–3 mg/ml. When disrupted in liquid nitrogen, samples such as liver biopsies and plant leaves contain 10–30% and 1–2% extractable protein, respectively



To diminish endogenous enzymatic activity:

— Disrupt the sample or place freshly disrupted

samples in solutions containing strong denaturing agents such as 7–9 M urea, 2 M thiourea, or 2% SDS. In this environment, enzymatic activity is often negligible

— Perform cell disruption at low temperatures

to diminish enzymatic activity

— Lyse samples at pH >9 using either sodium

carbonate or Tris as a base in the lysis solution (proteases are often least active at basic pH)

— Add a chemical protease inhibitor

to the lysis buffer. Examples include phenylmethylsulfonyl ﬂuoride (PMSF), aminoethyl-benzene sulfonyl ﬂuoride (AEBSF), tosyl lysine chloromethylketone (TLCK), tosyl phenyl chloromethyletone (TPCK), ethylenediaminetetraacetic acid (EDTA), benzamidine, and peptide protease inhibitors (for example, leupeptin, pepstatin, aprotinin, bestatin). For best results, use a combination of inhibitors in a protease inhibitor cocktail

— If protein phosphorylation is to be studied,

include phosphatase inhibitors such as ﬂuoride and vanadate



When working with a new sample, use at least two different cell disruption protocols and compare the protein yield (by protein assay) and qualitative protein content (by SDS-PAGE)



Optimize the power settings of mechanical rupture systems and incubation times for all lysis approaches. Mechanical cell lysis usually generates heat, so employ cooling where required to avoid overheating of the sample



Following cell disruption, check the efﬁcacy of cell wall disruption by light microscopy and centrifuge all extracts extensively (20,000 × g for 15 min at 15°C) to remove any insoluble material; solid particles may block the pores of the electrophoresis gel



Direct application of clariﬁed lysate to IPG strips is appropriate only for samples with high protein content and minimal interfering substances. Preparation of many sample types (for example, plant tissues and dilute bodily ﬂuids) should incorporate a precipitation step to remove interfering substances and allow application of a more concentrated sample

Protein Solubilization



Prepare fresh sample solubilization solutions daily or store them frozen in aliquots, preferably at –80°C; always use high-quality reagents and proteomics-grade water. Use urea stock solutions soon after they are made, or treat them with a mixed-bed ion exchange resin to avoid protein carbamylation by cyanate, which forms in old urea. If solutions are prepared in advance and stored, it is best to prepare them without reductant (DTT) and add the reductant directly before use



Dissolve pelleted protein samples in 1× 2-D sample solution



Perform a protein quantitation assay to determine the amount of total protein in each sample. Use a protein assay that is tolerant to chemicals in your samples. For samples in 2-D sample solution, for example, use the RC DC

™

protein assay,

which can tolerate up to 2% detergent



Dilute or concentrate samples as needed to yield a ﬁnal protein concentration of 1–5 mg/ml. Make dilutions in 2-D sample solution and concentrate the sample using the ReadyPrep 2-D cleanup kit



Use protein extracts immediately or aliquot them into appropriately sized batches and store them at –80°C to avoid freeze-thaw cycles



Highly viscous samples likely have a very high DNA or carbohydrate content. Fragment DNA with ultrasound during protein solubilization or by adding endonucleases like benzonase. Use protein precipitation (for example, with the ReadyPrep 2-D cleanup kit) to diminish carbohydrate content



Do not heat samples containing urea and thiourea above 35°C as this can lead to protein modiﬁcation

Buffers and Solutions

2-D sample solution (50 ml)

7 M urea, 2 M thiourea, 4% (w/v) CHAPS, 40 mM DTT,

0.2% (w/v) ampholytes (pH 3–10)

Urea/thiourea stock solution 48 ml CHAPS 2.0 g Bio-Lyte

ampholytes, pH 3–10 250 µl DTT 0.31 g Bromophenol blue (1%) 10 µl Distilled or deionized H



2-D sample solution is used for sample application

O to 50 ml

and IPG strip rehydration. Bio-Rad offers various types of 2-D sample buffers, which differ in solubilizing power (see Ordering Information)



For pH control, Tris base may be added to the 2-D sample solution at 10–40 mM. Addition of Tris increases the conductivity of the sample solution and extends the time required to focus the IPG strips



Ampholytes are added to all IPG rehydration and sample solubilization solutions to maintain solubility of the proteins. The choice of ampholytes depends on the pH range of the IPG strip. Higher concentrations (up to 1% (w/v)) may be used, but they result in lower IEF voltage and correspondingly longer focusing times

Urea/thiourea stock solution (50 ml)

Urea 22 g Thiourea 8 g Distilled or deionized H

O to 50 ml

Filter through Whatman No. 1 paper

™

using a Buchner funnel

Store at –80°C

1% Bromophenol blue (10 ml)

Bromophenol blue will not dissolve in unbuffered water. Prepare 10 ml of 50 mM Tris base by dissolving

60.6 mg of Tris in 10 ml of water. Add 100 mg of bromophenol blue and vortex until dissolved. Store at 25°C.

Cell washing buf fer (1 L)

10 mM Tris-HCl, pH 7.0, 250 mM sucrose

Tris base 1.21 g Sucrose 85.58 g Distilled or deionized H

O 800 ml

Dissolve Adjust pH to 7.0 with HCl Distilled or deionized H

O to 1 L

Store at 4°C

Protein precipitation solution (100 ml)

20% (w/v) trichloroacetic acid (TCA), 0.2% DTT (w/v) in ice-cold acetone (–20°C)

Trichloroacetic acid 20 g DTT 0.2 g Acetone 80 ml

Dissolve Acetone to 100 ml Store at –20°C

Wash solution (100 ml)

0.2% DTT in ice-cold acetone (–20°C)

DTT 0.2 g Acetone 80 ml Dissolve Acetone to 100 ml Store at –20°C

SDS sample solubilization buffer (50 ml)

1% (w/v) SDS, 100 mM Tris-HCl (pH 9.5)

SDS 0.5 g Tris base 0.6 g Distilled or deionized H

O 40 ml

Titrate to pH 9.5 with diluted HCl Distilled or deionized H

O to 50 ml

Store at 25°C

76 77

2-D Electrophoresis Guide MethodsChapter 8: Sample Preparation

Cell Lysis and Protein Extraction Procedures

Suspension Cultured Human Cells

Use the MicroRotofor™ cell lysis kit (mammalian) or the protocol below, which uses 2-D sample solution and a sonicator for cell lysis and protein extraction. Use 0.5 ml of 2-D sample solution with 3 × 10

Reagents



2-D sample solution



Cell washing buffer

Protocol

Pellet the cells by centrifugation at 2,000 × g for 5 min at 4°C.

Discard the supernatant and wash pelleted cells in cold cell washing buffer. Repeat steps 1 and 2 two times.

Add 2-D sample solution to the pelleted cells and suspend the pellet with a pipet.

Place the cell suspension on ice, incubate 5 min, and sonicate at appropriate intervals. Check lysis efﬁcacy by light microscopy.

Centrifuge cell debris at 14,000 × g for 15 min and transfer supernatant to a new vial.

Perform a protein assay of the supernatant. A protein concentration of 3–5 mg/ml is best for 2-D electrophoresis.

cells.

Monolayer Cultured Human Cells

Use the MicroRotofor cell lysis kit (mammalian) or the protocol below, which uses 2-D sample solution and a sonicator for cell lysis and protein extraction. Use 0.5 ml of 2-D sample solution with 3 × 10

Reagents



2-D sample solution



Cell washing buffer

Protocol

Carefully remove (decant) culture medium from cells. Wash cells twice with cell washing buffer.

Add 2-D sample solution to the cells and keep on ice for 5 min. Swirl the plate occasionally to spread the buffer around the plate.

Use a cell scraper to collect the lysate and transfer to a microcentrifuge tube.

Place the cell suspension on ice, incubate 5 min, and sonicate at appropriate intervals. Check lysis efﬁcacy by light microscopy.

Centrifuge the cell debris at 14,000 × g for 15 min and transfer the supernatant to a new vial.

Perform a protein assay of the supernatant. A protein concentration of 3–5 mg/ml is best for 2-D electrophoresis.

cells.

Mammalian Tissue

Use the MicroRotofor cell lysis kit (mammalian) or the protocol below, which involves freezing tissue samples (for example, biopsy samples) in liquid nitrogen. Use liquid nitrogen and a mortar and pestle to grind the samples while they are still frozen. Break up any larger pieces beforehand (for example, wrap the frozen tissue sample in aluminum foil and crush with a hammer).

Reagents



2-D sample solution

Protocol

Chill a mortar with liquid nitrogen, then grind small tissue pieces in the presence of liquid nitrogen to a ﬁne powder.

Immediately after grinding, transfer 60 mg tissue powder to a microcentrifuge tube containing

1.0 ml of 2-D sample solution.

Optional: sonicate the sample on ice 5 times, for 2 sec each time. Pause between sonication steps to avoid overheating.

Incubate the sample at room temperature for 30 min. Vortex from time to time.

Centrifuge at 35,000 × g for 30 min at room temperature.

Perform a protein assay to determine the protein concentration of the supernatant, which should be 5–10 mg/ml.

Dilute the supernatant with 2-D sample solution and incubate for 20 min at room temperature.

Microbial Cultures

Reproducible sample preparation from bacteria and yeast is challenging because the cells may release proteases and other enzymes into the growth medium (Harder et al. 1999, Drews et al. 2004, Poetsch and Wolters 2008). Wash the cultures thoroughly with isotonic buffers and take precautions to inactivate the proteolytic activity after cell lysis. Extensive disruption of microbial cells is required and is usually performed with the help of a French press, bead impact instruments, or sonicator.

Use the MicroRotofor cell lysis kit (bacteria), the MicroRotofor cell lysis kit (yeast), or the protocol below. This protocol relies on cell lysis with ultrasonic waves in combination with a solubilization in SDS under elevated temperature to ensure deactivation and denaturation of proteases.

Reagents



SDS sample solubilization buffer



2-D sample solution



Cell washing buffer

Protocol

Centrifuge cells (~5 × 10 for 3 min and resuspend the pellet in an equal volume of 2-D cell washing buffer heated at 37°C and centrifuge again. Repeat two more times to remove all interfering material (extracellular proteases and growth media).

Add ~150 µl hot (95°C) SDS sample solubilization buffer to the pellet and vortex thoroughly.

Sonicate the sample solution 10 times for 1 sec each at ~60 W and ~20 kHz.

Incubate the sample at 95°C for 5 min.

) at 5,000 × g

Cool the sample to 20°C and dilute with ~500 µl of 2-D sample solution. Incubate for another 20 min at room temperature. The ﬁnal SDS concentration should not exceed 0.25% in the extract to be applied onto the IPG strip; therefore, be sure that the total volume is maintained during the SDS boiling step.

Centrifuge the sample solution at 20°C for 30 min at 14,000 × g and harvest the supernatant.

Perform the protein assay. The protein concentration should be ~5 µg/µl.

78 79

2-D Electrophoresis Guide MethodsChapter 8: Sample Preparation

Cell Lysis and Protein Extraction Procedures (c on td.)

Plant Leaves

Plant leaf cells contain reactive compounds (such as proteases, phenol oxidases, organic acids, phenols, and terpenes). To minimize the deleterious effects of these compounds on protein integrity, use the MicroRotofor cell lysis kit (plant) or follow this protocol, which involves grinding the tissue in a mortar and pestle with liquid nitrogen. Precipitate the proteins with 20% trichloroacetic acid (TCA) in prechilled acetone (–20°C). To remove the plant phenols, rinse the pellet at least twice with cold acetone (–20°C) and air-dry samples in a vacuum (Damerval 1986).

Reagents



Protein precipitation solution



Wash solution



2-D sample solution

Protocol

Cool protein precipitation and wash solutions to –20°C and chill a mortar with liquid nitrogen.

Place leaves in the mortar, add liquid nitrogen, and grind the leaves in the liquid nitrogen to a ﬁne powder.

Transfer leaf powder into 20 ml protein precipitation solution and incubate for 1 hr at –20°C. Stir solution occasionally.

Centrifuge the solution at –20°C for 15 min at 35,000 × g.

Discard the supernatant, add wash solution, and suspend the pellet. Incubate for 15 min at –20°C and stir the solution occasionally.

Repeat steps 4 and 5 until the wash solution turns from dark to light green.

Centrifuge the solution at –20°C for 15 min at 35,000 × g and discard the supernatant.

Add 2 ml of wash solution and suspend the pellet.

Transfer the suspension into a shallow ceramic shell and cover with perforated Paraﬁlm wrap.

Put the shell into a dessicator and apply a vacuum until the pellet (acetone powder) is dry.

Mix 5 mg of sample powder with ~0.5 ml of 2-D sample solution and incubate for 30 min at room temperature. Vortex from time to time.

Centrifuge the solution at room temperature for 15 min at >16,000 × g.

Collect the supernatant and perform the protein assay.

Sample Cleanup

Prior to IEF, remove contaminating salts, buffers, and other chemicals from samples by dialysis, precipitation, or buffer exchange. A protocol for buffer exchange using Bio-Rad’s Micro Bio-Spin here. Another alternative is the use of the ReadyPrep 2-D cleanup kit to effectively precipitate sample protein and remove contaminants. It has the additional beneﬁt of concentrating the sample to a desired volume.

™

P-6 columns is provided

Buffer Exchange (Desalting)

Bio-Rad’s Micro Bio-Spin columns are suitable for use with 1.5 or 2.0 ml microcentrifuge tubes and are completely autoclavable. They accommodate volumes of 20–75 µl; volumes less than 20 µl may affect recovery. The gel in the Micro Bio-Spin columns is suspended in either SSC buffer, pH 7.0, or Tris-HCl buffer, pH 7.4. For 2-D electrophoresis, it is best to exchange the sample into the 2-D sample solution (7 M urea, 2 M thiourea, 4% CHAPS) using the following protocol. DTT and ampholytes are added after the buffer exchange procedure.

Protocol

Invert the column sharply several times to resuspend the settled gel and remove any bubbles. Snap off the tip and place the column in a

2.0 ml microcentrifuge tube (included). Remove the top cap. If the column does not begin to ﬂow, push the cap back on the column and then remove it again to start the ﬂow. Allow the excess packing buffer to drain by gravity to the top of the gel bed (about 2 min). Discard the drained buffer, then place the column back into the 2.0 ml tube.

Centrifuge for 2 min in a microcentrifuge at 1,000 × g to remove the remaining packing buffer. Discard the buffer.

Apply the new buffer in 500 μl aliquots. After each application, let the buffer drain out by gravity, then centrifuge the column at 1,000 × g for 1 min to remove the buffer. Discard the buffer from the collection tube. Repeat as required. Three washes result in >99% of the buffer exchanged. Four washes result in >99.9% of the buffer exchanged.

Place the column in a clean 1.5 or 2.0 ml microcentrifuge tube. Carefully apply the sample (20–75 μl) directly to the center of the column. Application of more or less than the recommended sample volume may decrease column performance.

Centrifuge the column for 2–4 min at 1,000 × g. Following centrifugation, the puriﬁed sample is in the new buffer. Molecules smaller than the column’s exclusion limit are retained by the column.

80 81

2-D Electrophoresis Guide MethodsChapter 8: Sample Preparation

Sample Quantitation (RC DC Protein Assay)

The RC DC protein assay is based on a modiﬁcation of the Lowry protocol (Lowry et al. 1951) and is both reducing agent compatible (RC) and detergent compatible (DC). Protein quantitation can be performed in complex mixtures including 2-D sample solution. It involves addition of detection reagents to a protein solution and subsequent measurement of absorbance at 750 nm with a spectrophotometer. Comparison to a standard curve provides a relative measurement of protein concentration.

Microfuge Tube Assay Protocol (1.5 ml)

Add 5 μl of DC Reagent S to each 250 μl of DC Reagent A needed. This solution is referred to as Reagent A assayed requires 127 μl Reagent A

Prepare 3–5 dilutions of a protein standard (0.2–1.5 mg/ml protein). Use distilled or deionized water as the diluent.

Pipet 25 µl of protein standard or sample into clean 1.5 ml microcentrifuge tubes. Add 125 µl of RC Reagent I into each tube and vortex. Incubate the tubes for 1 min at room temperature.

Add 125 µl of RC Reagent II into each tube and vortex. Centrifuge the tubes at 15,000 x g for 5 min. Position the tubes with the cap hinge facing outward.

. Each standard or sample

Add 127 µl of Reagent A and vortex. Incubate tubes at room temperature for 5 min, or until the precipitate is dissolved. Vortex.

Add 1 ml of DC Reagent B to each tube and vortex immediately. Incubate at room temperature for at least 15 min, but no longer than 1 hr.

Read absorbance of each sample at 750 nm. The absorbances are stable for at least 1 hr.

Plot absorbance measurements as a function of concentration for the standards.

Interpolate the concentration of the protein samples from the plot and sample absorbance measurements.

to each tube

Remove the tubes as soon as centrifugation is complete. A small pellet should be visible on the hinge side of the tube. Decant the supernatant. Reposition the tubes as before. Brieﬂy centrifuge again to bring any remaining liquid to the bottom of the tube. Use a micropipet to remove the remaining liquid.

82 83

2-D Electrophoresis Guide Methods

TABLE OF CONTENTSTABLE OF CONTENTS

CHAPTER 9

First-Dimension IEF with IPG Strips

84 85

2-D Electrophoresis Guide MethodsChapter 9: First-Dimension IEF with IPG Strips

Tips for IEF



Master 2-D separation techniques using the ReadyPrep before using your own samples. The kit contains premixed reagents, a standard sample, and a detailed and optimized protocol, which allows you to become familiar with the 2-D workﬂow and techniques while validating the performance of your 2-D system



When preparing solutions, use clean and dust-free vessels to avoid keratin contamination



Use highly puriﬁed laboratory water (conductivity <2 µS)



Use deionized urea prepared with a mixed-bed ion exchange resin to avoid protein carbamylation by cyanate, which forms in old urea



Do not heat urea-containing buffers to >37°C to

™

2-D starter kit (catalog #163-2105)

IPG Strip Rehydration and Sample Loading

Prior to their use in IEF, IPG strips must be rehydrated (with or without sample) to their original thickness with rehydration solution (Table 9.1), which is often the 2-D sample solution (see Chapter 8).

Tips for Rehydration and Sample Loading



Rehydrate IPG strips for 12 hr–overnight at 20°C

(or room temperature)



After rehydration in a rehydration/equilibration tray, rinse and blot the IPG gel strips to remove excess rehydration solution before transferring to the focusing tray; otherwise, urea may crystallize on the surface of the IPG strips



Moisten electrode wicks with deionized water. They should be moist, not wet

avoid protein carbamylation

Table 9.1. Rehydration volumes a nd sample loads. Protein load recommendations are intended as a starting point, and the optimum amount for the sample must be determined empirically. For narrow-range IPG strips, use more protein (proteins outside the range will not remain on the strip). For single-pH-unit IPG strips, use up to 4– 5 times more protein to improve the detection of low-abundance proteins.

IPG Strip Length, cm

7 11 17 18 24

Rehydration solution 125 µl 200 µl 300 µl 315 µl 450 µl

Protein load

Coomassie (Brilliant) Blue 50–100 µg 100–200 µg 200–400 µg 200– 400 µg 400 –80 0 µg

Fluorescent stains 5–100 µg 20 –200 µg 50– 400 µg 50– 400 µg 80–800 µg

Silver stains 5–20 µg 20–50 µg 50 –80 µg 50–80 µg 80–150 µg

Mineral oil 4 ml 5 ml 7 ml 7 ml 9 ml

Performing IEF

IPG Strip Rehydration in Rehydration/ Equilibration Trays Followed by IEF

The instructions in this chapter pertain to the use of the PROTEAN details about the components of this system and their assembly and use, please refer to the PROTEAN i12 cell instruction manual (bulletin 10022069).

Protocol

i12™ cell and accessories. For more

Pipet the rehydration solution (with or without sample, see Table 9.1 for volumes and protein loads) along the center of the channel(s) of the i12 rehydration/equilibration tray. Take care not to introduce air bubbles when expelling the solution.

Using forceps, remove the cover sheet from the IPG strip, then gently place the IPG strip gel-side down onto the solution in the channel. Move the IPG strip back and forth slightly to ensure that the solution is distributed along its length and that the strip is not sticking to the bottom of the tray. Take care to avoid trapping air bubbles beneath the IPG strip.

Overlay each IPG strip with mineral oil to prevent evaporation and precipitation of urea during rehydration (see Table 9.1 for recommended volumes). Apply the mineral oil to both ends of the channel and allow it to ﬂow toward the middle.

Cover the tray and leave it on a level bench overnight (12–18 hr) for complete rehydration.

IEF with Gel-Side Up

The following protocol is for IPG strips that have been rehydrated in the presence of sample (in-gel sample loading).

Protocol

Using forceps, remove the IPG strips from the rehydration tray, remove excess mineral oil, and place the rehydrated IPG strips gel-side up in the channels of the focusing tray. Position the positive (+) ends of the IPG strips against the positioning stops in each channel.

Recommended: Wet the gel-side up wicks (notched) with distilled or deionized water and blot off excess water. Use two wicks per IPG strip: place a wick at each end of each IPG strip.

Position the electrode assemblies in the focusing tray and press down on the green tabs to snap the electrode assemblies into place. Place the focusing tray with the rehydrated IPG strips on the Peltier platform and connect the electrodes to the instrument.

Overlay each IPG strip with mineral oil (see Table 9.1 for recommended volumes).

Select or program the protocol(s) and start the run.

Rehydration

With sample

(in-gel sample loading)

Without sample

Fig. 9.1. Sample loading.

the focusing tray for IEF (see below).

Transfer IPG str ips

to focusing tray

Transfer IPG str ips

to focus ing tr ay

IEF

With gel-side up

With gel-side down

With gel-side up

(cup loading)

86 87

Transfer the rehydrated IPG strips to

2-D Electrophoresis Guide MethodsChapter 9: First-Dimension IEF with IPG Strips

Performing IEF (contd.)

IEF with Gel-Side Down

The following protocol is for IPG strips that have been rehydrated in the presence of sample (in-gel sample loading).

Protocol

Position the electrode assemblies in the channels of the focusing tray and press down on the green tabs to snap the electrode assemblies into place.

Recommended: Wet the rectangular (gel-side down) wicks with distilled or deionized water and blot off excess water. Use two wicks per IPG strip: place a wick on top of each electrode.

Using forceps, place the rehydrated IPG strips gel-side down in the channels of the focusing tray. Position the positive (+) ends of the IPG strips against the positioning stops in each channel.

Place the focusing tray on the Peltier platform and connect the electrodes to the instrument.

Overlay each IPG strip with mineral oil (see Table 9.1 for recommended volumes).

Place the IPG strip retainers on top of the IPG strips at both the positive and the negative ends. Without IPG strip retainers in place, gases formed during electrolysis may lift IPG strips off the electrodes, interrupting electrical contact.

Select or program the protocol(s) and start the run.

Cup Loading (IEF with Gel-Side Up)

This protocol is for IPG strips that have been rehydrated in the absence of sample. Sample cups offer an alternative method of sample loading, and their use can often improve resolution, especially at extreme pH ranges. The PROTEAN i12 sample cup assembly consists of a sample cup holder that holds 1–12 disposable sample cups.

Protocol

Using forceps, place the rehydrated IPG strips gel-side up in the channels of the focusing tray. Position the positive (+) end of the IPG strips against the positioning stops in each channel.

Recommended: Wet the gel-side up electrode wicks (notched) with deionized water and blot off excess water. Use two wicks per IPG strip: place a wick at each end of each IPG strip.

Prepare the sample cup assembly by placing the sample cups into the slots of the sample cup holder corresponding to the channel with the rehydrated IPG strip.

Clamp the sample cup assembly onto the edges of the focusing tray, on top of the IPG strips and next to either electrode. Placement depends on the pH gradient and the sample. In general, focusing is most effective towards the end of the IPG strip opposite the site of the sample cup placement. Use anodic sample cup placement when using basic pH ranges or when resolution of basic proteins is desired.

Load 25–250 μl of sample into the sample cups (larger volumes of dilute samples of up to 400 μl may be loaded). Overlay both the sample in the sample cup and the IPG strip with mineral oil.

IPG Strip Rehydration in the Focusing Tray Followed by IEF

For rehydration and IEF in the focusing tray, place the IPG strip gel-side down on top of the rehydration solution in the focusing tray. Rehydration can be programmed as a part of the IEF run, and the protocols can be programmed next. Alternatively, the strips can be rehydrated independently and the protocol(s) started when most convenient.

Protocol

Rehydration

Fig. 9.2. Rehydration in the focusing tray.

Position the electrode assemblies in the focusing tray.

Pipet the rehydration solution containing the protein sample along the center of the channel(s) of the focusing tray (see Table 9.1 for recommended volumes and protein loads). Do not introduce air bubbles when expelling the solution.

Using forceps, remove the cover sheet from the IPG strip, then gently place the IPG strip gel-side down onto the sample in the channel of the tray. To ensure even rehydration, move the IPG strip back and forth slightly to distribute the solution along its length. Check that no bubbles are trapped beneath the strips and that some rehydration solution extends beyond the electrode contacts.

Place the focusing tray with the IPG strips on the Peltier platform and connect the electrodes to the instrument.

Immediately overlay each IPG strip with mineral oil to prevent evaporation and precipitation of urea during rehydration. Apply the mineral oil to both ends of the channel and allow it to ﬂow toward the middle. See Table 9.1 for recommended volumes of mineral oil.

With sample

(passive or active)

IPG str ips remain

in focusing tray

Position the IPG strip retainers on top of the IPG strips at both the anode and the cathode to maintain electrical contact with the IPG strips. Without the IPG strip retainers, gases formed during electrolysis may lift the IPG strips off the electrodes, interrupting electrical contact.

Rehydration in the focusing tray with in-gel sample application can be programmed as a part of the IEF run or be performed separately.

To program rehydration as part of the run:

a. Select or program the protocol(s)

for the lanes containing IPG strips

b. Program the global rehydration

conditions. If electrode wicks are used, include a post-rehydration pause to insert electrode wicks when the rehydration step is completed

c. Start the run

For rehydration not programmed as part of the run, leave the tray on the Peltier platform or on a level bench overnight (11–16 hr) for complete rehydration.

Start the run (perform IEF).

IEF

With gel-side down

Select or program the protocol(s) and start the run.

88 89

2-D Electrophoresis Guide MethodsChapter 9: First-Dimension IEF with IPG Strips

IEF Programming Recommendations

The protocols and settings described are for IEF using the PROTEAN i12 IEF cell. Preprogrammed protocols serve as convenient starting points for optimization of IEF conditions (Tables 9.2 to 9.5).



The recommended focusing temperature for most samples is 20°C



For better sample entry, start IEF with a low voltage gradient (200 V for 30–180 min) and limit current to 50 µA per IPG strip for the whole run

™

Table 9.2. Preprogrammed protocols for 7 cm ReadyStrip

Protocol Name

7 cm pH 3–10 R 7 cm pH 3–10 NL R 7 cm pH 4–7 R 7 cm pH 5–8 R

7 cm pH 3–10 G 7 cm pH 3–10 NL G 7 cm pH 4–7 G 7 cm pH 5–8 G

7 cm pH 3–6 R

7 cm pH 3–6 G

7 cm pH 3.9 – 5.1 7 cm pH 4.7–5.9

7 cm pH 5.5 – 6.7 7 cm pH 6.3 – 8.3

7 cm pH 7–10 R

7 cm pH 7–10 G

R = rapid, G = gradual

Step Voltage, V Ramp Time Units

1 4,00 0 Rapid 15,000 Vh

2 500 Hold

1 250 Rapid 0:20 HH:MMr

2 4,000 Gradual 1:00 HH:MM

3 4,000 Rapid 15,000 Vh

4 500 Hold

1 4,00 0 Rapid 10,000 Vh

2 500 Hold

1 250 Rapid 0:15 HH:MMr

2 4,000 Gradual 1:00 HH:MM

3 4,000 Rapid 20,000 Vh

4 500 Hold

1 250 Rapid 0:15 HH:MMr

2 4,000 Gradual 1:00 HH:MM

3 4,000 Rapid 20,000 Vh

4 500 Hold

1 250 Rapid 0:15 HH:MMr

2 4,000 Gradual 1:00 HH:MM

3 4,000 Rapid 25,000 Vh

4 500 Hold

1 4,00 0 Rapid 16,000 Vh

2 500 Hold

1 250 Rapid 0:15 HH:MMr

2 4,000 Gradual 1:00 HH:MM

3 4,000 Rapid 16,000 Vh

4 500 Hold

IPG strips.



Focusing time depends on gel length, pH gradient, gel additives, and protein amount loaded. Vertical streaking is often caused by overfocusing — isoelectric precipitation (pI fallout) increases with focusing time. For this reason, do not conduct ﬁrstdimension IEF for any longer than is necessary



After completion of the IEF run, IPG strips should be stored frozen at –80°C in rehydration trays or immediately applied to a second-dimension SDS-gel. Frozen IPG strips can be stored for about 3–6 months

Table 9.3. Preprogrammed protocols for 11 cm ReadyStrip IPG strips.

Protocol Name

11 cm pH 3–10 R 11 cm pH 3–10 NL R 11 cm pH 4–7 R 11 cm pH 5–8 R

11 cm pH 3–10 G 11 cm pH 3–10 NL G 11 cm pH 4–7 G 11 cm pH 5–8 G

11 cm pH 3–6 R

11 cm pH 3–6 G

11 cm pH 3.9– 5.1 11 cm pH 4.7–5.9

11 cm pH 5.5– 6.7 11 cm pH 6.3– 8.3

11 cm pH 7–10 R

11 cm pH 7–10 G

R = rapid, G = gradual

Step Voltage, V Ramp Time Units

1 8,00 0 Rapid 26,000 Vh

2 750 Hold

1 250 Rapid 0:20 HH:MMr

2 8,000 Gradual 1:00 HH:MM

3 8,000 Rapid 26,000 Vh

4 1,500 Hold

1 8,00 0 Rapid 20,000 Vh

2 750 Hold

1 250 Rapid 0:20 HH:MMr

2 8,000 Gradual 1:00 HH:MM

3 8,000 Rapid 20,000 Vh

4 750 Hold

1 250 Rapid 0:20 HH:MMr

2 8,000 Gradual 1:00 HH:MM

3 8,000 Rapid 32,000 Vh

4 750 Hold

1 250 Rapid 0:20 HH:MMr

2 8,000 Gradual 1:00 HH:MM

3 8,000 Rapid 40,000 Vh

4 750 Hold

1 8,00 0 Rapid 29,000 Vh

2 750 Hold

1 250 Rapid 0:20 HH:MMr

2 8,000 Gradual 1:00 HH:MM

3 8,000 Rapid 29,000 Vh

4 750 Hold

90 91

2-D Electrophoresis Guide MethodsChapter 9: First-Dimension IEF with IPG Strips

IEF Programming Recommendations (contd.)

Table 9.4. Preprogrammed protocols for 17 and 18 cm ReadyStrip IPG strips.

Protocol Name

17 cm pH 3–10 R 17 cm pH 3–10 NL R 17 cm pH 4–7 R 17 cm pH 5– 8 R

17 cm pH 3–10 G 17 cm pH 3–10 NL G 17 cm pH 4–7 G 17 cm pH 5– 8 G

17 cm pH 3– 6 R 18 cm pH 3–6 R

17 cm pH 3– 6 G 18 cm pH 3 –6 G

17 cm pH 3.9–5.1 17 cm pH 4.7–5.9

17 cm pH 5.5–6.7 17 cm pH 6.3–8.3

17 cm pH 7–10 R 18 cm pH 7–10 R

17 cm pH 7–10 G 18 cm pH 7–10 G

R = rapid, G = gradual

18 cm pH 3–10 R 18 cm pH 3–10 NL R 18 cm pH 4–7 R 18 cm pH5–8 R

18 cm pH 3–10 G 18 cm pH 3–10 NL G 18 cm pH 4–7 G 18 cm pH 5– 8 G

18 cm pH 3.9 –5.1 18 cm pH 4.7–5.9

18 cm pH 5.5 –6.7 18 cm pH 6.3–8.3

Step Voltage, V Ramp Time Units

1 10,000 Rapid 43,000 Vh

2 1,000 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 Rapid 43,000 Vh

4 1,000 Hold

1 10,000 Rapid 32,000 Vh

2 1,000 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 Rapid 32,000 Vh

4 1,000 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 Rapid 50,000 Vh

4 1,000 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 Rapid 63,000 Vh

4 1,000 Hold

1 10,000 Rapid 46,000 Vh

2 1,000 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 Rapid 46,00 0 Vh

4 1,000 Hold

Table 9.5. Preprogrammed protocols for 24 cm ReadyStrip IPG strips.

Protocol Name

24 cm pH 3–10 R 24 cm pH 3–10 NL R 24 cm pH 4–7 R 24 cm pH 5–8 R

24 cm pH 3–10 G 24 cm pH 3–10 NL G 24 cm pH 4–7 G 24 cm pH 5–8 G

24 cm pH 3–6 R

24 cm pH 3–6 G

24 cm pH 3.9 – 5.1 24 cm pH 4.7–5.9

24 cm pH 5.5 – 6.7 24 cm pH 6.3 – 8.3

24 cm pH 7–10 R

24 cm pH 7–10 G

R = rapid, G = gradual

Step Voltage, V Ramp Time Units

1 10,000 R apid 60,000 Vh

2 1,500 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 R apid 60,000 Vh

4 1,500 Hold

1 10,000 Rapid 44,000 Vh

2 1,500 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 Rapid 44,000 Vh

4 1,500 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 R apid 70,000 Vh

4 1,500 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 R apid 70,000 Vh

4 1,500 Hold

1 10,000 Rapid 63,000 Vh

2 1,500 Hold

1 250 Rapid 0:30 HH:MMr

2 10,000 Gradual 2:00 HH:MM

3 10,000 Rapid 63,000 Vh

4 1,500 Hold

92 93

2-D Electrophoresis Guide Methods

TABLE OF CONTENTSTABLE OF CONTENTS

CHAPTER 10

Second-Dimension SDS-PAGE

94 95

2-D Electrophoresis Guide MethodsChapter 10: Second-Dimension SDS-PAGE

Tips for SDS-PAGE



Ensure that gels have the same composition by either using precast gels, which are manufactured in lots and so are virtually identical, or hand casting the gels at the same time in a multicasting chamber



Save time by preparing the overlay solution and running buffers during the 10 min equilibration incubations



Vertical streaking on second-dimension gels is often caused by gaps between the IPG strips and the gels. Ensure that the second-dimension gel has a straight and level top edge, and that the IPG strip is in direct contact with the gel along its entire length



When preparing running buffers, make the solution as speciﬁed in the protocol and do not titrate to a pH. The ion balance is set by the concentration of reagents; adjusting the pH alters this balance and leads to undesirable results



Do not reuse running buffers



Use 5–10 V per cm of gel for 10 to 30 min during sample entry (until the sample has concentrated at the starting point of the separation gel). Then continue with the voltage setting recommended in the instruction manual for the electrophoresis system you are using



Use the voltage setting recommended in the instruction manual for the electrophoresis system you are using; excessive voltage leads to decreased resolution and distortions



When running multiple cells, use the same voltage for multiple cells as you would for one cell. Be aware that the current drawn from the power supply will double with two — compared to one — cells. Use a power supply that can accommodate this additive current and set the current limit high enough to permit this additive function



To maximize reproducibility, maintain the temperature of the electrophoresis buffer at about 20°C with the help of a recirculating cooler

IPG Strip Equilibration

Equilibrate the IPG strips twice, each time for 10 min, in two different equilibration buffers. Use disposable rehydration/equilibration trays for this purpose.

Reagents

Tris-HCl buffer (25 ml)

1.5 M Tris-HCl (pH 8.8)

Dissolve 4.55 g of Tris base in ~20 ml of deionized or distilled H diluted HCl and adjust the volume to 25 ml with distilled or deionized H

Equilibration stock buffer (500 ml)

6 M urea, 30% (w/v) glycerol, 2% (w/v) SDS in 0.05 M Tris-HCl buffer, (pH 8.8). Pre-prepared equilibration buffers can also be purchased.

Combine 180 g of urea, 150 g of glycerol, 10 g of SDS, and 16.7 ml of Tris-HCl buffer. Dissolve in deionized distilled H Store frozen.

Equilibration buffer 1 (10 ml)

Add 100 mg of DTT to 10 ml of equilibration stock buffer.

O. Adjust the pH of the solution with

O and adjust the volume to 500 ml.

Protocol

Place one IPG strip gel-side up in each channel of a rehydration/equilibration tray, and ﬁll the channels with the recommended volume of equilibration buffer.

Incubate with gentle agitation for 10 min, then decant.

Fill the channels with the recommended volume of equilibration buffer 2, and incubate again for 10 min.

After equilibration, remove the IPG strips and brieﬂy rinse with the SDS-PAGE running buffer you will be using. This step rids the IPG strip of excess iodoacetamide and serves to lubricate the IPG strip for placement on the second dimension.

Equilibration buffer 2 (10 ml)

Add 400 mg of iodoacetamide to 10 ml of equilibration stock buffer.

Table 10.1. Recommended equilibration volumes.

IPG Str ip Length 7 cm 11 cm 17 cm 18 cm 24 cm

Equilibration buffer 1 2.5 ml 4 ml 6 ml 6 ml 8 ml

Equilibration buffer 2 2.5 ml 4 ml 6 ml 6 ml 8 ml

10 min is recommended for each equilibration step.

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2-D Electrophoresis Guide MethodsChapter 10: Second-Dimension SDS-PAGE

Sealing IPG Strips onto SDS-PAGE Gels SDS-PAG E

In this stage, the equilibrated IPG strips are placed on the top of polyacrylamide gels. This enables smooth movement of the focused proteins into the gel for separation by SDS-PAGE.

Reagents

Agarose solution (0.5% [w/v]): Suspend 0.5 g of low-melting agarose (low electroendosmosis, EEO) in 100 ml of SDS-PAGE running buffer, and dissolve it in a boiling water bath or in a microwave oven. Add a few crystals of bromophenol blue (or 100 µl of 1% bromophenol blue) to color the solution slightly.

The agarose solution can be aliquoted into sealed

1.5 ml or 2.0 ml plastic tubes, which can then be melted individually in a 100°C heat block when needed.

Caution: Wear protective gloves, goggles, and a lab coat when handling molten agarose. SDS in the molten agarose can cause the solution to bubble over. Molten agarose and the vessel containing it can cause severe burns if not handled carefully.

Molecular weight standards: SDS-PAGE standards can be applied to gels that have no reference lane. Trim a thin ﬁlter paper to ~4 × 5 mm and pipet 10 μl of SDS-PAGE standards onto the wick. Remove excess solution with ﬁlter paper. Alternatively, use Precision Plus Protein vertical 2-D gels with or without a reference well.

™

standard plugs, which can be used on

Protocol

Position the second-dimension gel cassette so that it is leaning slightly backwards (approximately 30° from vertical). Use AnyGel if available.

Place the equilibrated IPG strip (anodic side on the left) onto the long plate with the plastic backing against the plate.

Slide the strip between the plates using a spatula to push against the plastic backing. Ensure that the plastic backing remains fully in contact with the long plate and be careful not to damage the gel with the spatula. Make sure the IPG strip is positioned directly on top of the second-dimension gel without any bubbles in the interface between the two gel surfaces.

Optional: Slip a wick soaked with molecular weight standards or use a Precision Plus Protein standard plug in the slot in the gel sandwich next to or overlapping an end of the IPG strip.

To secure the strip in place, overlay it with molten agarose solution. Use warm molten agarose, as hot agarose may accelerate decomposition of the urea in the equilibration buffer. Avoid trapping air bubbles between the IPG strip and second-dimension gel. Dislodge any bubbles by tapping the plastic backing on top of the strip.

Stand the gel upright and allow the agarose to set for 5–10 min before loading the gel into the electrophoresis cell.

™

stands,

Buffers and Solutions

This step requires the use of running buffer appropriate for the gel chemistry you are using.

SDS-PAGE Running Buffer (Tris-HCl and TGX™ formulations)

Prepare sufﬁcient 1× Tris/glycine/SDS running buffer to run the number of gels in the system selected:

1 L of 1× Tris/glycine/SDS (25 mM Tris, 192 mM glycine, 0.1% SDS)

Tris base 3.03 g Glycine 14.4 g SDS 1.0 g Distilled or deionized H

Alternatively, dilute 10× stock solution (catalog #161-0732) to the desired volume.

Protocol

Perform SDS-PAGE according to the running conditions speciﬁed for the electrophoresis system you are using. In general:

Insert the gel cassettes in the electrophoresis apparatus and ﬁll the buffer chamber(s) with SDS running buffer. SDS running buffer temperature should be kept constant at 20°C if the chamber design allows for external cooling.

Connect the electrophoresis cell to a power supply and perform electrophoresis at 5–10 V per cm of gel until the sample has concentrated at the starting point of the separation gel. Then continue with the voltage settings recommended by the instruction manual for the electrophoresis system you are using.

After electrophoresis, carefully open the cassettes and use a spatula to separate the agarose overlay, including the IPG strip, from the polyacrylamide gel.

Carefully peel the gel from the cassette and place it in a container with ﬁxative or staining solution, depending on the staining procedure used (see Chapter 11).

O to 1 L

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2-D Electrophoresis Guide MethodsMethods

TABLE OF CONTENTSTABLE OF CONTENTS

CHA P TER 11

Protein Detection

100 101

2-D Electrophoresis Guide MethodsChapter 11: Protein Detection

Tips for Total Protein Staining



Stain gels at room temperature with gentle agitation (for example, on an orbital shaker), making sure the gel is completely covered with stain solution at all times



Use any convenient glass or plastic container that is appropriate to the method chosen. Use glass containers with silver staining methods or with Flamingo

™

stain. Use plastic trays with

SYPRO Ruby stain



Use Bio-Rad’s Dodeca™ stainers for high-throughput staining



Wear gloves during the staining process, and handle gels only by the edges and corners. Wet gloves with water or buffer before handling the gel to keep the gel from sticking and tearing



Use clean and dust-free containers for gel staining. Place a lid on the container to avoid contamination of the staining solution



Use pure chemicals and highly puriﬁed water (conductivity <2 μS)



When performing gel staining with ﬂuorescent dyes, cover the staining tray with foil during incubations

Long-Term Storage of Stained Gels

Gels stained with a visible stain can serve as a permanent record of the SDS-PAGE separation. Stained gels may be stored indeﬁnitely when dried between cellophane sheets. To dry stained gels, the gel is placed on a sheet of wet cellophane. A second sheet of wet cellophane is carefully laid over the gel with care taken not to introduce bubbles or wrinkles. The gel, sandwiched between two sheets of wet cellophane, is clamped into a frame and allowed to dry.

The most common problem associated with drying gels is cracking. Cracking is best prevented by soaking the gel for at least 30 min in a 2% (w/v) solution of glycerol in water prior to drying. Alternatively, a commercially available gel-drying solution may be used.



Fluorescent dyes like Flamingo and Oriole™ ﬂuorescent gel stains have a higher dynamic range than Coomassie (Brilliant) Blue or silver staining techniques and are, therefore, recommended for quantitative protein analysis



Gels stained with ﬂuorescent dyes can be counterstained with Bio-Safe

™

Coomassie stain for further reference and to enhance sensitivity of the Coomassie stain



Silver staining is not generally recommended when protein spots will be identiﬁed by mass spectrometry, though some formulations are compatible with mass spectrometry at the expense of promised sensitivity. Use Bio-Safe Coomassie or ﬂuorescent dyes like Flamingo or Oriole instead



As an alternative to drying gels, seal them in zip-top plastic bags in either water or, for long-term storage, water with 0.005% sodium azide. Fill the bag with water, insert the gel, expel the water, and seal the bag

Total Protein Staining

For more detailed instructions, refer to the respective instruction manuals.

Bio-Safe Coomassie Stain

Instruction manual: bulletin 4307051.

Protocol

Fig. 11.1. 2-D gel stained with Bio-Safe Coomassie stain.

Wash gels three times for 5 min each in distilled or deionized H

Remove water from staining container and add Bio-Safe Coomassie stain to completely cover the gel. Agitate for at least 1 hr.

Rinse in distilled or deionized H at least 30 min. Stained gels can be stored in water.

O for

Flamingo Fluorescent Gel Stain

Instruction manual: bulletin 10003321. Refer to Table 11.1 for solution volumes.

Protocol

Table 11.1. Flamingo ﬂuorescent gel stain.

Volume of ﬁxing Volume of staining Gel size solution per gel solution per gel

Mini (8.6 × 6.8 cm) 100 ml 50 ml

Midi (13.3 × 8.7 cm) 200 ml 100 ml

Large 500 ml 250 ml (16 × 16 cm or 16 × 20 cm)

Larger (25.6 × 23 cm) 1,000 ml 500 ml

Fig. 11.2. 2-D gel stained with Flamingo stain.

Place gel in a staining tray with ﬁxing solution (40% ethanol, 10% acetic acid). Cover the tray and agitate gently for at least 2 hr.

Pour off the ﬁxing solution and add 1× stain solution (dilute 1 part Flamingo ﬂuorescent gel stain with 9 parts deionized or distilled H

O). Cover the

tray and agitate gently. Stain for at least 3 hr.

Optional background reduction: Carefully pour off the stain solution and replace with an equal volume of

0.1% (w/v) Tween 20. Cover the tray and agitate gently for 10 min.

Rinse gel with deionized or distilled H

O prior to imaging.

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2-D Electrophoresis Guide MethodsChapter 11: Protein Detection

Total Protein Staining (con td.)

Oriole Fluorescent Gel Stain

Instruction manual: bulletin 10017295. Refer to Table 11.2 for solution volumes.

Protocol

Note: Do not ﬁx or wash gel prior to staining. This will

make staining less sensitive.

Table 11.2. Oriole ﬂuorescent gel stain.

Gel size Volume of staining solution per gel

Mini (8.6 × 6.8 cm) 50 ml

Midi (13.3 × 8.7 cm) 100 ml

Large (16 × 16 cm or 16 × 20 cm) 250 ml

Larger (25.6 × 23 cm) 500 ml

Fig. 11.3. 2-D gel stained with Oriole stain.

If using the 5 L conﬁguration, prepare the Oriole stain solution by adding 400 ml of methanol to the 1 L bottle of diluent. Then add 10 ml of Oriole ﬂuorescent gel stain concentrate and mix well by shaking.

Place gel in a staining tray with Oriole ﬂuorescent gel stain. Cover the tray and agitate for ~1.5 hr. For best results, do not leave gel in stain for more than 2 hr.

Rinse the gel in deionized distilled H

O prior to imaging. Destaining is

not necessary.

SYPRO Ruby Protein Gel Stain

Instruction manual: bulletin 4006173. Refer to Table 11.3 for solution volumes.

Protocol

Table 11.3. SYPRO Ruby ﬂuorescent gel st ain.

Gel size Volume of staining solution per gel

8 × 108 cm 50 ml

16 × 20 cm 330 ml

20 × 20 cm 50 0 ml

Fig. 11.4. 2-D gel stained with SYPRO Ruby stain.

Wash the gel in one of the following gel ﬁxing solutions for 30 min:



10% methanol, 7% acetic acid



25% ethanol, 12.5% trichloroacetic acid



10% ethanol, 7% acetic acid



50% ethanol, 3% acetic acid



40% ethanol, 10% acetic acid

Remove the wash solution and cover the gel with SYPRO Ruby protein gel stain. In general, use ~10 times the volume of the gel. Using too little stain will reduce sensitivity.

Stain the gel with continuous gentle agitation for at least 3 hr for best sensitivity. Speciﬁc staining can be seen in 30–90 min. For convenience, gels can be left in the stain solution overnight (16–18 hr).

Rinse the gel in 10% methanol (or ethanol), 7% acetic acid for 30–60 min to decrease background ﬂuorescence. Rinse the gel in water before imaging.

Silver Stain Plus™ Kit

Instruction manual: bulletin LIT-442. Refer to Table 11.4 for solution volumes and incubation times.

Components:



Fixative enhancer concentrate



Silver complex solution



Reduction moderator solution



Image development reagent



Development accelerator reagent



Empty 1L bottle for development accelerator reagent

Protocol

Prepare the development accelerator reagent solution. Add the entire contents (50 g) of development accelerator reagent to deionized distilled H

O and bring volume up to 1 L.

Store at 4°C and use within 3 months.

Fixative step. Make ﬁxative enhancer solution by mixing 50% (v/v) reagentgrade methanol, 10% (v/v) reagent-grade acetic acid, 10% (v/v) ﬁxative enhancer concentrate, and 30% (v/v) deionized distilled H

O. After gel electrophoresis,

place gels in the ﬁxative enhancer solution with gentle agitation.

Water wash steps. Decant the ﬁxative enhancer solution from the staining vessel. Rinse gels in deionized or distilled H

O with gentle agitation.

Decant water and replace with fresh rinse water and rinse. Decant rinse water.

Staining step. To prepare staining solution, add 35 ml of deionized or distilled H

O to a beaker or ﬂask with

a Teﬂon-coated stir bar. Add in the following order: 5.0 ml of silver complex solution, 5.0 ml of reduction moderator solution, and 5.0 ml of image development reagent. Immediately before use, quickly add 50 ml of development accelerator solution. Stir well. Stain gels with gentle agitation.

Stop step. After the desired staining is reached, place the gels in 5% acetic acid solution to stop the staining reaction. After stopping the reaction, rinse the gels in high purity water for 5 min. Then the gels are ready to be dried or photographed.

Table 11.4. Silver Stain Plus.

Gel Thickness

0.75 –1. 0 m m

Step Time Mini Gel Large G el

Fixative* 20 min 400 ml 800 ml

Water washes 10 min 400 ml 800 ml

Stain** 20 min 100 ml 300 ml

Stop 15 min 400 ml 400 ml

Gel Thickness

1.5 –3. 0 m m

Step Time Mini Gel Large G el

Fixative* 30 min 400 ml 800 ml

Water washes 20 min 400 ml 800 ml

Stain** 20 min 100 ml 300 ml

Stop 15 min 400 ml 400 ml

* Gels may be lef t in this solution indeﬁnitely prior to staining;

therefore, it is not ne cessary to carry out the entire procedure directly following electrophoresis.

** Stain until the desired intensity is reached. It may take at least

15 min before the ﬁrst bands or spots become visible. Staining time is dependent on the sample and quantit y loaded.

Fig. 11.5. 2-D gel st ained with Silver stain.

104 105

2-D Electrophoresis Guide Methods

TABLE OF CONTENTS

CHAPTER 12

In-Gel Trypsin Digestion

106 107

2-D Electrophoresis Guide MethodsChapter 12: In-Gel Trypsin Digestion2-D Electrophoresis Guide

Tryptic Digestion Protocol

This protocol for tryptic digestion of gel pieces (plugs) excised from SDS-PAGE gels is derived from the protocol described by Speicher et al. (2000). It can be used in conjunction with any of the non-silver stains described in this guide.

Reagents and Solutions



Ammonium bicarbonate, NH4HCO



Acetonitrile



Iodoacetamide



HPLC-grade water (for example, Burdick and Jackson AH365)



Triﬂuoracetic acid (TFA) (for example, Thermo Scientiﬁc 28904)



Octyl b-D-glucopyranoside (for example, Sigma Aldrich 08001)



Sequencing-grade modiﬁed trypsin, porcine (for example, Promega V5111)

Destaining buffer (50:50 ACN:0.2 M NH4HCO3)

Dissolve 158 mg of NH4HCO3 in 5 ml HPLC-grade water and add 5 ml acetonitrile.

50 mM NH4HCO3

Dissolve 79 mg of NH4HCO3 in 20 ml of water.

Reducing solution

Dissolve 555 mg of DTT in 3 ml of 50 mM NH4HCO3.

Alkylating solution

Dissolve 54 mg of iodoacetamide in 3 ml of 50 mM NH

HCO3.

Trypsin solution (20 μg/ml)

Dissolve 20 μg of trypsin in 1 ml of 50 mM NH4HCO3.

Extraction solvent

Combine 950 µl of 1% TFA with 50 µl of 1% octyl D-glucopyranoside.

Destaining Gel Plugs from Silver-Stained Gels (Pre-Treatment)

Gels that have been stained with a mass spectrometry–compatible silver stain beneﬁt from an additional treatment to remove silver metal by oxidation.

All materials used should be ACS reagent grade or better.

Solution A (30 mM potassium ferricyanide)

To prepare 50 ml, dissolve 494 mg of potassium ferricyanide [K may be stored indeﬁnitely at room temperature.

Solution B (100 mM sodium thiosulfate)

To prepare 50 ml, dissolve 791 mg of anhydrous sodium thiosulfate [Na be stored for one year in a sealed bottle.

Protocol

Prepare the silver destain solution just prior to use. It is good for only one use. Discard any excess.

Fe(CN)6] in 50 ml of water. This solution

] in 50 ml of water. This solution may

2S2O3

Mix Solutions A and B in a 1:1 ratio. This is the silver destain solution.

Place each gel plug in a 0.5 ml or

1.5 ml plastic tube.

Add 50 µl of silver destain solution. Incubate 20 min at room temperature.

Using a laboratory pipet, remove the silver destain solution and add 50 µl of fresh solution.

Repeat steps 2 and 3 for a total of three treatments. Following the last incubation, remove the silver destain solution.

General Destaining Protocol

Add 100 μl of destaining buffer to the gel plug and incubate for 30 min. Remove and discard the solution.

Repeat step 1 two more times.

Reduction and Alkylation Protocol

This step is not necessary for 2-D gel plugs if they have already been reduced and alkylated during the sample preparation or equilibration steps.

Add 400 μl of destaining buffer to the gel plug and incubate overnight at room temperature.

Remove destaining buffer and dehydrate the gel by adding 50 μl of acetonitrile. Incubate 10 min at room temperature and remove excess solution (for example, by aspiration).

Dry the gel piece for 30 min in a laminar ﬂow hood.

Add 100 μl of reducing solution to the gel plug and incubate 30 min at room temperature. Remove excess liquid.

Add 100 μl of alkylating solution to the gel plug and incubate 30 min at room temperature in the dark. Remove excess liquid.

Digestion Protocol

Add 50 μl of acetonitrile to the gel plug and incubate for 10 min at room temperature. Remove excess liquid and proceed to digestion.

To the dried gel plug, add a volume of trypsin solution equivalent to the volume of the original hydrated plug (1.5 mm plug = 3.4 μl).

Incubate at room temperature for 10 min (center of gel will change from opaque to clear). If gel plugs aren’t swollen, add a few more μl of trypsin solution and incubate for an additional 10 min.

Add enough 50 mM NH to cover the gel plug (~10 μl).

Incubate at 37°C for at least 3 hr.

Extraction Protocol

Remove trypsin solution from the gel plug, and store it in another vial.

To the gel plug, add 2–8 µl of extraction solvent. For MALDI-MS analysis, keep this volume as small as possible (2–3 µl). For LC-MS analysis, add 8 µl.

Incubate 30 min at room temperature.

Combine extraction solvent with trypsin solution.

HCO3

Proceed with the procedure described below.

108 109

2-D Electrophoresis Guide Troubleshooting

2-D Electrophoresis Guide

TABLE OF CONTENTS

PART III

Troubleshooting

110 111

2-D Electrophoresis Guide Troubleshooting

Isoelectric Focusing

Problem Cause Solution

Initial low or zero current Poor contact between IPG strips Make sure that the gel side of the IPG strip

and electrodes is in contact with the electrode

For the gel-side down conﬁguration with

the PROTEAN

i12™ cell, use the IPG

strip retainers

Incomplete wetting of Wet the electrode wicks with distilled or electrode wicks deionized H

O until they are damp, but not

soaking wet

Incomplete IPG strip rehydration Check the rehydration volumes and times for the lengths of IPG strips used

No current in any lane No contact between the Make sure that:



electrode assembly and

The electrode assembly is properly

IPG strips seated in the focusing tray



The IPG strips are positioned correctly, (for example, that the gel is in direct contact with the electrode)

No contact between the Make sure that:



electrode assembly

The gold contact pin of the negative (–) and instrument assembly is in direct contact with the cathode bar on the instrument



The positive (+) assembly is completely inserted into the anode of the instrument

Voltage does not High levels of ionic contaminants Keep salt concentrations under 40 mM; increase beyond initial in sample solution (optimum salt if necessary, desalt the sample

™

low voltage steps concentration is ~10 mM, though (for example with Micro Bio-Spin up to 40 mM can be tolerated) columns or the ReadyPrep

™

2-D cleanup kit)

Salt collects in electrode wicks, so

replace electrode wicks from time to time (every 2 hr) during the initial low-voltage steps. Several hours may be needed for ionic contaminants to leave IPG strips

Voltage does not reach Programmed voltage is too Lower the voltage maximum set for the programmed value, high for the pH range and focusing step; the conductivity and the or maximum voltage is length of IPG strip length and type of IPG strip determine the reached very slowly. voltage maximum that can be reached

Note: good focusing may be obtained even if programmed voltage is never reached

Ampholyte concentration is Lower the ampholyte concentration too high. Up to 1% (v/v)

Bio-Lyte

ampholytes may be used, but ampholytes increase conductivity; therefore, voltage will be lower with increasing concentrations

Isoelectric Focusing (con td.)

Problem Cause Solution

Excess sample during rehydration Use correct rehydration volumes for did not enter gel, or IPG gels are the lengths of the IPG strips used overswelled with excess sample

Voltage is too high for the IPG Program Vh for the IEF step to ensure strip size and pH gradient complete focusing of the sample

Large ﬂuctuations in IPG strips contain poorly Check rehydration volumes and times voltage and current rehydrated regions, or IPG strips

have dried out during the run Make sure that the rehydration solution is evenly distributed during rehydration and that the IPG strips are completely covered with mineral oil

Burning of strips Current limit is too high Use a current limit of 50 µA/IPG strip

IPG strips have dried out Make sure that the IPG strips are covered

with mineral oil or equivalent

Electrode wicks are too wet or Wet the electrode wicks with distilled contain incorrect electrode solution or deionized H

O until they are damp,

not soaking wet

Incorrect rehydration Check the composition of the solution composition rehydration solution

Sample is leaking from Cup positioning is incorrect When positioning the cup holder, make the sample cups sure that it clicks into place at the edges

of the focusing tray

The cup is positioned in an Make sure that the IPG strips are area of the IPG strip that is rehydrated evenly and thoroughly not completely rehydrated

The cup is malfunctioning Replace cup

SDS-PAGE

Problem Cause Solution

Low or zero current, With a precast gel, the tape Remove the tape and samples do not at the bottom of the gel cassette migrate into the gel was not removed

Insufﬁcient buffer in the inner Fill the inner and outer buffer chambers or outer buffer chamber to ensure that the IPG well is completely covered

Electrical disconnection Check the electrodes and connections

Running time slower or Incorrect running buffer Check the buffer composition and type faster than expected concentration or type

Leaking from inner Incomplete gasket seal Wet the gasket with running buffer buffer chamber before use



Improper assembly of the gel

Ensure that the top edge of the short into the electrode/ companion plate ﬁts under the notch at the top assembly of the gasket



Ensure that the top of the short plate touches the green gasket

112 113

2-D Electrophoresis Guide Troubleshooting

Total Protein Staining

Problem Cause Solution

Spots not visible (see 2-D No protein in the gel Use another staining method to conﬁrm Gel Evaluation, below) that there is protein in the gel

Malfunctioning imaging Check the instrument manual for system or incorrect troubleshooting information, or contact imaging parameters the imaging instrument manufacturer

Poor staining Insufﬁcient protein in the gel Repeat the experiment with a load sensitivity higher protein quantity

Dirty staining trays (for example, Clean the staining trays and other with silver staining) equipment thoroughly with laboratory glassware cleaner

Insufﬁcient stain volume Follow the recommendations for stain volume appropriate to the gel size

Insufﬁcient staining time Increase staining time

Reuse of staining solution To ensure quantitative reproducibility of a 2-D experiment, never reuse staining solution

High or uneven Dir ty equipment or staining trays Clean the staining trays and other equipment background staining thoroughly with laboratory glassware cleaner

Too much time in staining solution Restrict the time in staining solution as recommended

Wash the gel in water or respective destaining solution for >30 min

Reagent impurities Make sure that the water and reagents used for staining are of the highest possible quality

Total Protein Staining (contd.)

Problem Cause Solution

Speckles or blotches in Particulate material from reagents, Clean the staining trays and other the gel image staining tray, dust, or gloves equipment thoroughly with laboratory

glassware cleaner

Limit exposure of gels and staining solution to open air

Use dust-free gloves, and handle gels only by the edges

Uneven staining Insufﬁcient shaking during staining Agitate the gel during staining

Gel shrinkage Some gel shrinkage occurs Transfer the gel to water

during staining

2-D Gel Evaluation*

Problem Cause Solution

No Spots or Fewer Spots than Expected

Across the gel Insufﬁcient sample was loaded Check the sample concentration by protein assay

Check that the protein assay is functioning properly and that it is not responding to interfering substances in your sample

Insufﬁcient sample entered Start IEF at a low ﬁeld strength the IPG strip Make sure that the IPG strips are in the correct orientation in the focusing tray

Diffuse, uneven Insufﬁcient washing Perform more washing steps. Use puriﬁed background in laboratory water and clean staining trays silver-stained gel

Do not place too many gels in one tray. Fully immerse the gels in the staining solution; they should not stick to the staining tray

Insufﬁcient ﬁxative (some uneven Apply a longer ﬁxing procedure background stain is normal when using a silver stain. Due to migration of different chemicals and ions into the gels, some regions can be stained with different colors or intensities)

Contaminant(s) in the agarose Prepare fresh overlay solution overlay solution

Check that the orientation of electrical connections

Increase the solubility strength of the

2-D sample solution; insoluble proteins will not enter the IPG strip

Failure of detection reagents Run a lane of unstained standards adjacent

to the second-dimension separation. If the standards are not detected, check the expiration dates and the formulations of all detection reagents

Staining method not See Chapter 3 for sample loading sensitive enough recommendations dependent on the staining technique used

Poor protein transfer from Perform the ﬁrst stage of SDS-PAGE at IPG strip to SDS-gel low voltage (50 V) for >20 min until the bromophenol blue front enters the separation gel (time depends on gel size)

* Also refe r to Berkelman et al. (2004) and Bio-Rad Laboratories (2005).

114 115

2-D Electrophoresis Guide Troubleshooting

2-D Gel Evaluation (co ntd .)

Problem Cause Solution

No Spots or Fewer Spots than Expected

In high molecular Sample may have undergone Include appropriate protease inhibitors weight regions proteolysis prior to IEF and keep the sample on ice or in a cold room during sample preparation

Insufﬁcient equilibration Incubate IPG strips in sufﬁcient volumes

of each equilibration buffer for up to 15 min with mild agitation

Poor entry of high molecular Use active sample loading in the focusing weight proteins during rehydration tray or cup loading (the pore size of the acrylamide in the IPG strip is very small during the early stages of rehydration)

Poor entry of high molecular Increase equilibration time (2 × 15 min) weight proteins into the second-dimension gel

Horizontal Streaking

Across the entire gel Protein overloading Use less sample

Horizontal Streaking (contd.)

Problem Cause Solution

Across the entire gel DNA contamination Treat the sample with a nuclease

Make sure that the nuclease is active and

that digestion is adequate; a very viscous sample implies that nuclease treatment has failed

Incomplete focusing Optimize the sample focusing time by or overfocusing running a time course. For example,

run the sample on 6 IPG strips and remove an IPG strip at each time point (20 kV-hr, 30 kV-hr, 40 kV-hr, etc.)

Incomplete IPG strip rehydration Check the rehydration volumes and times

for the lengths of IPG strips used

Partial Incomplete IPG strip rehydration Check the rehydration volumes and

times for the lengths of IPG strips used

If the sample appears unevenly distributed,

or if areas of the IPG strip are not wetted with sample, slide the IPG strip back and forth several times along the length of the channel in the focusing tray

Perform prefractionation to enrich the

protein of interest and lower the amounts of other abundant proteins

Use a longer IPG strip and larger gel size

to allow for a greater protein load

Proteins are not properly and Solubilize proteins completely using a stably solubilized strong chaotropic extraction reagent. The concentrations of urea, thiourea,

detergents, carrier ampholytes, and DTT are also critical. Every sample type typically requires a new sample preparation method

Allow sufﬁcient time for full denaturation

and solubilization; for example, incubate the sample in the solubilization solution at room temperature for 1 hr before applying it to the IPG strip

Regional Protein overloading Use less sample

Perform prefractionation to enrich the

protein of interest and lower the relative amounts of other abundant proteins

Use a longer IPG strip and larger gel size

to allow for a greater protein load

In the basic range Depletion of DTT in the basic Treat the sample with the ReadyPrep of the gel range of the IPG strip reduction-alkylation kit prior to IEF

116 117

2-D Electrophoresis Guide Troubleshooting

Horizontal Streaking (contd.)

Problem Cause Solution

Spots Incomplete IEF Optimize the sample focusing time by

running a time course. For example, run the sample on 6 IPG strips and remove an IPG strip at each time point (20 kV-hr, 30 kV-hr, 40 kV-hr, etc.)

Intermittent Contaminants such as salts, Use appropriate contaminant removal ionic detergents (for example, techniques, such as treatment with SDS), peptides, nucleic acids, the ReadyPrep 2-D cleanup kit lipids, polysaccharides, phenolic compounds

Vertical Streaking (contd.)

Problem Cause Solution

At one end of the gel Protein aggregation or Dilute the sample to 3–5 µg/µl for (cup loading) precipitation caused by cup loading

too much protein or sample loading problems Perform a protein assay prior to IEF to

ensure correct protein load. The total amount of protein that should be loaded onto an IPG strip depends on the length of the strip and the stain that will be used to visualize the results

Load the sample using in-gel sample loading

Prolong the time on the initial low-voltage

steps and increase the voltage gradually

Field strength used for sample Reduce the ﬁeld strength to ~10 V/cm loading is too high IPG strip length

Poor protein solubility Increase the solubilizing strength of

2-D sample solution

Isolated streaking Improper rehydration of IPG strip Check the rehydration volumes and times

for the lengths of IPG strips used

If the sample appears unevenly distributed,

or if areas of the IPG strip are not wetted with sample, slide the IPG strip back and forth several times along the length of the channel in the focusing tray

Vertical Streaking

Across the entire gel Leaking of the upper buffer Prior to inserting the gel(s) into the vertical

reservoir (cathode) of the vertical electrophoresis cell, wet the gaskets of the electrophoresis unit electrophoresis chamber with water or

use a small amount of vacuum grease

Incomplete equilibration Increase equilibration time to 15 min

Old DTT and iodoacetamide Use fresh reagents for the equilibration step preparations used in equilibration

Point streaking Dust or other particles in the Filter gel solutions through a 0.45 μm (handcast gels) gel solutions membrane and into a dust-free container

Vertical streaks Insufﬁcient binding of SDS Check the SDS concentration (>1%) in the connected to a spot to protein equilibration solution

Increase equilibration time: equilibrate IPG strips for 2 × 15 min

Incorrect pH in resolving gel buffer; Ensure that the pH of the Tris buffer used incorrect pH decreases mobility for gel casting is 8.8 of protein-SDS complexes and causes vertical streaks

Buffer leakage Ensure that the upper buffer reservoir

is not leaking

118 119

2-D Electrophoresis Guide Troubleshooting

Vertical Streaking (contd.)

Problem Cause Solution

Twin vertical spots Improper placement of the IPG Make sure that the focused IPG strip is or vertical doublets strip onto the gel in full contact with the gel

Temperature gradient in the gel Lower the power settings for the second-

dimension SDS-PAGE run, especially when using cells that provide only one-sided cooling of the gel

Use a better circulation system to improve

heat dissipation during a run

Blank vertical stripes Air bubble trapped in the agarose Ensure that the 2-D gel has a straight, that joins the IPG strip to the top level top edge and that the IPG strip is of the gel in direct contact with the 2-D gel along its

entire length. Squeeze out air bubbles by pressing on the plastic backing of the IPG strip

Use a 0.5% agarose overlay solution to

prevent the IPG strip from coming loose or moving. To minimize the number of bubbles in the overlay, melt the agarose overlay solution completely prior to loading

Vertical Streaking (contd.)

Problem Cause Solution

Blank stripes near pH 7 Excessive DTT (>50 mM) in the Lower the amount of DTT in the

IPG sample solution rehydration solution

Blank stripes at the Salt buildup Remove ionic contaminants from the electrodes, especially samples with Bio-Rad´s ReadyPrep 2-D at the cathode cleanup kit or by desalting

Blank vertical regions Interfering substances; impurities Remove contaminants from the samples

in the rehydration/sample solution with the ReadyPrep 2-D cleanup kit or by desalting

Use high-quality reagents and chemicals

for electrophoresis to minimize the risk of impurities. Replace chemicals of questionable or unknown shelf life, origin, or quality, as these products can also contribute to poor 2-D results

Air bubble trapped in the agarose Ensure that the 2-D gel has a straight, that joins the IPG strip to the top level top edge and that the IPG strip is of the gel in direct contact with the 2-D gel along

its entire length. Squeeze out air bubbles by pressing on the plastic backing of the IPG strip

Use a 0.5% agarose overlay solution to

prevent the IPG strip from coming loose or moving. To minimize the number of bubbles in the overlay, melt the agarose overlay solution completely prior to loading

Insufﬁcient rehydration of a region Make sure that the IPG strip is not sticking of the IPG strip, or tears resulting to the bottom of the rehydration tray from improper handling, resulting in the absence of focused protein Check the integrity of rehydrated IPG in that region strips prior IEF

Focusing of an amphoteric Apply sample cleanup nonprotein contaminant (for example, phospholipid or HEPES) prevents protein focusing around the pI of the contaminant

120 121

2-D Electrophoresis Guide Troubleshooting

Problem Cause Solution

Other Problems

Wavy spots Insufﬁcient overlay solution used Overlay the gel with water-saturated

in gel casting butanol (n-butanol, l-butanol, or t-butanol)

or t-amyl alcohol immediately after gel casting. These ensure that the gel has a clean, straight top edge

Use precast gels

Use the overlay recommended by the

manufacturer of the electrophoresis cell

Localized wavy Problems with casting second- Optimize the APS and TEMED disturbance of spots dimension acrylamide gel: concentrations

not evenly polymerized, gel cassette leaking, etc. Degas solutions prior to the addition of APS/TEMED

Perform casting at room temperature,

warming the glass plates if necessary. Be aware that the polymerization process is temperature dependent. If the temperature is too low, polymerization may be compromised

Use precast gels

Known proteins appearing Protein carbamylation Do not prepare samples too far ahead as multiple spots or at the of time in urea wrong position

Do not expose urea-containing samples to

high pH or temperatures that exceed 30°C

Protein oxidation Increase DTT concentration

Protein proteolysis Add protease inhibitors, perform (during sample preparation) manipulations as quickly as possible,

and keep solutions as cold as possible

For fur ther he lp or adv ice, please contact the Bio-Rad Technical Support department. In the United States, the Technical Support department is open Monday– Friday, 5:00 AM–5:00 PM, Paciﬁc time.

Phone: 1-800 -424-6723

Fa x: 1-510-741-58 02

Email: LSG_TechServ_US@bio-rad.com (for U.S. and international customers)

Online technical support and worldwide contact information are available at www.consult.bio-rad.com.

122 123

2-D Electrophoresis Guide Appendices

2-D Electrophoresis Guide

TABLE OF CONTENTS

PART IV

Appendices

124 125

2-D Electrophoresis Guide Appendices

Appendix A

Glossary

%C Cross-linker concentration; weight percentage of cross-linker in a polyacrylamide

gel. Effective pore size of a gel is a biphasic function of %C

%T Monomer concentration (acrylamide + cross-linker) in a gel (in g/100 ml).

Effective pore size of a gel is an inverse function of %T, and gels can be made with a single, continuous %T throughout the gel (single-percentage gels), or they can be cast with a gradient of %T through the gel (gradient gels)

2-D electrophoresis Two-dimensional electrophoresis. Proteins are separated ﬁrst according to

isoelectric point (pI) by isoelectric focusing (IEF) and then according to size by SDS-PAGE, yielding a two-dimensional protein map of spots

2-Mercaptoethanol Reducing agent used for cleavage of intra- and intermolecular disulﬁde bonds to

achieve complete protein unfolding and to maintain all proteins in a fully reduced state. Also known as b-mercaptoethanol or BME

Acrylamide Monomer used with a cross-linker to form the matrix used for separating proteins

or small DNA molecules

Ammonium persulfate Initiator used with TEMED (catalyst) to initiate the polymerization of acrylamide and (APS) bisacrylamide in making a polyacrylamide gel; (NH

Ampholyte Amphoteric molecule that exists mostly as a zwitterion in a certain pH range.

Ampholytes are used to establish a stable pH gradient for use in isoelectric focusing

Amphoteric Containing both acidic and basic groups

Anode Positively charged electrode. Negatively charged molecules (anions) move towards

the anode, which is usually indicated by the color red

Anionic dye Negatively charged compound used as a stain; used in blotting to stain proteins

immobilized on membranes such as nitrocellulose or PVDF

4)2S2O8

CHAPS Zwitterionic detergent (having both positively and negatively charged groups

with a net charge of zero) that is widely used for protein solubilization for IEF and 2-D electrophoresis; 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate

Comb Object used to cast wells in an agarose or acrylamide gel. In PAGE applications,

square-bottom combs are inserted into the gel sandwich before polymerization to form square-bottomed wells

Coomassie (Brilliant) Anionic dye used in the total protein staining of gels and blots and that comes in Blue two forms: Coomassie (Brilliant) Blue G-250 differs from Coomassie (Brilliant) Blue

R-250 by the addition of two methyl groups

Criterion blotters, and gels includes the Criterion and Criterion

™

cells, Family of Bio-Rad products used for midi-format vertical electrophoresis;

™

Dodeca™ cells, Criterion blotter, and

Criterion precast gels

Cross-linker Molecule (for example, bis-acrylamide) used to link polymerizing monomer

molecules together to form a netlike structure within the gel. The holes in the nets are called the pores, and the pore size is determined in part by the cross-linker concentration. The pores may or may not sieve the macromolecules

Cup loading Application of protein sample onto IPG strips through sample cups applied to the

strips; can improve resolution at extremes of a pH gradient and improve uptake of basic proteins

™

assay kit Bio-Rad’s detergent-compatible protein assay kit

Depletion Reduction in the amount of high-abundance proteins relative to

low-abundance proteins

Discontinuous Electrophoresis gel system that uses different buffers and sometimes buffer system different buffer compositions to focus and separate components of a sample.

Discontinuous systems typically focus the proteins into tighter bands than continuous gel systems, allowing larger protein loads

Antibody Immunoglobulin (Ig); protein produced in response to an antigen, which speciﬁcally

binds the portion of the antigen that initiated its production

Assay Analysis of the quantity or characteristics of a substance

Background Nonspeciﬁc signal or noise that can interfere with the interpretation of valid signals

Bio-Spin

columns Family of Bio-Rad sample preparation products that includes the Bio-Spin® 6 and

Micro Bio-Spin

™

6 columns; used for buffer exchange and desalting applications

Bis or bis-acrylamide A common cross-linker used with acrylamide to form a support matrix;

N,N'-methylene-bis-acrylamide

Blot Immobilization of proteins or other molecules onto a membrane, or a membrane

that has the molecules adsorbed onto its surface

Bromophenol blue Common tracking dye used to monitor the progress of electrophoresis

Carrier ampholytes Heterogeneous mixture of small (300–1,000 Da) polyamino-polycarboxylate

buffering compounds that have closely spaced pI values and high conductivity. Within an electric ﬁeld, they align according to pI to establish the pH gradient

Cathode Negatively charged electrode. Positively charged molecules (cations) move toward

the cathode, which is usually indicated by the color black

Chaotropic agent Chemical that disrupts inter- and intramolecular interactions (for example, urea

and thiourea)

Disulﬁde bond Chemical bond joining two sulfur atoms; commonly found in proteins,

contributing to their secondary and tertiary structures

Dithiotheithol (DTT) Reducing agent used for cleavage of intra- and intermolecular disulﬁde

bonds to achieve complete protein unfolding and to maintain all proteins in a fully reduced state

Electrophoresis Movement of charged molecules in a uniform electric ﬁeld

Equilibration Preparation of protein separated in an IPG strip for second-dimension SDS-PAGE;

reduces and alkylates sulfhydryl groups and saturates proteins with SDS

EXQuest

™

spot cutter Bio-Rad’s brand of spot cutter

Fractionation Separation of a sample into discrete parts for separate analysis; may improve

detection of low-abundance proteins and reduce sample complexity

Glycine Amino acid used as the trailing or slow ion in SDS-PAGE according to Laemmli

(L a e mmli, 1970)

Gradient gel Gel with gradually changing monomer concentration (%T) in the direction of

migration. In SDS-PAGE, gradients are used to separate wider molecular weight ranges of molecules than can be separated with single-percentage gels

Immobilized pH Strips in which buffering groups are covalently bound to an acrylamide gel gradient (IPG) strips matrix, resulting in stable pH gradients. This eliminates problems of gradient

instability and poor sample loading capacity associated with carrier ampholyte–generated pH gradients

126 127

2-D Electrophoresis Guide Appendices

Immunoblotting Blot detection by antibody binding

Immunodetection Detection of a molecule by its binding to an antibody

In-gel sample application Sample application to the IPG strip during IPG strip rehydration; may be passive (In-gel rehydration) or active (in the presence of a low applied voltage)

Ionic strength Measure of the ionic concentration of a solution that affects its resistance

Isoelectric Electrophoresis technique that separates proteins according to their focusing (IEF) isoelectric point (pI)

Isoelectric point (pI) pH value at which a molecule carries no net electrical charge, or at which the

negative and positive charges are equal

–

Leading ion Ion in a discontinous buffer system with a greater mobility, typically Cl

™

MicroRotofor

cells Family of Bio-Rad sample preparation products, including the MicroRotofor

(chloride ion)

and kits liquid-phase IEF cell and MicroRotofor cell lysis kits

Monomer Unit that makes up a polymer (acrylamide is a monomer that is polymerized

into polyacrylamide)

Mini-PROTEAN and gels includes the Mini-PROTEAN Tetra and Mini-PROTEAN

cells Family of Bio-Rad products used for mini-format vertical electrophoresis;

3 Dodeca™ cells

and Mini-PROTEAN precast gels

Molecular weight Mixtures of well-characterized or recombinant proteins used to help monitor markers separation as well as estimate the size of the proteins separated in a gel

Ohm’s Law Describes the mutual dependence of three electrical parameters

(V, voltage; I, current; R, resistance): V = I × R

PAGE Polyacrylamide gel electrophoresis, a common method of separating proteins

based on molecular weight

™

PDQuest

software Bio-Rad’s 2-D gel analysis software

Polyacrylamide Anticonvective, sieving matrix used in gel electrophoresis. Polyacylamide gels

are cast using mixtures of acrylamide monomers with a cross-linking reagent, usually N,N'-methylenebisacrylamide (bis), both dissolved in buffer

Polyacrylamide gel Electrophoresis technique that uses polyacrylamide as the separation medium electrophoresis (PAGE)

™

PowerPac

Family of Bio-Rad power supplies

power supplies

Power supply Instrument that provides the electric power to drive electrophoresis

and electrophoretic blotting experiments

™

Precision Plus Protein

Bio-Rad’s family of recombinant molecular weight markers

standards

PROTEAN

cells Family of Bio-Rad products used for large-format vertical electrophoresis

and isoelectric focusing; includes PROTEAN II xi, PROTEAN II XL,

Plus Dodeca™ cells, and the PROTEAN® i12™ IEF cell

ProteoMiner

PROTEAN

™

beads, Protein enrichment technology that operates on the principle of dynamic range

reagents, and kits reduction; uses a bead-based library of combinatorial peptide ligands to enrich the

amounts of medium- and low-abundance proteins relative to high-abundance proteins

Prestained standards Mixture of molecular weight marker proteins that have covalently attached dye

molecules, which render the bands visible during electrophoresis and transfer

™

RC DC

ReadyStrip

ReadyPrep

assay kit Bio-Rad’s reductant- and detergent-compatible protein assay kit

™

IPG strips Bio-Rad’s brand of IPG strips

™

kits Bio-Rad’s brand of sample preparation and 2-D electrophoresis kits and reagents

Rf value Relative distance a protein has traveled compared to the distance traveled by

the ion front. The R

value is used to compare proteins in different lanes and

even in different gels. It can be used with standards to generate standard curves, from which the molecular weight or pI of an unknown may be estimated

Running buffer Buffer that provides the ions for the electrical current in an electrophoresis run.

It may also contain denaturing agents. The running buffer provides the trailing ions in discontinuous electrophoresis

Sample solution Solution in which a sample is prepared or suspended prior to loading onto

an IPG strip

Sodium dodecyl sulfate Separation of molecules by molecular weight in a polyacrylamide gel matrix in polyacrylamide gel the presence of a denaturing detergent, such as sodium dodecyl sulfate (SDS). electrophoresis SDS denatures polypeptides and binds to proteins at a constant charge-to-mass-ratio. (SDS-PAGE) In a sieving polyacrylamide gel, the rate at which the resulting SDS-coated proteins

migrate in the gel is relative only to their size and not their charge or shape

Sodium dodecyl Anionic detergent that denatures proteins and binds to polypeptides in a constant sulfate (SDS) weight ratio of 1.4 g/g of polypeptide (SDS:polypeptide)

Stain-free technology Protein detection technology involving UV-induced additive that modiﬁes protein

tryptophan residues. Continued exposure to UV light causes ﬂuorescence of the modiﬁed proteins, which are then detected by a CCD imager. Sensitivity of this technique is generally equal to or better than Coomassie staining

Stained standards Mixture of molecular weight marker proteins that have covalently attached dye

molecules; the bands are visible during electrophoresis and transfer

Standard Collection of molecules with known properties, such as molecular weight,

isoelectric point, or concentration. Often used to create standard curves, from which the properties of an unknown may be determined

™

TGX

Bio-Rad’s Tris-glycine extended shelf life precast gels

Total protein stain Reagent that binds nonspeciﬁcally to proteins; used to detect the entire protein

pattern on a blot or gel

Trailing ion Ion in a discontinous buffer system with a lower mobility, typically glycinate

Tri s Organic component of buffer solutions that has an effective buffering range of

pH 7.0–9.2; tris(hydroxymethyl)aminomethane

Trit o n X-10 0 Nonionic detergent widely used for protein solubilization

(for IEF and 2-D electrophoresis)

Twe en 20 Nonionic detergent; used in blot detection procedures as a blocking reagent

or added to wash buffers to minimize nonspeciﬁc binding and background

Unstained standards Mixture of molecular weight marker proteins that do not have covalently attached

dye molecules; the bands are invisible during electrophoresis and transfer, but are useful for molecular weight determination in stained gels

Urea Chaotrope usually included at rather high concentrations (9.5 M) in sample

solubilization buffers for denaturing IEF and 2-D PAGE

Volt-hour (Vh) Voltage multiplied by time is used as a unit for the duration of an IEF run

Western blotting Immobilization of proteins onto a membrane and subsequent detection by

protein-speciﬁc binding and detection reagents

Zwitterion Neutral molecule with positive and negative charges at different locations

128 129

2-D Electrophoresis Guide Appendices

Appendix B

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Sanchez JC et al. (1997). Improved and simpliﬁed in-gel sample applic ation using reswelling of dry immobilized pH gradients. Electrophoresis 18, 324–327.

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Related Bio-Rad Literature

Bio-Rad Laboratories, Inc. (2005) 2-D gel electrophoresis troubleshooting. BioRadiations 116, 29–29.

Bulletin 1069 Colorimetric Protein Assays

Bulletin 2414 The Little Book of Standards

Bulletin 2587 High-Performance 2-D Gel Electrophoresis Using Narrow pH-Range ReadyStrip IPG Strips

Bulletin 2895 Protein Blotting Guide

Bulletin 2998 Protein Standards Application Guide

Bulletin 3103 Removal of Abundant Myofilament Proteins from Rabbit Myocardium Using the ReadyPrep Protein Extraction Kit (Membrane I)

Bulletin 3110 Tips to Prevent Streaking on 2-D Gels

Bulletin 3131 The Rotofor System As a Prefractionation Device Used Prior to Electrophoresis

Bulletin 3133 Molecular Weight Determination by SDS-PAGE

Bulletin 3144 Using Precision Plus Protein Standards to Determine Molecular Weight

Bulletin 3145 Strategies for Protein Sample Preparation

Bulletin 5241 Important Factors Influencing Protein Solubility for 2-D Electrophoresis

Bulletin 5344 Fractionation by Liquid-Phase Isoelectric Focusing in the MicroRotofor Cell: Improved Detection of Low-Abundance Proteins

Bulletin 5398 Enriching Basic and Acidic Rodent Brain Proteins with Ion Exchange Spin Columns for Two-Dimensional Gel Electrophoresis

Bulletin 5754 Compar ison of SYPRO Ruby and Flamingo Fluoresce nt Gel Stains with Respect to Compatibility with Mass Spectrometry

Bulletin 5782 In-Gel Protein Quantitation Using the Criterion Stain Fre e Gel Imaging System

Bulletin 5841 Quantitation of Serum and Plasma Proteins after Enrichment of Low-Abundance Proteins with the ProteoMiner Protein Enrichment System

Bulletin 5911 Mini-PROTEAN TGX Precast Gel: A Versatile and Robust L aemmli-Like Precast Gel for SDS-PAGE

Bulletin 5939 Overcoming the Coomassie Blues

Bulletin 6040 A Guide to Polyacrylamide Gel Electrophoresis and Detection

Bulletin 6138 PROTEAN i12 IEF System: Independent Voltage and Current Control Enables Optimization of First-Dimension IEF Conditions

Bulletin 6139 Versatile Se paration Capabilities of the PROTEAN i12 IEF System

Bulletin 6140 Use of the PROTEAN i12 IEF System for In-Gel Peptide Fractionation Prior to LC-MS and Comparison with Off-Gel Fractionation

Bulletin 4006173 Instruction Manual, SYPRO Ruby Protein Stains

Bulletin 4307051 Instruction Manual, Bio-Safe Coomassie Stain

Bulletin 10003321 Instruction Manual, Flamingo Fluorescent Gel Stain

Bulletin 10017295 Instruction Manual, Oriole Fluorescent Gel Stain

Bulletin 10022069 Instruction Manual, PROTE AN i12 IEF System

Bulletin LIT-442 Instruction Manual, Silver-Stain Plus.

Appendix C

Ordering Information

Catalog # Description

Protein Sample Preparat ion Kits and Reagents

Protein Extraction

163- 2141 MicroRotofor

includes 50 ml protein solubilization buffer (PSB), ReadyPrep

163- 214 2 MicroRotofor Cell Lysis Kit (Plant), 10 preps,

includes 50 ml protein solubilization buffer (PSB), ReadyPrep 2-D cleanup kit (50 reaction size)

163-2143 MicroRotofor Cell Lysis Kit (Yeast), 15 preps,

includes 50 ml protein solubilization buffer (PSB), 15 ml yeast suspension buffer, 2 × 0.5 ml lyticase (1.5 U/µ l)

163- 214 4 MicroRotofor Cell Lysis Kit (Bacteria), 15 preps,

includes 50 ml protein solubilization buffer (PSB), 25 ml bacteria suspension buffer, 1 ml lysozyme (1,5 0 0 U/ µl)

163 -208 6 ReadyPrep

Protein), 20 preps, general purpose protein preparation kit, includes strong detergent ASB-14

163- 214 6 ReadyPrep Mini Grinders, pkg of 20, 1.5 ml

grinding tube, contains grinding resin and matching pestle, sufﬁcient for twent y 100 mg extractions

163 -208 3 ReadyPrep 2-D Rehydration/Sample Buffer 1,

10 ml, protein solubilization reagent, includes 7 M urea, 2 M thiourea, 1% ASB-14, 40 mM Tris, 0.001% bromophenol blue

163 -210 6 ReadyPrep 2-D Starter Kit Rehydration/Sample

Buffer, 10 ml, protein sample buffer, includes 8 M urea, 2% CHAPS, 50 mM DTT, 0.2% Bio-Lyte ampholyte, 0.001% bromophenol blue

163- 214 5 Protein Solubilization Buffer (PSB), pkg of 1,

strongly chaotropic protein solubilization buffer, contains NDSB 201, urea, thiourea, and CHAPS, makes 50 ml solution

163 -2091 ReadyPrep Proteomics Grade Water, 500 ml

161-0730 Urea, 250 g

161-0 719 Tr is, 1 kg

161-04 60 CHAPS, 1g

161-0611 Dithiothreitol (DTT), 5 g

163 -2101 Tributylphosphine (TBP), 0.6 ml, 200 mM

163 -210 9 Iodoacetamide, 30 g

161-0404 Bromophenol Blue, 10 g

Protein Sample Cleanup

163 -213 0 ReadyPrep 2-D Cleanup Kit, 50 preps

163- 214 0 ReadyPrep 2-D Cleanup Kit, 5 preps

732-6 221 Micro Bio-Spin

in Tris buffe r, 50 collection tubes

732-6 227 Bio-Spin

Tris buffer, 50 collection tubes

732-6 228 Bio-Spin 6 Columns, includes 100 columns in

Tris buffer, 200 collection tubes

163 -209 0 ReadyPrep Reduction-Alkylation Kit, 100 preps

™

Cell Lysis K it (Mammal), 15 preps,

™

mini grinders (2 packs of 10 each)

™

Protein Extraction Kit ( Total

™

6 Columns, includes 25 columns

6 Columns, includes 25 columns in

Catalog # Description

Protein Fractionation

163 -210 0 ReadyPrep Sequential Extraction Kit, 5–15 preps

163 -208 5 ReadyPrep Protein Extraction Kit

(Soluble/Insoluble), 20 preps

163-2089 ReadyPrep Protein Extraction Kit

(Cytoplasmic/Nuclear), 50 preps

163 -208 8 ReadyPrep Protein Extraction Kit (Membrane I),

50 preps

163 -208 4 ReadyPrep Protein Extraction Kit (Membrane II),

10 preps

163 -2087 ReadyPrep Protein Extraction Kit (Signal),

50 preps

™

73 2 - 6 711 Aurum

CEX Mini Kit, 2 preps

732- 6710 Aurum A EX Mini Kit, 2 preps

™

170-2800 MicroRotofor

Cell Kit, 100/120 V

170 -28 0 1 MicroRotofor Cell Kit, 220/240 V

170-2986 Rotofor

Puriﬁcation System, 100/120 V

170 -298 7 Rotofor Puriﬁcation System, 220/240 V

170 -292 6 Model 491 Prep Cell, 100/120 V

170-2927 Model 491 Prep Cell, 220/240 V

170 -2908 Mini Prep Cell without Reagent Star ter Kit

Protein Sample Depletion

732-6701 Aurum Serum Protein Mini Kit, 10 preps

™

732-6712 Aurum

163 -3 0 06 ProteoMiner

Afﬁ-Gel® Blue Mini Kit, 2 preps

™

Protein Enrichment Small-

Capacity Kit, 10 preps for 10 mg total protein

163 -3 0 07 ProteoMiner Protein Enrichment Large-

Capacity Kit, 10 preps for 50 mg total protein

Protein Assay Kits and Instruments

500-0001 Bio -Rad Protein Assay Kit I, includes 450 ml dye

reagent concentrate, bovine g-globulin standard; sufﬁcient for 440 standard assays or 2,200 microplate assays

500-0002 Bio-Rad Protein Assay Kit II, includes 450 ml

dye reagent concentrate, bovine se rum albumin standard; sufﬁcient for 440 standard assays or 2,200 microplate assays

™

50 0 - 0111 DC

Protein Assay K it I, includes 250 ml alkaline

copper tartrate solution, 2 L dilute Folin reagent, 5 ml surfactant solution, bovine g -globulin standard; sufﬁcient for 450 standard assays

500-0112 DC Protein Assay Kit II, includes 250 ml alkaline

copper tartrate solution, 2 L dilute Folin reagent, 5 ml surfactant solution, bovine serum albumin standard; sufﬁcient for 450 standard assays

™

500-0120 RC D C

Protein Assay Reagents Package,

includes RC reagents package and DC reagents package, and suf ﬁcient for 450 standard assays

500-0121 RC DC Protein Assay Kit I, includes RC reagents

package, DC reagents package, bovine g-globulin standard; sufﬁcient for 450 sta ndard assays

500-0122 RC DC Protein Assay Kit II, includes RC reagents

package, DC reagents package, bovine serum albumin standard; suf ﬁcient for 450 standard assays

™

500-0201 Quick Start

Bradford Protein Assay Kit 1,

includes 1× dye reagent (1 L), bovine serum albumin standard (5 × 2 mg/ml); sufﬁcient for 200 standard assays or 4,000 microplate assays

132 133

2-D Electrophoresis Guide Appendices

Catalog # DescriptionCatalog # Description Catalog # DescriptionCatalog # Description

500-0202 Quick Start Bradford Protein As say Kit 2,

includes 1× dye reagent (1 L), bovine ser um albumin standard set (2 sets of 7 concentration standards,

0.125 –2.0 mg/ml, 2 ml)

500-0203 Quick Star t Bradford Protein Assay K it 3,

includes 1× dye reagent (1 L), bovine g -globulin standard (5 × 2 mg/ml)

500-0204 Quick S tar t Bradford Protein Assay K it 4,

includes 1× dye reagent (1 L), bovine g -globulin standard set (2 sets of 7 concentration standards,

0.125 –2.0 mg/ml, 2 ml)

™

170-2525 SmartSpec

Plus Spectrophotometer

170 -25 0 2 Standard Cuvette, 1–3.5 ml, quartz

™

170 -2511 trUView

Cuvettes, pack of 100, individually

packaged, disposable DNase- and RNase-free cuvettes

Protein Standards

™

161-0378 Precision Plus Protein

Standard Plugs,

pkg of 24, 1 mm thick aga rose plugs containing 10 Strep-tagged recombinant proteins (10–250 kD), including three reference bands

161-03 63 Precision Plus Protein Unstained Standards,

100 applications

161-03 9 6 Precision Plus Protein Unstained Standards

Value Pack, 500 applications

161-0373 Precision Plus Protein All Blue Standards,

50 applications

161-03 93 Precision Plus Protein All Blue St andards Value

Pack, 500 applications

16 1- 0374 Precision Plus Protein Dual Color Standards,

50 applications

161-03 94 Precision Plus Protein Dual Color S tandards

Value Pack, 250 applications

™

161-0375 Precision Plus Protein

Kaleidoscope™

Standards, 50 applications

161-03 95 Precision Plus Protein Kaleidoscope Standards

Value Pack, 250 applications

161-0377 Precision Plus Protein Dual Xtra Standards,

50 applications

161-03 97 Precision Plus Protein Dual Xtra Standards

Value Pack, 250 applications

™

161-0385 Precision Plus Protein

WesternC™ Pack,

50 applications

161-03 98 Precision Plus Protein WesternC Standards Pack

Value Pack, 250 applications

161-03 99 Precision Plus Protein WesternC Standards

Value Pack, 250 applications

™

161-03 24 Kaleidoscope

Prestained Standards,

broad range, 500 μl

161-03 25 Kaleidoscope Polypeptide Standards, 500 μl

161-03 0 9 Prestained SDS-PAGE Standards, high range,

500 μl

161-03 0 5 Prestained SDS-PAGE Standards, low range,

500 μl

161-0318 Prestained SDS-PAGE Standards, broad range,

500 μl

161-0303 SDS-PAGE Standards, high range, 200 μl

161-0304 SDS-PAGE Standards, low range, 200 μl

161-0317 SDS-PAGE Standards, broad range, 20 0 μl

™

163 -209 3 ReadyStrip

100× pH 7–10 Buffer, includes only

ampholytes, 1 ml

163 -209 8 ReadyStrip 100× pH 3.9 – 5.1 Buffer, includes only

ampholytes, 1 ml

163 -2097 ReadyStrip 100× pH 4.7–5.9 Buf fer, includes only

ampholytes, 1 ml

163 -209 6 ReadyStrip 100× pH 5.5 – 6.7 Buf fer, includes only

ampholytes, 1 ml

163-2095 ReadyStrip 100× pH 6.3–8.3 Buffer, includes only

ampholytes, 1 ml

Bio-Lyte® Ampholyte

pH Range

3/10 3/5 4/6 6/8 5/7 5/8 7/9 8/10

1 ml 163-2094 — — — — — — —

10 m l 16 3 -1112 1 6 3 -1132 1 6 3 -11 42 16 3 -116 2 163-115 2 16 3-1192 1 6 3 -117 2 1 6 3 -11 8 2

25 ml 163-1113 — 163-1143 163-1163 163-1153 163-1193 — —

IPG Strips and Buffers

ReadyStrip IPG strips, 12 per package.

7 cm 11 cm 17 cm 18 cm 24 cm

pH 3–10 163-2000 163-2014 163-2007 163-2032 163-2042

pH 3–10 NL 163-2002 163-2016 163-2009 163-2033 163-2043

pH 3– 6 163-2003 163-2017 163-2010 163-2035 163-2045

pH 4–7 163-2001 163-2015 163-2008 163-2034 163-2044

pH 5–8 163-2004 163-2018 163-2011 163-2036 163-2046

pH 7–10 163-2005 163-2019 163-2012 163-2037 163-2047

pH 3.9– 5.1 163-2028 163-2024 163-2020 163-2038 163-2048

pH 4.7–5.9 163-2029 163-2025 163-2021 163-2039 163-2049

pH 5.5– 6.7 163-2030 163-2026 163-2022 163-2040 163-2050

pH 6.3– 8.3 163-2031 163-2027 163-2023 163-2041 163-2051

Electrophoresis Instrumentation

PROTEAN

i12™ IEF System

164-6000 PROTE AN i12 IEF System, 90 –240 VAC, includes

basic unit, positive and negative electrode assemblies, 7 cm, 11 cm, and 17 cm focusing trays with IPG strip retainers, 1 pack each of 7 cm, 11 cm, and 17 cm rehydration/equilibration trays, 2 pairs of forceps, 2 packs electrode wicks for gel-side down and gel-side up applications, mineral oil, 2 cleaning brushes, cleaning concentrate, 2 USB ﬂash drives, 3 styluses, pH 3 –10 ReadyStrip

™

IPG strips in 7 cm, 11 cm, and 17 cm lengths, rehydration sample buffer, and instruction manual. 13 cm, 18 cm, and 24 cm trays and cup loading accessories can be purchased separately

164-6 0 01 PROTE AN i12 IEF Cell, 90–240 VAC basic

unit includes cell, positive and negative electrode assemblies

™

164-6107 7 cm i12

Focusing Tray, includes 2 IPG strip retainers

16 4 - 6111 11 cm i12 Focusing Tray, includes 2 IPG strip retainers

16 4 - 6113 13 cm i12 Focusing Tray, includes 2 IPG strip retainers

16 4 - 6117 17 cm i12 Focusing Tray, includes 2 IPG strip retainers

16 4 - 6118 18 cm i12 Focusing Tray, includes 2 IPG strip retainers

164 - 6124 24 cm i12 Focusing Tray, includes 2 IPG strip retainers

165-4035 7 cm i12 Rehydration/Equilibration Tray,

with lids, pkg of 25

165 -4 025 11 cm i12 Rehydration/Equilibration Tray,

with lids, pkg of 25

164-6313 13 cm i12 Rehydration/Equilibration Tray,

with lids, pkg of 25

165 -4015 17 cm i12 Rehydration/Equilibration Tray,

with lids, pkg of 25

165-4041 18 cm i12 Rehydration/Equilibration Tray,

with lids, pkg of 25

165-4043 24 cm i12 Rehydration/Equilibration Tray,

with lids, pkg of 25

164-6 0 40 IPG Strip Retainers, pkg of 2

164-6 020 i12 Sample Cup Holder, pkg of 1, 12-position

sample cup holder, includes 25 disposable sample cups

164-6 021 i12 Sample Cups, pkg of 25

164-6 0 30 Gel-Side Up Electrode Wicks, pkg of 100

164-6 0 31 Gel-Side Down Electrode Wicks, pkg of 500

164 - 6 012 Negative Electrode Assembly, pkg of 1

16 4 - 6011 Positive Electrode Assembly, pkg of 1

164-6 010 Electrode Assembly Pair, pkg of 1 pair, positive

and one negative electrode assemblies

165-4 072 Cleaning Brushes, pkg of 2

161-0722 Cleaning Concentrate

164-6060 USB Flash Drive, pkg of 2

164-6050 Stylus, pkg of 3

165 -4 070 Forceps, pkg of 1

163 -2129 Mineral Oil

163-2105 ReadyPrep 2-D S tar ter Kit

Mini-PROTEAN

165-8000 Mini-PROTEAN Tetra Cell, 10-well, 0.75 mm

165-8001 Mini-PROTEAN Tetra Cell, 10-well, 1.0 mm

165-8002 Mini-PROTEAN Tetra Cell, 10-well, 0.75 mm

165-8003 Mini-PROTEAN Tetra Cell, 10-well, 1.0 mm

165-8004 Mini-PROTEAN Tetra Cell for Mini Precast G els,

165-8005 Mini-PROTE AN Tetra Cell for Mini Precast Gels,

165-8006 Mini-PROTEAN Tetra Cell, 10-well, 1.5 mm

165-8007 Mini-PROTEAN Tetra Cell, 10-well, 1.5 mm

165-8025 Mini-PROTEAN Tetra Cell and PowerPac

165-8026 Mini-PROTEAN Tetra Cell and PowerPac

165-8027 Mini-PROTEAN Tetra Cell and PowerPac

165-8028 Mini-PROTEAN Tetra Cell and PowerPac

165-8029 Mini-PROTEAN Tetra Cell and Mini Trans-Blot®

165-8030 Mini-PROTEAN Tetra Cell for Ready Gel Precast

165-8033 Mini-PROTEAN Tetra Cell, Mini Trans-Blot

Tetra Cells a nd Systems

thickness; 4-gel system includes 5 combs, 5 sets of glass plates, 2 casting stands, 4 casting frames, sample loading guide, electrode assembly, companion running module, tank, lid with power cables, mini cell buf fer dam

thickness; 2-gel system includes 5 combs, 5 sets of glass plates, casting stand, 2 casting frames, sample loading guide, electrode assembly, tank, lid with power cables, mini cell buffe r dam

4-gel system includes electrode assembly, clamping frame, companion module, tank, lid with power cables, mini cell buf fer dam

2-gel system includes electrode assembly, clamping frame, tank, lid with power cables, mini cell buffer dam

thickness; 2-gel system includes 5 combs, 5 sets of glass plates, casting stand, 2 casting frames, sample loading guide, electrode asse mbly, tank, lid with power cables, mini cell buffe r dam

™

Basic

Power Supply, includes 165-8 001 and 164-5050

™

Universal Power Supply, includes 165-8001 and 164-5070

™

Power Supply, includes 165-8 001 and 164-5052

™

Power Supply, includes 165-8 001 and 164-5056

Module, includes 165-8001 and 170-3935

Gels and Mini Trans -Blot Module, includes

165-8004 and 170-3935

Module, and PowerPac Basic Power Supply, includes 165-8001, 170-3935, and 164-5050

134 135

2-D Electrophoresis Guide Appendices

Catalog # DescriptionCatalog # Description Catalog # DescriptionCatalog # Description

Mini-PROTEAN® Tetra Cells a nd Systems ( con td.)

165-8034 Mini-PROTEAN Tetra Cell for Ready Gel Precast

Gels, Mini Trans- Blot Module, and PowerPac Basic Power Supply, includes 165-8004, 170-3935,

and 164-5050

165-8035 Mini-PROTEAN Tetra Cell, Mini Trans-Blot

Module, and PowerPac HC Power Supply, includes 165-8001, 170-3935, and 164-5052

165-8036 Mini-PROTEAN Tetra Cell for Ready Gel Precast

Gels, Mini Trans- Blot Module, and PowerPac HC Power Supply, includes 165-8 004, 170-3935,

and 164-5052

Mini-PROTEAN Dodeca Cells and Systems

165- 410 0 Mini-PROTEAN

3 Dodeca™ Cell, includes

electrophoresis tank with built-in cooling coil, lid with power cables, 6 electrophoresis clamping frames, 2 buffer dams, drain line, 2 gel releasers

165- 410 1 Mini-PROTEAN 3 Dodeca Cell with Multi-Casting

Chamber, same as 165-4100 with multi-casting chamber, 15 separation sheets, 8 acrylic blocks, tapered luer connector, stopcock valve

™

Criterion

Cells and Systems

165 -60 01 Criterion Cell, includes buffer tank, lid with power

cables, 3 sample loading guides (12 + 2-well, 18-well, 26-well)

165 -6019 Criterion Cell and PowerPac Basic Power Supply,

100–120/220–240 V, includes 165- 6001 and 164-5050

™

Criterion

Dodeca™ Cells and Systems

165-4130 Criterion Dodeca Cell, includes electrophoresis

buffer tank with built-in cooling coil, lid with power cables

165- 413 8 Criterion Dodeca Cell and PowerPac HC Power

Supply, includes 165-4130 and 164-5052

165- 413 9 Criterion Dodeca Cell and PowerPac Universal

Power Supply, includes 165-4130 and 164-5070

™

165 - 513 3 Criter ion Dodeca Cell and 6 -Row A nyGel

Stand,

includes 165-4130 and 165-5131

PROTEAN

II xi Cells

165-1801 PROTEAN II xi Cell, 16 cm, without spacers

and combs

165-1802 PROTEAN II xi Cell, 16 cm, 1.5 mm spacers (4),

15-well combs (2)

165-1803 PROTEAN II xi Cell, 16 cm, 1.0 mm spacers (4),

15-well combs (2)

165-1804 PROTEAN II xi Cell, 16 cm, 0.75 mm spacers (4),

15-well combs (2)

16 5 -1811 PROTEAN II xi Cell, 20 cm, without spacers

and combs

16 5 -1812 PROTEAN II xi Cell, 20 cm, 1.5 mm spacers (4),

15-well combs (2)

16 5 -1813 PROTEAN II xi Cell, 20 cm, 1.0 mm spacers (4),

15-well combs (2)

16 5 -1814 PROTEAN II xi Cell, 20 cm, 0.75 mm spacers (4),

15-well combs (2)

PROTEAN II XL Cells

165-3188 PROTEAN II XL Cell, wide format 1-D vertical

electrophore sis cell, 1.0 mm, includes PROTEAN II xi basic unit (#165-1834) and 1.0 mm IPG conversion kit (#165-3183)

165 -3189 PROTEAN II XL Cell, wide format 1-D vertical

electrophore sis cell, 1.5 mm, includes PROTEAN II xi basic unit (#165-1834) and 1.5 mm IPG conversion kit (#165-3186)

165 -3190 PROTEAN II XL Cell, wide format 1-D vertical

electrophore sis cell, 2.0 mm, includes PROTE AN II xi basic unit (#165-1834) and 2.0 mm IPG conversion kit (#165-3184)

16 5 -1815 PROTEAN II xi Cell 2-D Conversion Kit,

conver ts PROTEAN II xi cell into a tube gel IEF 2-D system; includes 2 tube gel adaptors, 24 glass tubes (1.5 mm ID, 180 mm length), gaskets, grommets, stoppers

165-3183 PROTEAN II xi Cell IPG Conversion Kit, 1.0 mm,

18.5 × 20 cm, for conversion to IPG PROTEAN II XL system; includes IPG clamps, 20 × 20 cm glass plates (2), IPG spacers, 2-D combs, and central cooling core gaskets

165 -3186 PROTEAN II xi Cell IPG Conversion Kit, 1.5 mm,

18.5 × 20 cm, for conversion to IPG PROTEAN II XL system; includes IPG clamps, 20 × 20 cm glass plates (2), IPG spacers, 2-D combs, and central cooling core gaskets

165 -3184 PROTEAN II xi Cell IPG Conversion Kit, 2.0 mm,

18.5 × 20 cm, for conversion to IPG PROTEAN II XL system; includes IPG clamps, 20 × 20 cm glass plates (2), IPG spacers, 2-D combs, and central cooling core gaskets

165-1834 PROTEAN II xi Basic Unit With Casting

Stand, vertical electrophoresis system, includes electrophore sis cell with ce ntral cooling core, gel casting stand

16 5 -19 51 PROTEAN II xi Multi- Cell, multi-cell electrophoresis

system, includes 3 central cooling cores, buffer tank, PROTEAN II xi multi-casting chamber with accessories

16 5 -19 5 6 PROTE AN II xi Multi-Cell 2-D Conversion Kit,

for proper cooling in 2-D electrophoresis applications; includes 2 cooling coils and manifold

16 5-3176 PROTEAN II XL Multi-Cell, wide format vertical

electrophoresis multi-cell, 1.0 mm, compatible with ReadyStrip IPG strips; includes catalog #165-1951, #165-1956, and 3 PROTEAN II xi cell IPG conversion kits of desired thickness

16 5-317 7 PROTE AN II XL Multi-Cell, wide format ver tical

electrophoresis multi-cell, 1.5 mm, compatible with ReadyStrip IPG strips; includes catalog #165-1951, #165-1956, and 3 PROTEAN II xi cell IPG conversion kits of desired thickness

16 5-3178 PROTEAN II XL Multi-Cell, wide format vertical

electrophoresis multi-cell, 2.0 mm, compatible with ReadyStrip IPG strips; includes catalog #165-1951, #165-1956, and 3 PROTEAN II xi cell IPG conversion kits of desired thickness

PROTEAN

Plus Dodeca™ Cells and Systems

165- 415 0 PROTEAN Plus Dodeca Cell, 100/120 V, includes

electrophoresis buffer tank with built-in ceramic cooling core, lid, buffer recirculation pump with tubing, 2 gel releasers

165- 414 0 PROTEAN Plus Dodeca Cell (100/120 V) and

PowerPac HC Power Supply, includes 165-4150 and 164-5052

165- 414 2 PROTEAN Plus Dodeca Cell (100/120 V) and

PowerPac Universal Power Supply, includes 165 -415 0 a nd 164- 5070

165-4144 PROTEAN Plus Dodeca Cell (100/120 V),

Trans-Blot Plus Cell, and PowerPac Univer sal Power Supply, includes 165-4150, 170-3990,

and 164-5070

PROTEAN

Plus Dodeca™ Cells and Systems (c on td.)

165 - 513 4 PROTEAN Plus Dodeca Cell (100/120 V) and

Two 6-Row AnyGel Stands, includes 165-4150

and two 165-5131

165- 4151 PROTEAN Plus Dodeca Cell, 220/240 V, includes

electrophoresis buffer tank with built-in ceramic cooling core, lid, buffer recirculation pump with tubing, 2 gel releasers

165- 4141 PROTEAN Plus Dodeca Cell (220/240 V) and

PowerPac HC Power Supply, includes 165-4151 and 164-5052

165- 414 3 PROTEAN Plus Dodeca Cell (220/240 V ) and

PowerPac Universal Power Supply, includes 165 -4151 a n d 16 4- 5070

165- 414 5 PROTEAN Plus Dodeca Cell (220/240 V )

Trans-Blot Plus Cell, and PowerPac Univer sal Power Supply, includes 165-4151, 170-3990,

and 164-5070

165 - 513 5 PROTE AN Plus Dodeca Cell (220/240 V ) and

Two 6-Row AnyGel Stands, includes 165-4151 and two 165-5131

Power Supplies

164-5050 PowerPac

™

Basic Power Supply,

100–120/220–240 V

164-5052 PowerPac HC Power Supply, 100–120/220–240 V

164-5056 PowerPac HV Power Supply, 100–120/220–240 V

164-5070 PowerPac Universal Power Supply,

100–120/220–240 V

IEF and SDS-PAGE Buffers and Reagents

16 3 - 2 111 ReadyPrep Overlay Agarose, 1 bottle, 50 ml

161-0732 10× Tris/Glycine/SDS, 1 L

161-0734 10× Tris/Glycine, 1 L

161-0744 10× Tris/Tricine/SDS, 1 L

161-0788 XT MOPS Running Buffer, 20×, 500 ml

161-0789 XT MES Running Buf fer, 20×, 500 ml

161-0790 XT Tricine Running Buffer, 20×, 500 ml

161-0793 XT MOPS Buffer Kit, includes 500 ml 20× XT

MOPS running buffer, 10 ml 4× XT sample buf fer, 1 ml 20× XT reducing agent

161-0796 XT MES Buffer Kit, includes 500 ml 20× X T MES

running buffer, 10 ml 4× XT sample buffer, 1 ml 20× XT reducing agent

161-0797 XT Tricine Buffer Kit, includes 500 ml 20× XT

Tricine running buf fer, 10 ml 4× XT sample buffer, 1 ml 20× XT reducing agent

161-0729 EDTA , 500 g

161-0 718 Glycine, 1 kg

161-0713 Tricine, 500 g

161-0 719 Tr is, 1 kg

161-0404 Bromophenol Blue, 10 g

Precast Gels*

Mini-PROTEAN

TGX™ Precast Gels

(for 7 cm IPG Strips)

IPG well, 10 gels per box

45 6 -1021 7.5% Mini-PROTEAN TGX Precast Gel

45 6 -1031 10% Mini-PROTEAN TGX Preca st Gel

45 6 -1041 12% Mini-PROTE AN TGX Precast Gel

45 6 -1081 4 –15% Mini-PROTEAN TGX Precast Gel

45 6 -1091 4 –20% Mini-PROTEAN TGX Precast Gel

™

456-9031 Any kD

Mini-PROTEAN TGX Precast Gel

Mini-PROTEAN (for 7 cm IPG Strips)

456 -8021 7.5% Mini-PROTEAN TGX Stain-Free Precast Gel

456 -8 031 10% Mini-PROTEAN TGX Stain-Fre e Precast Gel

45 6 - 8041 12% Mini-PROTEAN TGX Stain-Free Precast Gel

45 6 -8121 Any kD Mini-PROTEAN TGX Stain-Free

Criterion Precast Gels (for 11 cm IPG Strips)

IPG +1 well, package of 1

345-0101 10% Criterion Tris-HCl Precast Gel

345- 010 2 12.5% Criter ion Tris-HCl Pre cast Gel

345- 010 3 4–15% Criter ion Tris-HCl Pre cast Gel

345- 010 4 4–20% Criterion Tris-HCl Precast Gel

345- 010 5 8–16% Criterion Tris-HCl Pr ecast Gel

345- 010 6 10.5–14% Criterion Tris-HCl Precast Gel

345-0107 10–20% Criterion Tris-HCl Precast Gel

34 5 - 0 115 10% Criterion XT Bis-Tris Precast Gel

34 5 -0121 12% Criterion XT B is-Tris Precast Gel

34 5 -0127 4–12% Criterion XT Bis-Tris Precast Gel

345-0133 3–8% Criterion XT Tris-Acet ate Precast Gel

34 5- 8161 8–16% Criterion Stain-Free Precast Gel

Criterion (for 11 cm IPG Strips)

56 7-1071 18% Criterion TGX Precast Gel

56 7-1081 4–15% Criterion TGX Preca st Gel

56 7-1091 4–20% Criterion TG X Precast Gel

567-110 1 8–16% Criterion TG X Precast Gel

567-1111 10–20% Criterion TGX Precast Gel

567-112 1 Any kD Criterion TGX Precast Gel

Criterion (for 11 cm IPG Strips)

56 7- 8 0 71 18% Criterion TGX Stain-Free Precas t Gel

567-8081 4–15% Criterion TG X Stain-Free Precast Gel

56 7- 8 0 9 1 4–20% Criterion TGX Stain-Free Precast Gel

56 7- 8 10 1 8–16% Criterion TGX Stain-Free Precast Gel

567-8111 10–20% Criter ion TGX Stain-Free Precast Gel

56 7- 8 121 Any kD Cr iterion TGX Stain-Free Precas t Gel

* For a complete selection of precast gels, visit www.bio-rad.com

Gel Casting Buffers and Reagents

161- 510 0 SDS-PAGE Reagent Starter Kit, includes

161-0100 Acrylamide, 99.9%, 100 g

161-0120 Acrylamide/Bis Powder, 19:1, 30 g

161-0122 Acrylamide/Bis Powder, 37.5:1, 30 g

161-0140 40% Acrylamide Solution, 500 ml

161-0144 40% Acrylamide/Bis Solution, 19:1, 500 ml

161-0146 40% Acrylamide/Bis Solution, 29:1, 500 ml

161-0148 40% Acrylamide/Bis Solution, 37.5:1, 500 ml

161-0154 30% Acrylamide/Bis Solution, 19:1, 500 ml

161-0156 30% Acrylamide/Bis Solution, 29:1, 500 ml

161-0158 30% Acrylamide/Bis Solution, 37.5:1, 500 ml

161-02 00 Bis Crosslinker, 5 g

TGX Stain-Free™ Precast Gels

Precast Gel

™

TGX™ Precast Gels

™

TGX Stain-Free™ Precast Gels

100 g acrylamide, 5 g bis, 5 ml TEMED, 10 g ammonium persulfate

136 137

2-D Electrophoresis Guide

Appendices

Catalog # Description Catalog # Description

Gel Casting Buffers and Reagents (c on td.)

161-0800 TEMED, 5 ml

161-0798 Resolving Gel Buffer, 1.5 M Tris-HCl, pH 8.8, 1 L

161-0700 Ammonium Persulfate (APS), 10 g

161-0799 Stacking Gel Buffer, 0.5 M Tris-HCl, pH 6.8, 1 L

Gel Casting Accessories

See catalog or www.bio-rad.com for a complete listing of accessories, including available empty gel cassettes and glass plates, spacers, combs, etc.

™

165 - 5131 AnyGel

Stand, 6-row, holds 6 PROTE AN gels,

12 Criterion gels, or 18 Ready Gel mini gels

165- 413 1 AnyGel Stand, single-row, holds 1 PROTEAN gel,

2 Criterion gels, or 3 Ready Gel mini gels

165- 412 2 Model 485 Gradient Former and Mini-PROTEA N

3 Multi-Casting Chamber, includes 165-4120 and 165-4110

165-4123 Model 495 Gradient Former and PROTEAN Plus

Multi-Casting Chamber, includes 165-4121 an d 16 5-4160

Total Protein Gel Stains

™

161-0786 Bio-Safe

Coomassie Stain, 1 L

161-0787 Bio-Safe Coomassie Stain, 5 L

™

TABLE OF CONTENTS

161-0449 Silver Stain Plus

concentrate, silver complex solution, reduction

Kit, includes ﬁxative enhancer

moderator solution, image development reagent, development accelerator reagent, stains 13 full size or 40 mini gels

™

161-04 96 Oriole

161-04 92 Flamingo

Fluorescent Gel Stain, 1× solution, 1 L

™

Fluorescent Gel Stain, 10× solution,

500 ml

170 - 3125 SYPRO Ruby Protein Gel Stain, 1× solution, 1 L

161-0440 Zinc Stain and Destain Kit, includes 125 ml of 10×

zinc stain solution A, 125 ml of 10× zinc stain solution B, 125 ml of 10× zinc destain solution

161-0470 Copper Stain and Destain Kit, includes 125 ml

of 10× copper stain, 125 ml of 10× copper destain solution

High-Throughput Stainers

165-3400 Dodeca Stainer, large, 100–240 V, includes

13 trays (12 clear, 1 white), 12 tray attachments, shaking rack, solution tank, lid with shaker motor, shaker control unit, gel clip

165-3401 Dodeca Stainer, small, 100–240 V, includes

13 trays (12 clear, 1 white), 12 Criterion tray attachments, shaking rack, solution tank, lid with shaker motor, shaker control unit, gel clip

Imaging Systems and Spot Cutter

™

170 -7 9 91 GS-900

Calibrated Densitometry System, gel

densitometry system, PC compatible, scanner, cables, Image L ab sof tware, optional 21 CFR Part 11 and Instrument Qualiﬁcation/Operations Qualiﬁcation

™

170 - 8 280 ChemiDoc

MP System, gel imaging system,

PC or Mac, includes darkroom, UV transilluminator, epi-white illumination, camera, power supply, cables, Image Lab

™

software

170-8270 Gel Doc EZ Sys tem, gel imaging system, PC or Mac, includes dark room, camera, cables, Image Lab software; samples trays (#170-8271, 170-8272, 170-8273, or 170-8274) are sold separately; sample trays are required to use the system

170-9460 Molecular Imager

PC or Mac, 110–240 V, includes Quantity One

PharosFX™ Plus System,

software, sample tray set, ﬂuorescence ﬁlters (170-7866, 170-7896) and phosphor imaging ﬁlters, USB2 cable

170-9450 Molecular Imager PharosFX System, PC or Mac,

110–240 V, includes Q uantity One software, sample tray set, ﬂuorescence ﬁlters (170-7866, 170-7896), USB2 cable

™

165 -7200 EXQuest

Spot Cutter, gel excision instrument,

includes enclosure, imaging system, ﬂuidics system, robotics, sensors, cutting head, gel tray, microplate rack, wash station

165-7201 E XQuest Spot Cutter with PC, gel excision

instrument, includes PC, enclosure, imaging system, ﬂuidics system, robotics, sensors, cutting head, gel tray, microplate rack, wash station

Benzonase is a trademark of Merck KGaA Corporation.

Coomassie is a trademark of BASF Aktiengesellschaft.

Cy is a trademark of GE Healthcare Group Companies.

Paraﬁlm is a trademark of American National Can Company.

Pro-Q, Qdot, and SYPRO are trademarks of Invitrogen Corporation.

Triton is a trademark of Dow Chemical Company.

Tween is a trademark of ICI Americas Inc.

Tygon is a trademark of Norton Company.

Whatman is a trademark of Whatman Limited Corporation.

ZipTip is a trademark of Millipore Corporation.

Bio-Rad Laboratorie s, Inc. is license d by Invitrogen Corporation to sell SYPRO products for research use only under U.S. Patent Number 5,616,502.

Precision Plus Protein standards are sold under license from Life Technologies Corporation, Carlsbad, CA, for use only by the buyer of the product. The buyer is not authorized to sell or resell this product or its components.

Purchase of Criterion X T Bis-Tris gels, XT MOPS running buffer, XT MES running buffer, XT MOPS buffer kit, and XT MES buffer kit is accompanied by a limited license under U.S. Patent Numbers 6,143,154; 6,096,182; 6,059,948; 5,578,180; 5,922,185; 6,162,338; and 6,783,651, and corresponding foreign patents.

StrepTactin is covered by German patent application P 19641876.3. Bio-Rad L aboratories, Inc. is licensed by Institut fur Bioanalytik GmbH to sell these products for research use only.

Analysis Software

170 - 9 6 9 0 Image Lab Software

170-9600 Quantity O ne 1-D Analysis Soft ware, PC or Mac

™

170 - 9 6 3 0 PDQuest

Advanced 2-D Analysis Software

Gel Drying Supplies

™

165 -1771 GelAir

Drying System, 115 V, 60 Hz, includes

165-1777, 2 drying frame s, 16 clamps, assembly table, 50 precut sheets of cellophane support, gel drying solution

165-1777 GelAir Dryer, 115 V, 60 Hz, gel drying oven only

138

139

Bio-Rad Laboratories, Inc.

Life Science Group

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13-0893 0413 Sig 1212Bulletin 2651 Rev F US/EG

Bio-Rad GS-900 Calibrated Densitometer User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual