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Labchip GX II
User Manual
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Perkinelmer Labchip GX II, Labchip GX User Manual

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LabChip GX/GX II
User Manual
Copyright 2008-2014, PerkinElmer Health Sciences, Inc. All rights reserved.
V4.2
Preface 2

Preface

Copyright
This manual is published by PerkinElmer Health Sciences, Inc., 68 Elm Street, Hopkinton, MA 01748 USA. Copyright 2008-2014, PerkinElmer Health Sciences, Inc and its parent, affiliated, and subsidiary companies. All rights reserved, including but not limited to those rights to reproduce this publication or parts thereof. Reproduction of this publication or parts thereof or the products it describes by any means or in any form is expressly prohibited without the written permission of PerkinElmer.
Trademarks
PerkinElmer, LabChip, the PerkinElmer logo, and the LabChip logo are registered trademarks of PerkinElmer Health Sciences, Inc and/or its parent, affiliates, and/or subsidiary companies (collectively “PerkinElmer”). Microsoft, Windows, and Windows NT are either registered trademarks or trademarks of Microsoft Corporation in the United States and/or other countries. All other trademarks and registered trademarks are the property of their respective holders.
Content
Any errors or omission which may have occurred in this publication, despite the utmost care taken in its production, will be corrected as soon as possible, but not necessarily immediately upon detection. PerkinElmer provides this publication “As Is” without warranty of any kind, either express or implied, including but not limited to the implied warranties of merchantability or fitness for a particular purpose. Some states or jurisdictions do not allow disclaimer of express or implied warranties in certain transactions; therefore, this statement may not apply to you. PerkinElmer reserves the right to revise this publication and to make changes from time to time in the content hereof without obligation of PerkinElmer to notify any person of such revision or changes. Further, PerkinElmer may make modifications to the product described in this manual at any time without any obligation to notify
Proper Equipment Operation
any person of such modifications.
WARNINGS
• To reduce the risk of electric shock, do not remove the cover. No user serviceable parts inside. Refer to qualified service personnel if help is required.
• Use this product only in the manner described in this manual. If the equipment is used in a manner not specified by the manufacturer, the protection provided by the equipment may be impaired.
AVERTISSEMENTS
• Pour réduire le risque de choc électrique, ne pas retirer le couvercle. Ce produit ne contient aucune pièce pouvant être réparée par l’utilisateur. Au besoin, confier l’appareil à un réparateur qualifié.
• Ce produit ne doit être utilisé que comme décrit dans ce manuel. Si cet appareil est utilisé d’une manière autre que celle spécifi ée par le fabricant, la protection fournie par l’appareil peut être entravée.
Preface 3
Contact Us
If you have a question about the LabChip GX that is not answered in this manual or online Help, or if you need assistance with this product, contact the PerkinElmer Technical Support Center:
Phone: (US Toll Free): 800-762-4000
(Worldwide): +1 203-925-4602
Fax: +1 203-944-4904 Email: global.techsupport@perkinelmer.com Internet: www.perkinelmer.com
For support outside the United States, contact your local PerkinElmer representative.
Before you call, you should have the following information available for the technical representative:
• Product serial number
• Software version (found by choosing About from the main Help menu)
• If applicable, the error number shown in the product software or in the log file.
Product Service and Customer Support Plans
PerkinElmer offers a full range of services to ensure your success. From our original factory warranty through a comprehensive line of customer support plans, PerkinElmer offers you Field Service Engineers and in-house Specialists who are dedicated to supporting your hardware, software and application development needs.
Call: (US Toll Free): 800-762-4000
(Worldwide): +1 203-925-4602
Fax: +1 203-944-4904 Email: global.techsupport@perkinelmer.com
Our programs can include such useful services as:
• Preventive maintenance
• Diagnostic servicing performed on-site by PerkinElmer field service engineers or remotely via Technical Support
• Validation performed on-site by PerkinElmer field service engineers
• Extended use of the PerkinElmer Technical Support Center
• Software updates
• Parts, labor, and travel expense coverage
• Other customized services upon request
Training For Your Product
Contact the PerkinElmer Center for Training and Development for information about the availability of training courses for your product:
Call: (508) 497-2634 Fax:
(508) 435-3439
FCC
CE
Preface 4
This device complies with part 15 of the FCC (United States Federal Communications Commission) Rules. Operation is subject to the following two conditions:
• This device may not cause harmful interference, and
• This device must accept any interference received, including interference that may cause undesired operation.
This device complies with all CE rules and requirements.
NOTE
Changes or modifications to this equipment not expressly approved by the party responsible for compliance could void the user’s authority to operate the equipment.
REMARQUE
Tout changement ou modification apporté à cet instrument non expresséme nt approuvé par l’entité responsable de la conformité peut annuler l’autorisation d’opérer l’appareil accordée à l’utilisateur.
Table of Symbols
Tab le 1 contains symbols that identify particularly important information and alert
you to the presence of hazards. These symbols may appear in this manual and/or on the product it describes.
Table 1. Important Symbols
Symbol Symbole
Description Description
DANGER: An imminently hazardous situation, which, if not
avoided, will result in death or serious injury. DANGER: Situation présentant un danger imminent qui, s’il
n’est pas éliminé, peut entraîner des blessures graves, voire la mort.
WARNING: Caution, risk of danger. Refer to the User’s documentation.
AVERTISSEMENT: Attention, danger potentiel. Se reporter à la documentation de l’utilisateur.
NOTE: A cautionary statement; an operating tip or maintenance suggestion; may result in instrument damage if not followed.
REMARQUE: Énoncé indiquant une précaution à prendre, un conseil de fonctionnement ou une suggestion d’entretien; son non-respect peut provoquer des dommages à l’instrument.
Table 1. Important Symbols (Continued)
Preface 5
Symbol Symbole
Description Description
Hazardous voltage; risk of shock injury. Tension dangereuse; risque de blessure par électrocution.
Crush hazard. Risk of body parts, hair, jewelry, or clothing getting caught in a moving part.
Danger d’écrasement. Faire attention que les parties corporelles, les cheveux, les bijoux ou les vêtements ne soient pas pris dans une pièce mobile.
Risk of puncture injury. Risque de blessure par piqûre.
Risk of eye injury; wear safety glasses. Risque de lésion oculaire; porter des lunettes de sécurité.
Risk of fire. Risque d’incendie.
Risk of poison. Risque d’empoisonnement.
Risk of explosion. Risque d’explosion.
Hazardous fumes. Émanations dangereuses.
Laser light; avoid exposure. Risk of eye injury. Rayonnement laser; éviter toute exposition. Risque de lésion
oculaire.
Lifting hazard. May result in injury. Levage dangereux. Peut entraîner des blessures.
Protective ground symbol. Symbole de terre de protection.
Ground symbol. Symbole de terre.
Fuse. Fusible.
Alternating current. Courant alternatif.
On (supply). Marche (alimentation).
Table 1. Important Symbols (Continued)
Preface 6
Symbol Symbole
Equipment labels are color coded:
Les étiquettes de l’appareil sont codées couleur:
Description Description
Off (supply). Arrêt (alimentation).
CE compliance mark. Marque de conformité CE.
Signifies that the unit has passed safety tests for grounding, power line transience, and current leakage.
Signifie que l’appareil a réussi les tests de sécurité pour la mise à la terre, le courant transitoire de ligne d’alimentation et la perte de courant.
Input. Entrée.
Output. Sortie.
Yellow Caution, risk of danger Red Stop Blue Mandatory action Green Safe condition or information
Jaune Attention, danger potentiel Rouge Arrêter Bleu Intervention obligatoire Vert Condition sûre ou informations de sécurité
Helpful hints, additional information Conseils utiles, informations supplémentaires

Instrument Safety

The following safety information about the LabChip GX is included in this documentation. Read and review all safety information before operating the LabChip GX.
• Required Training
• “Chemical Safety” on page 8
• “Laser Safety” on page 9
• “Electrical Safety” on page 10
• “Mechanical Safety” on page 11

Required Training

Ensure that all personnel involved with the operation of the instrument have:
• Received instruction in general safety practices for laboratories.
• Received instruction in specific safety practices for the instrument.
• Read and understood all related MSDSs.
Instrument Safety 7
WARNING
Use this product only in the manner d escri bed in this ma nual. If the equipment is used in a manner not specified by th e manufactur er, the protection provided by the equipme nt may be impaired.

Chemical Safety

WARNING
Some chemicals used with the LabChip GX are potentially hazardous and can cause ill ness.
• Read and understand the material safety data sheet (MSDS) provided by the chemical manufacturer before you store, handle, or work with any chemical or hazardous material.
• Minimize contact with and inhalation of chemicals and chemical wastes. Wear appropriate personal protective equipment when handling chemicals (e.g., safety glasses, gloves, or clothing). For additional safety guidelines consult the MSDS.
• Do not leave chemical containers open. Use only with adequate ventilation, including a fume hood, if necessary.
• Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the manufacturer’s cleanup procedures as recommended on the MSDS.
• Dispose of waste in accordance with good laboratory practices and local, state/provincial, or national environmental and health regulations.
Instrument Safety 8
• After emptying waste containers, seal them appropriately.
• Comply with all local, state/provincial, or national laws and regulations related to chemical storage, handling, and disposal.

Laser Safety

WARNING
BRIGHT LIGHT HAZARD. LabChip GX Instruments contain Class 3B laser diodes. The LabChip GX is classified as a Class 1 device because the lasers are appropriately enclosed (embedded) and indicated with Warning labels.
Complies with 21 CFR 1040.10 except for deviations pursuant to Laser Notice 50, dated June 24, 2007.
Complies with IEC 60825-1: 1993, A1: 1997, A2: 2001.
635 nm (visible red) laser source, 10 mW maximum continuous (CW)
Instrument Safety 9
Class 1
Laser
Product
WARNING
• Use of controls or adjustments or performance of procedures other than those specified herein may result in hazard ous radiation exposure.
• NEVER remove back, side, or front panels of the instrument while the laser is powered. Panels (which, if removed, could lead to laser exposure) are marked with the labels sh own be lo w:
• These panels are intended to be removed for service only by qualified personnel; they are not intended to be removed during operation or for maintenance by users. The only re movable maintenance panel is the lower panel at the back of the instrument, which can be removed to access the back of the robot, if cleaning is necessary.

Electrical Safety

The LabChip GX is powered by a UL/CSA/VDE approved 100-240 VAC, 50/60 Hz input, 5, 15, 24 VDC output power supply. Additionally, the LabChip GX High Voltage circuitry is current­limited to non-hazardous levels. Users should observe the following:
WARNING
Do not open the instrument enclosure. There are no user serviceable parts inside.
The wall outlet or the power cable connector on the back of the instrument should be accessible after the system's installation, to enable trained service personnel to safely disconnect power from the system during servicing.
The computer supplied with the LabChip GX instrument has internal lithium batteries. Batteries should not be incinerated.
Instrument Safety 10
WARNING
Danger of explosion if battery is incorrectly replaced. Replace only with the same or equivalent type recommende d by the manufacturer's instructions.

Power Cord Selection

United States and Canada
The LabChip GX instrument is shipped with a NEMA 5-15 / IEC 320 power cord. If the power cord needs to be replaced, substitute power cords must be UL Listed, Type SJT or equivalent, minimum No. 18 AWG, 3-conductor with ground conductor that for safety considerations should never be disconnected or defeated. The cord’s plug to the wall must be a three-pin grounding type connector with a NEMA 5-15P (15A, 125V) plug configuration. The cord’s connector at the unit must conform to requirements for an EN 60 320/IEC 320 Standard Sheet C13 connector.
The equipment is intended to be plugged into a standard NEMA 5­15R receptacle in the wall.
Instrument Safety 11
International
All power cord sets must be approved by an acceptable, accredited agency responsible for evaluation in the country where the power cord set and system will be used.
The flexible cord must be <HAR> Type H05VV-F, 3-conductor, minimum 0.75 - 1 mm set fittings that is, the appliance coupler and wall plug, must bear the certification mark of the agency responsible for evaluation in the country where it will be used. The appliance coupler must meet the mechanical configuration of an EN 60 320/IEC 320 Standard Sheet C13 connector for mating with appliance inlet on the system.

Fuses

The LabChip GX instruments do not contain any user replaceable fuses. Contact PerkinElmer Technical Support (see “Contact Us” on
page 3) if blown fuses are suspected.

Mechanical Safety

The LabChip GX instruments have a three axis robot that moves quickly and can be a pinch hazard. Keep the front door of the instrument closed when the robot is moving. Keep hands away from the robot when not actually placing microplates in the instrument or changing the ladder and buffer vials. Robot access areas are marked with the following warning label:
2
conductor size (230 volt input). Power cord
Table of Contents 12

Table of Contents

Preface ....................................................................................................................2
Instrument Safety ...................................................................................................7
Required Training................................................................................................7
Chemical Safety ..................................................................................................8
Laser Safety........................................................................................................ 9
Electrical Safety ................................................................................................10
Power Cord Selection ..................................................................................10
Fuses .......................................................................................................... 11
Mechanical Safety.............................................................................................11
Introduction...........................................................................................................18
Principles of Operation...................................................................................... 19
Software Modes Available ................................................................................. 21
Operation ..............................................................................................................22
Opening the LabChip GX Software....................................................................23
Creating Desktop Shortcuts............................................................................... 23
Creating a New Assay....................................................................................... 24
Running an Assay ............................................................................................. 25
Select the Auto Export Settings.........................................................................29
Monitoring the Run............................................................................................ 30
Stopping a Run .................................................................................................31
Continuing a Stopped Run ................................................................................32
Saving Data Files ..............................................................................................33
Saving Workspace Files....................................................................................34
Selecting Wells using a Sample Names File......................................................35
Data Analysis........................................................................................................42
Using a Barcode to Specify the Sample Names File .................................... 36
Adding a New Plate...........................................................................................38
Placing the Barcode on the Plate ...................................................................... 40
Calibrating the Optics........................................................................................ 41
How the Software Analyzes DNA Data ..............................................................43
How the Software Analyzes Protein Data .......................................................... 45
How the Software Analyzes RNA Data ..............................................................49
How the Software Analyzes Glycan Data........................................................... 54
How the Software Analyzes Protein Charge Variant Data..................................57
How the Software Analyzes Genomic DNA Data ...............................................58
Organizing, Retrieving, and Backing Up Data Files ...........................................59
Opening a New Workspace ............................................................................... 59
Opening a Data File ..........................................................................................60
Adding a Collection to a Workspace ..................................................................61
Selecting the Wells in a Collection .................................................................... 62
Using Sample Names Files ............................................................................... 63
Create a Sample Name File.........................................................................63
V4.2 LabChip GX User Manual PerkinElmer
Table of Contents 13
Sample Name File Format (.CSV Format).................................................... 65
Applying Different Window Values to Expected Peaks of the Same Size in
Different Wells ............................................................................................. 66
Sample Name File Import Errors.................................................................. 66
Using Expected Fragments/ Expected Proteins/ Expected Glycans................... 67
Entering EFs, EPs, or EGs in the Assay Analysis Window ...........................67
Exporting EFs, EPs, or EGs......................................................................... 68
Importing EFs, EPs, or EGs.........................................................................68
Forcing Expected Peaks .............................................................................. 69
Viewing the EFs/EPs/EGs in the Graph View...............................................69
Viewing the EFs/EPs/EGs in the Gel View ................................................... 70
Viewing the EFs/EPs/EGs in the Well Table ................................................71
Viewing the EFs/EPs/EGs in the Peak Table ............................................... 71
Modifying Analysis Parameters .........................................................................72
Changing the Peak Find Parameters ........................................................... 73
Adding a Peak ............................................................................................. 74
Excluding a Peak.........................................................................................74
Splitting a Peak............................................................................................75
Merging Two Peaks .....................................................................................75
Adjusting the Peak Baseline ........................................................................76
Setting the Baseline for a Range of Peaks................................................... 76
Removing a Manual Baseline....................................................................... 77
Selecting a Default Ladder........................................................................... 77
Using the Default Ladder for Alignment........................................................ 79
Exporting the Default Ladder in an Assay .................................................... 79
Clearing the Default Ladder in a Plate .........................................................79
Changing the Time Window for Analysis...................................................... 80
Aligning or Unaligning the Marker Peaks .....................................................80
Saving and Exporting Assays............................................................................ 84
Changing the View of the Data ..........................................................................85
Viewing Gels ...............................................................................................85
Viewing Zero Baselines ..............................................................................86
Adjust Pane Widths .....................................................................................87
Show or Hide Views..................................................................................... 87
Zoom In and Zoom Out................................................................................ 88
Viewing Graphs in the Overlay Electropherograms Tab ............................... 89
Viewing Graphs in the Electropherograms Tab ............................................ 90
Viewing Analysis Errors and Warnings.........................................................92
Viewing Multiple Properties in the Well Table View ......................................93
Copying Information .......................................................................................... 94
Reanalyzing a Data File ....................................................................................95
Printing Workspace Information......................................................................... 96
Exporting Data ................................................................................................ 102
Exporting Data Manually............................................................................ 105
Using the GX Software to Analyze GX Touch Data...........................................107
Understanding Peak Finding..............................................................................108
V4.2 LabChip GX User Manual PerkinElmer
Table of Contents 14
Data Smoothing .............................................................................................. 108
Peak Detection - Slope Threshold ...................................................................109
Peak Splitting - Inflection Threshold ................................................................ 112
Peak Identification...........................................................................................113
Software Security ............................................................................................... 114
Locking and Unlocking the Software................................................................ 116
Managing User Accounts ................................................................................117
Adding New Users ..................................................................................... 118
Changing User Information ........................................................................ 119
Printing User Information ........................................................................... 120
Activating and Deactivating User Accounts................................................120
Changing Access Rights............................................................................ 121
Printing Access Rights...............................................................................122
Setting Policies for User Accounts .............................................................123
Printing User Policies................................................................................. 124
Electronic Signatures ...................................................................................... 125
Automatically Exporting Copies of Data Files ..................................................126
Reverting to a Specific Data File Revision ....................................................... 126
Audit Trail........................................................................................................ 127
Viewing the Audit Trail ............................................................................... 128
Exporting the Audit Trail ............................................................................ 129
Central Data Repository (CDR) ....................................................................... 130
CDR Security Suggestions......................................................................... 130
Creating New Data Folders........................................................................ 131
Moving Data Files into Folders................................................................... 131
Deleting Data Folders ................................................................................ 131
Hiding Data Files in the CDR Manager Window ......................................... 132
Showing Hidden Data Files in the CDR Manager Window.......................... 132
Remote CDR Server Backup ........................................................................... 133
Setting Up the Remote CDR Server........................................................... 133
Backing Up Data Files to the Remote CDR................................................ 135
Restoring Data Files from the Remote CDR............................................... 136
Viewing the Files in the Remote CDR Folder ............................................. 137
Manually Backing Up and Restoring the CFR Files.......................................... 138
Backing Up CFR Files................................................................................ 138
Restoring CFR Files ..................................................................................140
Software Reference ............................................................................................142
LabChip GX Main Window............................................................................... 143
Menu Bar................................................................................................... 144
Chip Status and Run Status....................................................................... 151
Error Message Area................................................................................... 153
Plate View or Plate List.............................................................................. 154
Collection Pane ......................................................................................... 157
Graph View................................................................................................ 158
Graph View Properties............................................................................... 164
Gel View .................................................................................................... 167
V4.2 LabChip GX User Manual PerkinElmer
Table of Contents 15
Gel View Properties ................................................................................... 170
Well Table View......................................................................................... 172
Peak Table View........................................................................................ 174
Peak Table Properties ............................................................................... 179
Filter View ................................................................................................. 180
About LabChip GX Window ............................................................................. 183
Add New Expected Peak Window....................................................................184
Add Plate Window........................................................................................... 185
Assay Analysis Window................................................................................... 186
Assay Information Tab............................................................................... 187
Alignment Tab ........................................................................................... 188
Analysis Tab.............................................................................................. 189
Peak Find Tab ........................................................................................... 192
Expected Fragments/Proteins/Glycans Tab ...............................................196
Excluded Peaks Tab.................................................................................. 198
Smear Analysis Tab................................................................................... 200
Titer Tab.................................................................................................... 202
Advanced Tab ........................................................................................... 205
Audit Trail Window .......................................................................................... 208
Audit Trail Export Window ............................................................................... 209
Audit Trail Manage Columns Window..............................................................210
CDR Manager Window.................................................................................... 211
CDR Server Utility Window.............................................................................. 213
CDR Utility Window......................................................................................... 214
Change Password Window.............................................................................. 216
Data File Version Window ............................................................................... 217
Event Viewer Window ..................................................................................... 218
Export Window ................................................................................................219
Installation Qualification Window..................................................................... 222
Layout Options Window................................................................................... 223
Login Window..................................................................................................224
New Collection Window................................................................................... 225
Optics Calibration Window .............................................................................. 226
Perform Signature Window..............................................................................228
Plate Information Window................................................................................ 229
Print Window................................................................................................... 230
Print Validation Reports Window .....................................................................232
Rename Collection Window............................................................................. 233
Robot Teaching Wizard................................................................................... 234
Welcome Window ...................................................................................... 235
Teach Robot Window................................................................................. 236
Teach the X, Y and Z Reference Positions Window ................................... 237
Verify a Plate Window................................................................................ 238
Verify Positions Window ............................................................................ 239
Finished Window ....................................................................................... 240
Verify All Target Positions Window ............................................................ 241
Verify All Target Positions Correct Window ................................................ 242
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Table of Contents 16
Run File Editor Window...................................................................................243
Run Info Window............................................................................................. 244
Sample Name Editor Window.......................................................................... 245
Save Workspace As Window........................................................................... 247
Select a Data File Window .............................................................................. 248
Start Run Window ........................................................................................... 249
Run Tab..................................................................................................... 250
Output Tab ................................................................................................ 252
Advanced Tab ........................................................................................... 254
System Diagnostics Window ........................................................................... 256
Unlock Application Window ............................................................................. 258
Unlock Data File Window ................................................................................ 259
User Administration Window............................................................................ 260
Create New User ....................................................................................... 261
Edit Users..................................................................................................263
Show User Info .......................................................................................... 264
De/Activate User........................................................................................ 266
Define Access............................................................................................ 267
Set Policies................................................................................................ 269
LabChip GX Instrument Description ..................................................................270
Front View....................................................................................................... 270
Front Panel .....................................................................................................271
Rear Connectors ............................................................................................. 272
Optics ............................................................................................................. 273
Chip Pressure System..................................................................................... 273
Barcode Reader .............................................................................................. 273
DNA, RNA, and Protein Chips ......................................................................... 274
Chip Cartridge................................................................................................. 275
High Voltage Interface ............................................................................... 276
Microplate Carrier............................................................................................277
USB Key for 21 CFR Part 11 Option................................................................ 277
Specifications..................................................................................................278
General ..................................................................................................... 278
Environmental ........................................................................................... 278
Electrical....................................................................................................278
Assay Voltage ...........................................................................................279
Chip Pressure............................................................................................ 279
Chip Temperature Control ......................................................................... 279
Fluorescence Detection ............................................................................. 279
Light Source (Red laser diode) .................................................................. 279
Barcode Reader ........................................................................................ 279
Maintenance and Service ...................................................................................280
Cleaning the Chip Cartridge ............................................................................ 281
Cleaning the Instrument Electrodes................................................................. 281
Cleaning Test Chip C ...................................................................................... 282
Troubleshooting and Diagnostics......................................................................283
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Table of Contents 17
Searching for Events in the Events Tab........................................................... 283
Viewing Current Events in the Events Tab.......................................................284
Viewing Past Events in the Events Tab ........................................................... 284
Error Messages............................................................................................... 285
Device <Name> is Disconnected ............................................................... 286
Plate Carrier Motion Blocked ..................................................................... 286
Home Timeout ........................................................................................... 286
Move Timeout............................................................................................ 287
Pressure Leak Detected ............................................................................ 287
Focus Failed.............................................................................................. 287
Maximum Samples Exceeded .................................................................... 288
Chip Primed for Different Assay.................................................................288
HV Check Failed........................................................................................ 288
Current Leakage Check Failed .................................................................. 289
Chip Temperature Warning........................................................................289
Running Installation Qualification (IQ) ............................................................. 290
Running Operational Qualification (OQ) .......................................................... 290
Diagnostics ..................................................................................................... 291
Running the Diagnostics Tests .................................................................. 291
Description of Diagnostic Tests.................................................................. 292
Troubleshooting Assay Problems .................................................................... 298
Software Problems.......................................................................................... 298
Cannot Save a File .................................................................................... 298
Computer Software Lock-Ups .................................................................... 299
Zipping the Log Files....................................................................................... 300
Tips and Shortcuts .............................................................................................301
Glossary of Terms ..............................................................................................302
PerkinElmer Product Warranty ..........................................................................330
PerkinElmer Software License Agreement........................................................ 332
Index....................................................................................................................336
V4.2 LabChip GX User Manual PerkinElmer
Introduction 18

Introduction

This manual includes general instructions for using the LabChip GX hardware and software. It includes general procedures for operating the system, analyzing the data, using software security to comply with 21 CFR Part 11 requirements, instrument maintenance, and hardware and software troubleshooting.
DNA, gDNA, RNA, Protein, Glycan, and Protein Charge Variant (CZE) Chip and Reagent Kits are available to run specific assays on the LabChip GX. The Assay Kits include the reagents and consumables required to run the specific assay. Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.
Assay User Guides
Assay User Guides provide information about the assay. Instructions for preparing the chip, the plate, the ladder vial, and the buffer vial are included in the LabChip GX/GXII Assay User Guide for the specific assay that you are running. Detailed information about the assays, including Specifications, Safety Warnings, Preparation Procedures, Expected Results, Troubleshooting, LabChip Kit Essential Practices, and Reordering Information is also located in the LabChip GX/GXII Assay User Guide for the specific assay that you are running.
The current version of the Assay User Guides can be accessed on the PerkinElmer web site at:
www.perkinelmer.com/labchipguides.
Assay Quick Guides
Assay Quick Guides are included with each Assay Kit and include instructions for preparing the chip to run an assay.
The current version of the Assay Quick Guides can be accessed on the PerkinElmer web site at:
www.perkinelmer.com/labchipguides.

Principles of Operation

The LabChip GX assays are based on traditional gel electrophoresis principles that have been transferred to a chip format. The chip format dramatically reduces separation time and provides automated sizing and quantitation information in a digital format.
The chip contains an interconnected set of microchannels that join the separation channel and buffer wells. One of the microchannels is connected to a short capillary that extends from the bottom of the chip at a 90-degree angle. The capillary sips sample from the wells of a microplate during the assay.
Some of the channels in the chip are larger than others. The larger channels contain buffer. During the chip preparation, the smaller channels and some of the wells are filled with sieving gel and buffer.
Introduction 19
Figure 1. DNA/RNA Chip and Protein Chip Schematic s
After the channels are filled, the chip functions as an integrated electrical circuit. The circuit is driven by the 7 electrodes in the electrode cartridge that contact solutions in the chip's wells when the chip holder is closed. Each electrode is connected to an independent power supply that provides maximum control and flexibility.
The polymer filling the smaller channels in the chip is designed to sieve DNA/RNA fragments or proteins by size as they are driven through it by means of electrophoresis, similar to using agarose or polyacrylamide gels. The sample and sieving buffers also contain a fluorescent dye that gets brighter upon binding to double-stranded DNA, RNA, or protein/SDS complex. (Protein, Glycan, and Protein
Charge Variant assays are only supported on LabChip GX II instruments.)
Principles of Operation (Continued)
In the chip, each sample is sipped from the microplate by negative pressure until a sufficient quantity is loaded in the chip. The sample is then moved electrophoretically into the central channel. As the fragments move down the central channel, they separate by size, and then pass the laser, which excites the fluorescent dye bound to the molecule. The LabChip GX software plots fluorescence intensity versus time and produces electropherograms for each sample (see
Figure 2).
Introduction 20
Figure 2. Electro pherogram
The data can be viewed in a gel-like format on the Gel Tab to achieve the appearance of a slab gel. (The colors of the gel can be changed.)
Figure 3. Gel View
Principles of Operation (Continued)
For DNA, RNA, Protein, and Glycan assays, quantitating the concentration and accurately sizing each fragment are achieved by comparing against a sizing ladder and running internal standards or “markers” with each sample. Internal standards of known concentration are mixed with the sample to aid in quantitation.
The amount of sample sipped into the chip depends on pH, salt concentration, and buffer additives. The internal standards normalize these factors so that the software can use the ratio of the area of the curve of the standard to the unknown peak to determine concentration directly. The internal standards lie slightly outside the assay range so they do not interfere with analysis.
Capillary Zone Electrophoresis (CZE) is an electrophoretic separation technique used to evaluate the charge heterogeneity of proteins in a sample. For Protein Charge Variant assays, analytes are separated based on their net charges, with molecules with a higher net charge migrating faster than those with a lower net charge. The data is analyzed to calculate the % Relative Amount of the peaks.
Introduction 21

Software Modes Available

The LabChip GX software has three modes available: Instrument, Simulation, and Reviewer. The mode can be selected when the LabChip GX software is installed.
Instrument Mode is used to control the LabChip GX instrument and to review data generated by the LabChip GX.
• The 21 CFR Part 11 Compliance option is a purchased option that can be used when the software is installed in Instrument mode.
Simulation Mode is used to simulate running an instrument and to review data generated by the LabChip GX.
Reviewer Mode is used to review data and develop assays, but does not control an instrument or display the instrument controls.
If the LabChip GX software is installed in Instrument mode, shortcuts can be created on the desktop to run the LabChip GX software in Simulation or Reviewer mode (see “Creating Desktop
Shortcuts” on page 23).
Operation 22

Operation

This section includes general instructions for using the LabChip GX hardware and software to run an assay.
This section contains the following information:
• Opening the LabChip GX Software
• Creating Desktop Shortcuts
• Creating a New Assay
• Running an Assay
• Select the Auto Export Settings
• Monitoring the Run
• Stopping a Run
• Continuing a Stopped Run
• Saving Data Files
• Saving Workspace Files
• Selecting Wells using a Sample Names File
• Adding a New Plate
• Placing the Barcode on the Plate
• Calibrating the Optics
For assay-specific information, see the LabChip GX/GXII Assay User Guide for the specific assay that you are running. For instructions on preparing the chip and plate, see the LabChip GX/GXII Assay Quick Guide for the specific assay. The current version of the Assay User Guides and Quick Guides can be accessed on the PerkinElmer web site at:
http://www.perkinelmer.com/labchipguides.
To run an assay in the LabChip GX: 1 Open the LabChip GX software. (See “Opening the LabChip GX
Software” on page 23.)
2 If necessary, create a new assay. (See “Creating a New Assay”
on page 24)
3 Clean the electrodes and the O-Rings as directed in the
LabChip GX/GXII Assay User Guide.
4 If necessary, calibrate the optics (see page 41) and run
Diagnostics (see page 291).
5 Prepare the chip for the assay as directed in the LabChip
GX/GXII Assay Quick Guide.
6 Prepare the plate for the assay as directed in the LabChip
GX/GXII Assay Quick Guide. (See “Placing the Barcode on the
Plate” on page 40 if using barcodes on the sample plates.)
7 Run the assay. (See “Running an Assay” on page 25.)

Opening the LabChip GX Software

If the LabChip GX software was installed in Instrument mode, with or without the 21 CFR Part 11 security option, the desktop icon opens the software in Instrument mode. If desired, you can create shortcuts for Reviewer mode or Simulation mode as described below. If the LabChip GX software was installed in Reviewer mode, the desktop icon opens the software in Reviewer mode.
To open the LabChip GX software:
1 Double-click on the LabChip GX icon on the Windows desktop. 2 If 21 CFR Part 11Security is installed, the Login Window opens.
Type a valid LabChip GX user name and password into the text boxes and click the OK button. (For instructions on creating LabChip GX user names, see “Adding New Users” on
page 118.)
Operation 23
The LabChip GX Main Window opens.
3 See “Creating a New Assay” on page 24 or “Running an Assay”
on page 25.

Creating Desktop Shortcuts

If the LabChip GX software was installed in Instrument mode, you can create desktop shortcuts to run the LabChip GX software in Reviewer mode or Simulation Mode, if desired.
To create new software shortcuts on the Windows desktop: 1 Right-click on the LabChip GX icon on the Windows desktop
and click Copy.
2 Right-click on the Windows desktop and click Paste. A copy of
the LabChip GX icon is created on the desktop.
3 Rename the icon as desired. 4 Right-click on the new icon and click Properties. 5 On the Shortcut tab, enter the following in the Target text box:
•For Reviewer mode: "C:\Program Files\Caliper Life
Sciences\LabChip GX\LabChip.exe" /review
•For Simulation mode: "C:\Program Files\Caliper Life
Sciences\LabChip GX\LabChip.exe" /simulate
6 Click OK in the Properties window.

Creating a New Assay

The LabChip GX software enables you to create a new assay by opening and editing an existing assay and then saving the assay with a new name.
To create a new assay:
1 On the LabChip GX Main Window, select Tools Assay
Editor. The Select Assay To Edit window opens.
2 Select the name of the Assay file that you want to edit and click
the OK button. The Assay Analysis Window opens and displays the settings for the open assay.
Operation 24
3 Modify the settings as necessary for the new assay. (See
Modifying Analysis Parameters or Reanalyzing a Data File for
information on setting or changing analysis parameters.)
4 Click the Save Assay button at the bottom of the Assay
Analysis window, specify the desired name for the new assay file, and click the Save button.

Running an Assay

If a new chip has been inserted in the instrument, the chip is automatically primed at the start of the first run. Since priming is a lengthy process, you can start priming the chip before you are ready to start the run. (To save time, the sample plate can be prepared while the chip is priming.)
To prime a chip before starting the run: 1 Select Instrument Sta rt P r ime to start priming for a specific
assay.
2 Select the assay in the Choose Assay for Chip Prime window
and then click the OK button. (If the chip is not primed before starting the run, the chip is primed automatically when you click the Run button.)
To start an assay to read a plate: 1 Click the Run button on the LabChip GX Main Window (see
page 143) to open the Start Run Window.
Operation 25
If the maximum number of samples for the chip have already been run or if the chip was last primed for a different assay, a message displays instructions for resolving the problem.
2 Click the Run tab in the Start Run window. 3 Select the type of assay you want to run in the Assay Type
drop-down list. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.)
4 Type the operator's name in the Operator Name text box. 5 Select the name of the plate in the Plate Name drop-down list.
To use a plate that is not listed in the Plate Name list, see
“Adding a New Plate” on page 38.
6 To read the plate barcode, select the Use Barcode check box.
(The plate barcode can be used to name the data file if selected.)
Running an Assay (Continued)
7 On the Plate diagram, select the wells to be sampled.
• To select all wells and ladders on the plate, click the double-
arrow button in the lower-right corner of the plate.
• To select all rows on the plate, click the double-arrow button
at the top left corner of the plate.
• To select all columns on the plate, click the double-down-
arrow button at the top right corner of the plate.
• To select a single column, click the column number at the top
or bottom of the plate.
• To select or clear all wells in a quadrant, click the Q1, Q2,
Q3, or Q4 button.
• To select a single row, click the row letter on the left or right
side of the plate.
• Clear specific wells by clicking on a selected well.
• To use a Sample Names file to select the wells, see
“Selecting Wells using a Sample Names File” on page 35.
Operation 26
8 Select the desired sipping order for the selected wells, Row-
wise, Column-wise, or File Order.
9 Click the Output Tab in the Start Run window. 10 To change the Data Path, either type the desired path or click
the Browse button and select the desired location for the data files. Clicking the Default button restores the default data path.
NOTE
Data files should be saved to a local folder on the computer's hard drive. Saving data files to a network drive may ca use loss of data if the network connection is slow or interrupted.
11 If desired, select the Create Daily Sub-Directory check box to
create a new sub-directory for data files each day.
12 If the 21 CFR Part 11 option is installed and you want to save a
copy of the data files to a folder outside of the CDR or if the 21 CFR Part 11 option is not installed and you want to save a second copy of the data files, see “Automatically Exporting
Copies of Data Files” on page 126.
Running an Assay (Continued)
13 To add the File Prefix, Computer Name, Project Name,
Barcode, Date, and/or Time to the data file name, select or
clear the desired check boxes or type the desired file prefix and project name. The file name components are added to the data file name in the order in which they are selected. Leave the text box blank to omit the File Prefix or Project Name from the file name.
14 To automatically export data tables, graphs, or gels, select the
Automatic Export check box, click the Auto Export Settings
button, and then select the desired Auto Export settings (see
page 29).
15 Click the Advanced Tab in the Start Run window. 16 To perform the assay multiple times on the same plate, select
the desired number of times to run the assay in the Plate Cycles text box.
Operation 27
17 To randomly sample a specific percent of the selected wells,
select the Random Selection check box and specify the percent of wells to sample during the run.
18 To repeatedly run the selected wells and combine the data into
one data file, select the Sample Saver check box and select the number of times to repeatedly run the selected wells in the Repeats text box.
19 To use a file to supply the sample names, click the Browse
button next to Sample Name s File, select the name of the .csv file that contains the sample names, and click the Open button. The path and name of the file displays in the text box.
To use a Sample Names file to select the wells, see “Selecting
Wells using a Sample Names File” on page 35.
20 To use a file to supply the Expected Peaks, click the Browse
button next to Expected Peak s File , select the name of the .gep file that contains the expected peaks, and click the Open button. The path and name of the file displays in the text box. (See “Using Expected Fragments/ Expected Proteins/ Expected
Glycans” on page 67 for more information.)
21 To use a file to supply the Excluded Peaks, click the Browse
button next to Excluded Pe aks Fi le, select the name of the .gep file that contains the excluded peaks, and click the Open button. The path and name of the file displays in the text box.
Operation 28
22 Click the Start button to start the assay. A new workspace
opens to display the data.
See “Monitoring the Run” on page 30 for information about viewing data during the run.
Operation 29

Select the Auto Export Settings

The Auto Export settings specify which views to automatically export at the end of each run and specifies the format for each view. Click the Auto Export Settings button in the Output Tab on the
Start Run Window to open the Export Window.
To select the desired views to export:
1 Select the check boxes next to the views to export. Selecting
Export All selects all check boxes.
2 For each selected view, to change the location for the files, click
the Browse (...) button and select the desired location. If the default path is selected, the path displays in blue. If the
path is not the default path, the path displays in purple. To set the path to the default, right-click on the path and select Reset
to Default.
3 If Raw Data is selected, click the AIA Format check box to
export in Chromatography Data Interchange Format or clear the check box to export in CSV format. If CSV is selected:
•Select Include Size Data to align the data to the well's
ladder (for one file per well) or to the first well (for a single data file) and include the size data in the exported data. (Not available for CZE assays.)
•Select Export Single Table to export the data for all wells in
the plate to one CSV file. If not selected, the data from each
4 If Gel is selected:
well is exported to a separate CSV file.
a Select either Single File to include gels for all wells in the
run in the same image file, or select Separate Files to export each gel to a separate image file.
b To adjust the contrast minimum and maximum values for all
gels to a specific lane in the gel, choose the desired well in the Contrast Lane drop-down list. (Only available after the sample wells have been selected on the Run tab.)
c If desired, change the height, in pixels, of the exported gel
graphics in the Height text box.
5 If either Electropherogram or Gel is selected, choose the
desired format for the image files.
6 Click OK to save the Export settings. The specified files are
exported at the end of the run.

Monitoring the Run

The following occurs after a run is started in the LabChip GX software:
1 The priming and warming steps are performed.
• The priming step fills the channels of the chip with reagent.
(Only performed if the chip holder has been opened since the last run.)
• The warming step allows the heater plate located in the chip
holder to regulate chip temperature to 30°C.
• Data collection begins after the warming and priming steps
are completed.
2 After the run begins, the Start button on the LabChip GX main
window changes to Stop.
3 The Active Data Tab displays the electropherogram of the well
currently being read. Data is saved to a file with the name shown above the plate diagram after each well is completed.
Operation 30
4 To view the results for individual wells as data is acquired or
after the run is finished, click a well in the Plate View or Plate
List, a sample name in the Well Table View, or a lane in the Gel View. Data from the selected well displays in the Overlay Electropherograms Tab and the Peak Table View.
For more information on data analysis, see “Data Analysis” on
page 42.
5 To stop the run before it is complete, see Stopping a Run. 6 When the assay is complete, Run Successful displays in the
Status line.
7 If desired, remove the plate and/or remove the chip. To save the analyzed data: 1 Select File Sav e Workspace. The Save Workspace As
Window opens with the default workspace name as the name of
the data file.
2 If desired, change the location and/or the name of the
workspace file and click the Save button. (Workspace files have a .gxw file extension.)
To view or re-analyze the data, see Data Analysis.

Stopping a Run

If you need to stop the run before it is complete, click the Stop button.
A message box confirms that you want to stop the run in progress.
Click Yes to stop the run. The Status line displays Run stopped by user.
Operation 31
Data for any completed wells displays in the LabChip GX Main
Window.
To continue to read wells from an aborted run, see Continuing a
Stopped Run.

Continuing a Stopped Run

If a run is stopped before it is complete, you can restart the run to finish the reading the plate. When you select the wells for the assay, you should select only the wells that were not read so that the reading starts with the well that was not completed.
To continue a run: 1 Click Start in the upper-left corner of the main window to open
the Start Run Window.
2 Select the wells that were not read in the previous run,
beginning with the well that was in progress when the run was stopped.
3 Select the same options for this run as were selected for the
stopped run.
4 Click the Start button to begin.
Operation 32
The run starts with the well that was not completed in the previous run. A separate data file is created for the current run.

Saving Data Files

While running an assay, the raw time series data received from the instrument is automatically saved to the data file (.gxd), one well at a time as each well is completed. If a run is stopped before it is complete, the data for the completed wells is saved in the data file. The name of the data file is specified in the Output Tab on the Start
Run Window.
The analysis settings for a plate are saved at the end of the data file (.gxd). If analysis settings are changed in the Assay Analysis
Window and the data file is saved, the new settings are added to
the end of the data file, but the previous settings are not overwritten. This enables a plate to be restored to previous analysis settings using the Restore Plate button in the Assay Analysis window.
If the 21 CFR Part 11 option is installed, data files are saved in the Centralized Data Repository (CDR). The CDR is a secure folder that can only be accessed by the LabChip GX software. The location of the CDR is specified in the CDR Utility Window.
Operation 33
Updated analysis settings are saved when the plate data file is saved. To save the data file, either:
•select Workspace Save Plate on the Menu Bar,
• right-click on the plate name in the Plate View and select Save Plate, or
•select File Save Workspace or File Save Workspace As on the Menu Bar. (See Saving Workspace Files for more information.)
If the 21 CFR Part 11 option is installed and Require Signature on File Update is selected in the Set Policies tab on the User
Administration Window, the user must have signature rights to save
an updated data file. If the data file is locked, a user with Unlock rights must unlock the data file before changes can be saved.
To save the data file when the 21 CFR Part 11 option is installed and Require Signature on File Update is selected:
1 The Perform Signature Window opens when you save a data
file.
2 Select the name of the user who is signing the data file in the
Username drop-down list.
3 Type a Comme nt that meets the requirements of the
compliance policies.
Saving Data Files (Continued)
4 If appropriate, select the desired Approval State. 5 If desired, select the Lock check box to lock the data file and
prevent it from being changed.
6 Type the User Password for the signing user. 7 Click the Sign button. The Signature Performed window
confirms that the signature has been performed.
8 Click the OK button. The signature is recorded in the data file.
Note
Changing the analysis settings and sav ing the plate data file do es not change the raw data from the run. Only the display of the data is changed.
Operation 34
If you change the analysis settings without saving the new settings, and then try to close the workspace, exit the software, or acquire new data, you are prompted to save the changes. Selecting Yes opens the Save Workspace As Window.

Saving Workspace Files

When viewing plate data in the LabChip GX main window, you view the selected data files in a Workspace. When a new run starts, a new blank workspace opens, which contains the data file for the plate in the run. After the run is complete, saving the workspace saves the data file with the current analysis settings. (See Saving
Data Files for more information on the contents of the data files.)
The Data Files are not saved in the Workspace file. The workspace file contains links to the revision of the data file that was last open in the collection. If a Workspace file is moved to another folder or computer, the data files must be moved with the Workspace file. The data files must be in the same location relative to the Workspace file as they were, otherwise you are prompted to find the missing data files when you open the Workspace file. It is a good practice to save the workspace files in the same location as the data files that are included in the workspace.
Saving a Workspace file automatically saves any changes to the data files that are open in the workspace, and the settings for each collection in the workspace.
Operation 35
If the 21 CFR Part 11 option is installed, saving Workspace files does not require permission to save data files unless the data files in the workspace have been modified.

Selecting Wells using a Sample Names File

The wells to be sampled during the run can be selected using a Sample Names file. When using a Sample Names file to select the wells, only wells with an entry in the Sample Names file are selected for sampling. The format must match the file format described in “Sample Name File Format (.CSV Format)” on
page 65.
The Sample Names file used to select the samples contains one row for each well to be sampled, and does not contain rows for wells that are not sampled.
Using the Sample Names file in Figure 4 to select the wells in the run will select wells A1, A5, A11, A12, B1, B2, F5, and F6 for sampling.
Figure 4. Sample Names File for Selecting Samples
Figure 5. Selecte d Wells on Run tab in Start Run Window
This Sample Names file cannot be created in the Sample Names Editor window because the files created in the Sample Names Editor window always contain one row for each well in the plate. The Sample Names files for selecting wells are typically created by a LIMS or can be created in Microsoft Excel.
Operation 36
To select the wells using a Sample Names file: 1 Create the sample names file with one row for each well to be
sampled.
2 Click the Run button on the LabChip GX Main Window. The
Start Run Window opens.
3 Click the Advanced Tab. 4 Click the Browse button (...) next to the Sample Names text
box, select the sample names file, and click the Open button.
5 Select the Use this file for sample selection check box.
Figure 6. Use This File For Sample Selection 6 Click the Run Tab. 7 Select the desired Sipping Order: Row-wise, Column-wise, or
File Order. (See page 250 for details.)
8 Select any other run parameters as desired, and then start the
run.

Using a Barcode to Specify the Sample Names File

When using a LIMS, a Sample Names File can be specified by using the plate barcode as the name of the file. The Sample Names file is read at run-time, after reading the plate barcode.
To use the plate barcode as the name of the Sample Names file: 1 Decide on a location and file name format for the Sample
Names files. For example, the Sample Names files can be named “Sample Names” followed immediately by the barcode on the plate.
2 Create a temporary CSV file, using “%barcode%” as a
placeholder for the barcode string. For example, create a temporary file named “Sample Names%barcode%.csv” and save it in the location where the actual sample names files for the runs will be saved.
3 In the Run File Editor Window, select the desired run
parameters.
Operation 37
4 On the Advanced tab, click the Browse button next to Sample
Names File, and select the CSV file that contains the
%barcode% wildcard. The Use this file for Sample Selection check box is automatically selected when the sample names file contains the string %barcode%.
5 On the Run tab, select the desired Sipping Order: Row-wise,
Column-wise, or File Order.
6 Click the Export button and save the Run file. 7 To start the run, click the Run button. The Start Run Window
opens.
8 Click the Import button and select the saved Run file. 9 When the run is started, the plate barcode is read and the
Sample Names file with the corresponding barcode is used to select the wells to sample. In the example above, if the plate barcode is 12345, then the file named “Sample Names12345.csv” will be used to select the wells in the run.

Adding a New Plate

When using a plate other than the plates specified in the Start Run
Window, you must create a new plate in the Plate Information Window. Use caution adding new plates. Entering wrong values in
the Add Plate Window can result in damaged chips and broken sippers.
It is best to use the plate specifications provided by the plate manufacturer. If the specifications are not available, measure the plate with a caliper. Many plates have a large variation in the Z-axis location of the well bottom.
Make sure the Sip Height has enough margin to accommodate this variation:
• Minimum Sip Height is 2.5mm.
• Maximum Sip Height depends on the sample volume.
• Sip Height of 4mm is probably safe.
To add a new plate:
Operation 38
1 Select Tools Plate Editor to open the Plate Information
Window.
2 Click the Custom Plates tab. 3 Click the Add Plate button. The Add Plate Window opens. 4 Type the settings for the new plate. The diagram on the Add
Plate window shows the location for each measurement. Acceptable plate parameters are:
• PlateHeight: 0 to 16mm
• WellDepth: 0 to 36mm
• SipHeight >= 2mm
• (WellDepth – SipHeight) <= PlateHeight
5 Click the OK button. 6 Perform a Punch Test from the Plate Information window to
verify the new plate settings are acceptable.
• With a piece of the tape provided by PerkinElmer, cover the corner wells on the plate.
• Use an old, dead chip with a good sipper.
• In the Plate Editor, select the new plate name and click the Verify Plat e button.
• Follow the onscreen instructions.
Adding a New Plate (Continued)
• The instrument will move to the specified number of wells in each corner of the plate, punching holes in the tape.
• The Punch test is acceptable if the punched hole is >0.5mm from the edge of the well.
Operation 39
• Holes will never be perfectly centered.
Possible sources of errors:
• Sipper splay
• Plate tolerances
• Robot alignment error
• If the holes are too close to the edge (<0.5mm), adjust the X­Margin or Y-Margin values in the Add Plate window.
7 Select the new plate name in the Start Run Window when
starting the run.

Placing the Barcode on the Plate

Figure 7 shows the size limits for the barcode label and the location
on the microplate where the label should be placed. The barcode must be located on the short (portrait) end of the microplate, closest to well A1. If the barcode is not positioned properly, the barcode reader will not be able to read the barcode.
Operation 40
Figure 7. Ba rcode Label Po sition

Calibrating the Optics

The LabChip GX software provides an Optical Calibration function using Test Chip C to calculate a correction factor for each individual LabChip GX instrument. The correction factor is applied to all samples run on the instrument to provide a common absolute fluorescence across different instruments.
See “Maintenance and Service” on page 280 for recommendations on optical calibration frequency. Optics Calibration should also be run if the Optics Calibration Test in the Diagnostics fails.
To calibrate the optics:
1 Insert Test Chip C in the instrument. 2 Select Tools Calibrate Optics to open the Optics Calibration
Window. The laser and Test Chip warming step starts. Warm-up
takes 10 minutes.
3 Wait while the scan is performed. The scan takes 5 minutes.
When the scan is complete, the correction factor is calculated and displays in the New Correction Factor text box.
Operation 41
4 To apply the new calibration factor to the instrument, click the
Apply button. All future runs will be scaled by the new
calibration factor.
Walk-Away Operation
After the scan has started, you can leave the instrument. At the end of the scan, the chip warming and laser are turned off after one minute, but the correction factor displayed in the window can be applied when the user returns to the instrument.
Correction Factor Beyond Calibration Limi ts Error
If the New Correction Factor is not within the factory-set limits, the text box displays a red background and an error message displays. Please contact PerkinElmer technical support (see page 3) to determine the problem.
Failed to Find Focus Point
If the focus point cannot be found during a scan, retry the scan. If the error still displays and another Test Chip C is available, try the scan with a different Test Chip C. The laser and chip warming remain on for one minute to allow you to retry the scan.
Data Analysis 42

Data Analysis

After a run is complete, use the LabChip GX software to view and analyze the plate data. The LabChip GX software can open multiple data files in the same workspace to compare the data from different plates. Analysis settings can be changed for single wells, entire plates, or all plates in the workspace.
This section contains the following information:
• How the Software Analyzes DNA Data
• How the Software Analyzes Protein Data
• How the Software Analyzes RNA Data
• How the Software Analyzes Glycan Data
• How the Software Analyzes Protein Charge Variant Data
• How the Software Analyzes Genomic DNA Data
• Organizing, Retrieving, and Backing Up Data Files
• Opening a New Workspace
• Opening a Data File
• Adding a Collection to a Workspace
• Selecting the Wells in a Collection
• Using Sample Names Files
• Using Expected Fragments/ Expected Proteins/ Expected
Glycans
• Modifying Analysis Parameters
• Saving and Exporting Assays
• Changing the View of the Data
• Copying Information
• Reanalyzing a Data File
• Printing Workspace Information
• Exporting Data

How the Software Analyzes DNA Data

The LabChip GX DNA Assay Analysis calculates the size and concentration of nucleic acid fragments. Results for each well are calculated after all data for that well has been read.
The data analysis process for DNA assays consists of the following steps:
1 Raw data is read and stored by the system for each individual
well.
2 The data is filtered (see “Data Filtering” on page 307) and the
resulting electropherograms of all wells are plotted.
3 Peaks are identified (see “Understanding Peak Finding” on
page 108) for all wells and are tabulated by migration time. The
settings of the peak find algorithm can be changed and the data can be reanalyzed after the run has finished. (See “Reanalyzing
a Data File” on page 95.) The peak find settings can be changed
for all wells or only for specific wells.
Data Analysis 43
4 A sizing ladder (see Figure 8), which is a mixture of DNA
fragments of different known sizes, is run first from the ladder vial. The concentrations and sizes of the individual base pairs in the ladder can be changed on the Analysis Tab.
Figure 8. Ladde r Graph - DNA
How the Software Analyzes DNA Data (Continued)
5 The ladder is analyzed (see “Ladder Analysis” on page 311) and
a standard curve of migration time versus DNA size is plotted from the DNA ladder by interpolation between the individual DNA fragment size/migration points. The standard curve derived from the data of the ladder well should resemble Figure 9.
Data Analysis 44
Figure 9. Standard Curve Window - DNA
6 Two DNA fragments, the Lower Marker and Upper Marker, are
run with each of the samples, bracketing the DNA sizing range. The Lower Marker and Upper Marker are internal standards used to align the ladder data with data from the sample wells.
Figure 10 shows an example of assigned marker peaks in a
sample well.
Figure 10. Markers - DNA
How the Software Analyzes DNA Data (Continued)
7 The standard curve and the markers are used to calculate DNA
fragment sizes for each well from the migration times measured.
8 To calculate the concentration of the individual DNA fragments
in all sample wells, the upper marker, in conjunction with a calibration curve plotting assay-specific concentration against base-pair size, is applied to the individual sample peaks in all sample wells.
If a titer is being used, the ladder is not used for quantization. Instead, peak sample areas are normalized using the upper marker and then quantization is performed using the titer standard curve to convert normalized area to concentration; see
“Titer” on page 328.
NOTE
Data Analysis 45
The software allows you to define upper and lower markers. Changing the markers causes quantitative changes in the calibration procedure, however, and therefore in the entire data evaluation.

How the Software Analyzes Protein Data

Protein assays are only supported on LabChip GX II instruments.
The LabChip GX Protein Assay Analysis consists of the following steps:
1 Raw data is read and stored by the system for each individual
well.
2 The data is filtered (see “Data Filtering” on page 307) and the
resulting electropherograms of all wells are plotted.
3 Peaks are identified (see “Understanding Peak Finding” on
page 108) for all wells and are tabulated by migration time. The
settings of the peak find algorithm can be changed and the data can be reanalyzed after the run has finished. (See “Reanalyzing
a Data File” on page 95.) The peak find settings can be changed
for all or only certain wells.
Data Analysis 46
How the Software Analyzes Protein Data (Continued)
4 A sizing ladder (see Figure 11), which is a mixture of protein
fragments of different known sizes, is run from the ladder vial before and after every 12 samples. The concentration and sizes of the individual proteins (in kDa) in the ladder can be changed on the Analysis Tab.
Figure 11. Ladder Graph - Protein
5 The ladder is analyzed (see “Ladder Analysis” on page 311) and
a standard curve of migration time versus mobility is plotted
from the ladder by interpolation between the individual protein size/migration points. The standard curve derived from the data of the ladder well should resemble Figure 12.
Data Analysis 47
How the Software Analyzes Protein Data (Continued)
Figure 12. Standard Curve - Protein
6 A Lower Marker is the internal standard used to align the ladder
data with data from the sample wells. Figure 13 shows an example of the assigned Lower Marker peak (marked LM) in a sample well.
Figure 13. Marke rs - Protein
Data Analysis 48
How the Software Analyzes Protein Data (Continued)
7 Before calculating either the protein size or concentration, the
sample data is processed relative to the two ladders that bracket every 12 samples. First, all of the data is aligned to the lower marker and then stretched, relative to the highest molecular weight protein in the ladder.
8 The concentration of the sample proteins is determined relative
to the bracketed ladders. There are seven proteins in the ladder (not including the lower marker). The ladder concentration can be changed on the Analysis Tab (see page 189).
9 If a titer is being used, the ladder is not used for quantization.
Instead, peak sample areas are normalized using the lower marker and then quantization is performed using the titer standard curve to convert normalized area to concentration; see
“Titer” on page 328.
NOTES
• The seven proteins are assumed to represent th e average staining behavior of proteins and are used to determine an average peak area per g/mL o f protei n. Thi s factor is used to convert sample peak areas into relative concentration. The total relative concentration of all proteins is calcula ted by addition of the relative concentration of the individ ual proteins and is displayed in the Well Table View (see page 172).
• Since the conversion factor is determined for each ladder, the factor can be linearly interpolated for each sample and thus account for any assay drift.
• The software allows you to define the lower marker. Changing the selection of the marker will lead to quantitative changes in the calibration procedure, and theref ore in the entire data evaluation.

How the Software Analyzes RNA Data

The LabChip GX RNA Assay Analysis determines the quality of the RNA sample by measuring the relative amounts of know RNA fragments relative to the total RNA present in the sample. Results for each well are calculated after all data for the well has been read.
The data analysis process for RNA assays consists of the following steps:
1 Raw data is read and stored by the system for each individual
well.
2 The data is filtered (see “Data Filtering” on page 307) and the
resulting electropherograms of all wells are plotted. The filtering algorithm settings can be changed and the data can be reanalyzed after the run is finished. (See “Reanalyzing a Data
File” on page 95.)
3 A curve spline fit to the data is performed to generate a baseline
above which RNA fragment peaks are detected. This baseline is displayed as a blue line on the electropherogram when Show Peak Baselines is selected in the Graph View Properties (see
page 164).
Data Analysis 49
4 Peaks extending above the baseline are identified (see
“Understanding Peak Finding” on page 108) for all wells and are
tabulated by migration time. The settings of the peak find
algorithm can be changed and the data can be reanalyzed after the run has finished. The peak find settings can be changed for all or only certain wells.
5 A sizing ladder (see Figure 14), which is a mixture of RNA
fragments of different known sizes, is run first from the ladder vial. The concentrations and sizes of the individual nucleotides in the ladder can be changed on the Analysis Tab.
How the Software Analyzes RNA Data (Continued)
Data Analysis 50
Figure 14. Ladder Graph - RNA
6 The ladder is analyzed (see “Ladder Analysis” on page 311) and
a standard curve of migration time versus RNA size is plotted
from the RNA ladder by interpolation between individual RNA fragment size/migration points. The standard curve derived from the data of the ladder well should resemble Figure 15.
Figure 15. Standard Curve - RNA
How the Software Analyzes RNA Data (Continued)
7 A dye matching the lowest peak in the ladder is run with each of
the samples. This lower marker, labeled LM in the RNA sample (see Figure 16) is used to align the ladder data with data from the sample wells.
Data Analysis 51
Figure 16. Markers - RNA
8 The standard curve and the markers are used to calculate RNA
fragment sizes for each well from the migration times measured.
How the Software Analyzes RNA Data (Continued)
9 The Total RNA present is computed by finding the area under
the electropherogram trace. The baseline for this integration is a straight line starting at the end of the lower marker and ending at the baseline end time. The height of the baseline endpoints is computed from an average of a five second window around the baseline Start Time and End Time (shown on the Peak Find
Tab ). View the baseline by selecting Show Peak Baselines in
the Graph View Properties. Adjust the Start Time and End Time by dragging the left (Start) and right (End) vertical dashed lines to areas that more properly reflect the signal baseline. (Right­click in the graph, select Set Scale, and change the X axis Minimum and Maximum values if the start and end times are not shown in the graph.)
Data Analysis 52
Figure 17. Pea k Baseline - RNA
10 The Total RNA concentration in the sample is computed from
the ratio of the RNA area in the sample to the RNA area in the ladder multiplied by the ladder concentration specified in the assay.
If a titer is being used, the ladder is not used for quantization. Instead, peak sample areas are normalized using the lower marker and then quantization is performed using the titer standard curve to convert normalized area to concentration; see
“Titer” on page 328.
How the Software Analyzes RNA Data (Continued)
11 Assay-defined RNA fragments are identified from the peaks in
the peak table. Fragments are located by finding the largest peak within a size range associated with the fragment. For Eukaryote RNA assays, 5S, 18S and 28S fragments are located. For Prokaryote assays, 5S, 16S and 23S fragments are identified.
12 The following values are calculated for RNA assays:
Fragment_Area: Area of each rRNA Fragment. %_of_Total_Area: Each Fragment area as a percent of total
area. Corrected RNA Area: Total RNA Area corrected with Lower Marker height. RNA Concentration (ng/ul): Estimated Total RNA Concentration in the sample.
rRNA Area Ratio [28S / 18S]: 28S area divided by 18S area. rRNA Height Ratio [28S / 18S]: 28S height divided by 18S
height or 23S height divided by 16S height. rRNA Fast Area Ratio: Region between 5S and 18S or 16S, percent of total area. RNA quality metrics: rRNA Area and Height Ratios (28S/18S or 23S/16S) and Fast/Total RNA area ratio are computed.
Data Analysis 53
Figure 18. rRNA Graph Analysis
13 Messenger RNA Assay: The RNA contamination ratio is
computed. This is the ratio of the area of all the fragments to total RNA area.
Data Analysis 54

How the Software Analyzes Glycan Data

Glycan assays are only supported on LabChip GX II instruments.
The LabChip GX Glycan Assay Analysis consists of the following steps:
1 Raw data is read and stored by the system for each individual
well.
2 The data is filtered (see “Data Filtering” on page 307) and the
resulting electropherograms of all wells are plotted.
3 Peaks are identified (see “Understanding Peak Finding” on
page 108) for all wells and are tabulated by migration time. The
settings of the peak find algorithm can be changed and the data can be reanalyzed after the run has finished. (See “Reanalyzing
a Data File” on page 95.) The peak find settings can be changed
for all or only certain wells.
4 A sizing ladder (see Figure 19), which consists of multiples of a
basic sugar molecule, is run from the ladder vial before and after every 12 samples. The simplest molecule is assigned a size unit of 1 CGU (Caliper Glucose Unit). The sequence of ladder peaks is assigned integer size values, providing a migration time to size ruler for sizing other sugar molecules.
Figure 19. Ladder Graph - Glyc an
5 The ladder is analyzed (see “Ladder Analysis” on page 311) and
a standard curve of migration time versus mobility is plotted
from the ladder by interpolation between the individual glycan/migration points. The standard curve derived from the data of the ladder well should resemble Figure 20.
Data Analysis 55
How the Software Analyzes Glycan Data (Continued)
Figure 20. Standard Curve - Glycan
6 A Lower Marker is the internal standard used to align the ladder
data with data from the sample wells. Figure 21 shows an example of the assigned Lower Marker peak (marked LM) in a sample well.
Figure 21. Markers - Glycan
Data Analysis 56
How the Software Analyzes Glycan Data (Continued)
7 The standard curve and the markers are used to calculate
glycan sizes in each well from the migration times measured.
8 The area under each peak is calculated. 9 All the sample peak areas are added together and an area ratio
is calculated for the %Area for each peak.
NOTES
• In Glycan assays, the lower marker does not precede all ladder peaks but appears between the 6th an d 7th ladder peak. The concentration of the lower marker has been made sufficiently large to avoid confusion with ladder peaks. Si nce peaks befo re the lower marker are ignored, the ladder peaks used for the sizing ruler range from 7 to 13 CGU.
• The software allows you to define the lower marker. Changing the selection of the lower marker will lead to quantitative changes in the calibration, and therefore in the entire data evaluation.
Data Analysis 57

How the Software Analyzes Protein Charge Variant Dat a

Protein Charge Variant assays are only supported on LabChip GX II instruments.
The LabChip GX Protein Charge Variant Assay Analysis consists of the following steps:
1 Raw data is read and stored by the system for each individual
well.
2 The data is filtered (see “Data Filtering” on page 307) and the
resulting electropherograms of all wells are plotted.
3 A baseline is generated for the data using the settings on the
Peak Find tab on the Assay Analysis Window. This baseline is displayed on the electropherogram when Show Peak Baselines is selected in the Graph View Properties (see page 164).
4 Peaks are identified (see “Understanding Peak Finding” on
page 108) for all wells and are tabulated by migration time. The
settings of the peak find algorithm can be changed and the data can be reanalyzed after the run has finished. (See “Reanalyzing
a Data File” on page 95.) The peak find settings can be changed
for all or only certain wells.
5 The % Relative Amount for each peak is calculated as a percent
of total area.
Data Analysis 58

How the Software Analyzes Genomic DNA Data

The Genomic DNA (gDNA) assay analyzes data similar to the other DNA assays, except that the alignment of the sample data with the ladder data is based solely on the Lower Marker. To improve the accuracy of the alignment of the 12 samples between ladders, gDNA assays use the bracketed alignment described in “How the
Software Analyzes Protein Data” on page 45.
For calculating concentration, the Genomic DNA assay uses a GQS Smear, starting at 0.175 kb and extending to 300 kb, by default (see
Figure 22). The start size of the gDNA smear can be changed on
the Advanced Tab in the Assay Editor window. The calculation of concentration is similar to that used for individual peaks, as described in How the Software Analyzes DNA Data; however, the GQS Smear is used in place of individual sample peaks, and the lower marker is used in place of the upper marker to normalize areas. The Total gDNA Concentration of each sample is reported in the Well Table.
The Genomic DNA assay also reports a Genomic Quality Score (GQS) for each sample in the Well Table. The GQS represents the degree of degradation of a sample, with 5 corresponding to intact gDNA and 0 corresponding to highly degraded gDNA. The GQS is calculated using the size distribution of the sample.
Figure 22. Genomic DNA GQS Smear (in orange)
Data Analysis 59

Organizing, Retrieving, and Backing Up Data Files

As you work in the LabChip GX software, it's a good practice to organize the LabChip GX files.
• Create a folder in which to save the data files. If desired, each person can save data files to their own subfolder to organize the data files.
• Save Workspace files in the same directory as the data files to prevent missing data files in the workspaces.
• Review the files periodically, even if only one person uses the LabChip GX software. Archive files you are no longer using but want to save to a backup disk, and discard unneeded files. Verify there is enough free space on the hard drive to save new plate data files. If you are using the 21 CFR Part 11 option, see
“Software Security” on page 114 for backup options.
• Each user in the laboratory can specify a particular data file name prefix to easily differentiate data files.
• A new folder can be created each day to store the data from all runs. To automatically create the folders, select the Create Daily Sub-Directory check box on the Output Tab in the Start
Run Window.

Opening a New Workspace

A workspace displays data from one or more plate data files from the same type of assay. Each workspace can contain one or more
Collections to display the data.
To open a new workspace: 1 On the menu bar, select File New Workspace. If changes
have been made to an open workspace, you are prompted to save any unsaved changes. A blank workspace opens in the
LabChip GX Main Window.
To view data, see:
• Opening a Data File
• Adding a Collection to a Workspace
• Selecting the Wells in a Collection
• Modifying Analysis Parameters
• Saving and Exporting Assays

Opening a Data File

Open a data file to view the data, to compare the data to other data files in the same workspace, or to change analysis setting and view the reanalyzed data. Data files generated by the LabChip GX software have a .gxd file extension. Data files generated by the LabChip HT software, which have a .cla file extension, can also be opened in the LabChip GX software if the 21 CFR Part 11 option is not installed.
To open a data file: 1 Open a new workspace (see page 59) or a workspace that
already contains compatible data files.
2 On the menu bar, select File Import Data File. If the 21 CFR
Part 11 option is not installed, the Select a Data File Window opens. If the 21 CFR Part 11 option is installed, the CDR
Manager Window opens.
Data Analysis 60
3 Select the name of the data file to open and click the Open
button. The selected data file is imported into the open workspace. Use Ctrl+click or Shift+click to select multiple files.
• To select a .cla file, select CLA from the Files of Type drop-
down list in the Select a Data File window. The selected .cla file is converted to a .gxd file, and the new .gxd file is imported into the open workspace. The new .gxd data file is saved in the same folder as the original .cla file. Any changes are saved to the .gxd file. The .cla file cannot be changed.
NOTE
After the .cla file is converted to a .gxd file, use the .gxd file in any workspaces. Re-importing the same .cla file will over-write the existing .gxd file and any analysis changes saved in the .gxd file will be lost.
4 If desired, right-click on the data file name in the Plate View or
Plate List and select Rename Plate to change the name of the
plate in the display. (If desired, select the Rename File to Match check box to change the name of the data file.)
5 Select the desired wells to view in each collection in the
workspace (see page 62).
6 See “Modifying Analysis Parameters” on page 72 for information
about changing analysis parameters.

Adding a Collection to a Workspace

Collections are used to specify the wells selected for view in each plate data file, the layout of the views in the Collection tab, and the display properties for each view in each collection.
To add a new collection to an open workspace: 1 On the menu bar, select Collection New Collection. The
New Collection Window opens.
2 Select the desired option for creating the new collection:
• Template - Opens a new collection with the same settings
as a saved collection template file.
• Blank Collection - Opens a new template using the default
collection settings.
• Current Collection - Opens a new template based on the
current settings in the currently open collection.
3 If no plates are open in the collection, choose the desired Assay
Type for the collection: DNA, Protein, RNA, Glycan, CZE, or gDNA. (Protein, Glycan, and CZE are only supported on LabChip GX II instruments.) Only data files from the selected assay type can be imported into the workspace.
Data Analysis 61
4 If desired, type a new name for the collection in the Name text
box.
5 Click the OK button to open the new collection.

Selecting the Wells in a Collection

Each collection can display different wells or the same wells in different orders. To select the wells to display in a collection:
1 Select the collection where the wells will be displayed. 2 In the plate diagram in the Plate View, select the wells to
display:
Figure 23. Selecting Wells
Data Analysis 62
• Select individual wells: click on the well.
• Select a block of wells: click on the well in one corner and
drag to the opposite corner well.
• Select an entire row: click the row letter at the left.
• Select an entire row and the corresponding ladder: click
the row letter at the right (if the plate sip order is row-wise).
• Select an entire column: click the column number at the
top.
• Select an entire column and any corresp onding ladd er:
click the column number at the bottom (if the plate sip order is column-wise).
• Select all the wells by rows: click the button in the top left
corner of the microplate.
• Select all the wells by columns: click the button in the top
right corner of the microplate.
• Select all ladder wells and microplate wells: click the
button at the bottom right corner of the microplate.
• Select individual ladders: click on the ladder.
• Clear individual ladders: right-click on the ladder and
select Remove Ladder.
• Select all ladder wells: click the “L” icon at the bottom left
corner of the microplate.
• Clear individual wells: right-click on the well and select
Remove Well.
3 Save the workspace to save the wells selected in the collection.

Using Sample Names Files

Sample Names files are used to import sample names into a data file. The Sample Name file can also contain expected peaks. A sample names file can be selected in the Advanced Tab on the Start
Run Window to assign the sample names and expected peaks as
the assay is running. Before the run, a Sample Name file can also be used to select the wells and sipping order for the run (see
“Selecting Wells using a Sample Names File” on page 35).
After the run is complete, you can use the Sample Name Editor
Window to rename the samples or to import an existing sample
name file. Sample name files are saved as .CSV files and can be edited with a spreadsheet program such as Microsoft Excel.
The Color, Name, and Display Property for an Expected Peak cannot be set in the Sample Name Editor window. When new Expected Peaks are created in the Sample Name Editor window, default values are assigned for these properties.
Data Analysis 63

Create a Sample Name File

Sample Names files created in the Sample Name Editor contain a row for each well in the plate. To use the Sample Name file to select the wells in the run, manually create the CSV file in Microsoft Excel or use a LIMS to create the Sample Names file.
To create a Sample Names file to specify the sample names, comments, and Expected Peaks:
1 Select Tools Sample Name Editor on the LabChip GX Main
Window. The Sample Name Editor Window opens.
2 Modify the sample names as desired in the Sample Name
Editor window.
3 Enter any desired comments for the samples in the Sample
Comment column.
4 For DNA, gDNA, Protein, or Glycan assays, if desired, click the
Edit Expected Peaks check box and enter the desired
Expected Peaks and Window (%) in the columns. Separate each peak size or window value with a semi-colon (;). If only one Window % value is entered, the same value applies to all expected peaks. If multiple values are entered, separated by semi-colons, each expected peak will use the corresponding Window value. If more expected peaks are entered than Window values, the last Window applies to all remaining expected peaks in the list.
Data Analysis 64
5 Click the Export button, navigate to the desired location for the
file, type the desired name for the file, and click the Save button.
To import the sample names into a data file: 1 Open the data file in an open workspace in the LabChip GX
Main Window.
2 Select Tools Sample Name Editor on the LabChip GX Main
Window. The Sample Name Editor Window opens.
3 Click the Import button, navigate to the file location, select the
name of the .csv file that contains the sample names, and click the Open button.
If a Sample Names file is imported into the Sample Name Editor window, rows are added for any wells that are not listed in the original Sample Names file. All wells are included in the new Sample Names file.
4 Click the Apply button in the Sample Name Editor window to
apply the sample names to the active plate.

Sample Name File Format (.CSV Format)

Data Analysis 65
The Sample Names created in the Sample Name Editor Window
can be exported to a .CSV file. A .CSV file can also be created in
Microsoft Excel or generated automatically with a LIMS to import the Sample Names into the data file.
Figure 24 shows a Sample Names file open in Microsoft Excel.
Figure 24. Sample Nam e .CSV File
A Sample Name .CSV file must use the following format: Column A: The well label (A1 to P24). The wells labels can be
entered in any order and do not need to cover the entire plate.
Column B: The desired sample name for each well. Column C: A user comment to be added to the well properties. Column D: A list of Expected Peak sizes for the well. This list is
separated by semi-colons (;).
Data Analysis 66
Column E: The search window size for each Expected Peak in column D as a % (10 = +/-10% of Expected Peak size). If all Expected Peaks use the same window size, enter a single value; otherwise enter unique values as a semicolon separated list. If fewer windows than EPs are entered, the last window applies to all remaining EPs in the list.
Column F… Any higher columns are ignored.

Applying Different Window Values to Expected Peaks of the Same Size in Different Wells

Only one Expected Peak of a particular size can exist in the assay analysis settings. If the same Expected Peak size with a different Expected Peak window is entered in the Sample Name Editor window, only the first Expected Peak is created. All other Expected Peaks of the same size use the same window as the first Expected Peak. To overcome this restriction, use Expected Peaks of slightly different sizes; e.g. 200, 200.1, 200.2, etc. to apply different windows to the same Expected Peak in different wells.

Sample Name File Import Errors

Any row in the .CSV file that does not match the expected format and cannot be interpreted is ignored. If none of the rows can be interpreted, usually because the first column does not contain the well label, the following error message displays: “No rows found matching format: label, name, comment, EP, window.”
Data Analysis 67

Using Expected Fragments/ Expected Proteins/ Expected Glycans

You can track expected DNA fragments (EFs), proteins (EPs), Glycans (EGs), or peaks (EPs) for the samples in a DNA, gDNA, Protein, Glycan, or Protein Charge Variant assay, respectively. (Protein, Glycan, and Protein Charge Variant assays are only supported on LabChip GX II instruments.) You enter the EFs, EPs, and EGs in the Assay Analysis Window.

Entering EFs, EPs, or EGs in the Assay Analysis Window

1 Select Analysis Analysis Settings on the Menu Bar. The
Assay Analysis Window opens.
2 Click on the Expected Fragments/Proteins/Glycans Tab. 3 Click in the bottom (empty) row in the table. 4 In the Size column, type the size of the expected fragment (bp
for DNA or kb for gDNA), protein (kDa), or glycan (CGU).
5 For CZE assays, type the time of the expected peak, in
seconds, in the Time Column.
6 In the Window (%) column, if desired, change the tolerance
value to allow for variations in the expected fragment/protein/ glycan size or peak time. This value is specified as a percent of the expected size for that fragment/protein/glycan or time for a peak. The default is 10% for DNA, protein, and CZE, and 2.5% for Glycan.
Note: If there are multiple peaks in the tolerance range, the largest peak is labeled as the expected peak, even if it is not the exact size specified. To change the peak identified as an expected peak, see “Forcing Expected Peaks ” on page 69.
7 A default color is automatically assigned. To change the color,
click on the color block in the Color column and select the desired color in the Color window.
8 If desired, change the name shown in the Name column. 9 If desired, change the Property Displayed in the Well Table.
This setting specifies the property that will be displayed in the Expected Peak column for each expected peak listed in the Well
Table View.
10 To align the data to one or more specific peaks, select the For
Aligning check box. The data is realigned so the selected
peaks match their aligned size. Note: Incorrect alignment settings can cause analysis errors.
11 To apply the expected peak only to specific wells, click in the
Apply to Wells column. The Select Wells window opens. Click
(or click and drag) to select the wells that you want to apply the expected peaks to, and then click the OK button.
12 To apply the EFs, EPs, or EGs to the active plate, click the
Apply button.
13 To apply the EFs, EPs, or EGs to all plates in the workspace,
click the Apply Global button.

Exporting EFs, EPs, or EGs

1 After the EFs, EPs, or EGs are entered in the Expected
Fragments/Proteins/Glycans Tab, click the Export button at the
bottom of the window. The Export Expected Fragments/Proteins/Glycans Window opens.
Data Analysis 68
2 Navigate to the desired location for the file, type the desired
name for the file in the File Name text box, and then click the Save button. A .GEP file is created to save the expected peak settings.

Importing EFs, EPs, or EGs

After an Expected Peak file (*.GEP) has been exported, you can import the settings into another plate or workspace.
1 With the plate open in a workspace, in the Expected
Fragments/Proteins/Glycans Tab, click the Import button at the
bottom of the window. The Import Expected Fragments/Proteins/Glycan Table window opens.
2 Navigate to the location of the file, select the name of the file to
import, and then click the Open button. The expected peak settings are imported into the tab.
3 To apply the EFs, EPs, or EGs to the active plate, click the
Apply button.
4 To apply the EFs, EPs, or EGs to all plates in the workspace,
click the Apply Global button.

Forcing Expected Peaks

If there are multiple peaks in the tolerance range, the largest peak is labeled as the expected peak, even if it is not the exact size specified. If a different nearby peak should have been selected as the expected peak, you can specify which peak is labeled the expected peak.
1 In the Graph View, right-click on the peak that should be labeled
as the expected peak.
2 On the shortcut menu, select Force Expected Fragment/Peak
and then select the desired fragment or peak from the menu.
To clear a forced peak and revert to the default expected peak, right-click on the forced expected peak and select Clear Forced
EP.

Viewing the EFs/EPs/EGs in the Graph View

Data Analysis 69
Expected Fragments, Expected Proteins, and Expected Glycans are identified in the electropherogram by open triangles
over the peaks. The triangles are the same color as specified in the
Expected Fragments/Proteins/Glycans Tab.
To display the expected peak indicators in the Graph view: 1 Click the Properties tab on the right side of the Graph view to
open the Graph View Properties.
2 To view the size of all expected peaks, select Expected
Fragments, Expected Proteins, or Expected Glycan in one of
the Annotation list boxes.
Figure 25. Exp ected F ragments
Figure 26. Expected Peaks

Viewing the EFs/EPs/EGs in the Gel View

Expected Fragments/Proteins/Glycans are indicated in the Gel
View by colored lines. The color of the line matches the color
specified in the Expected Fragments/Proteins/Glycans Tab.
Data Analysis 70
To display the expected peaks in the Gel View: 1 Click the Properties tab on the right side of the Gel View to
open the Gel View Properties.
2 Select the Show Expected Peaks check box.
To display the legend that identifies the colors and sizes of the expected peaks:
1 Click the Properties tab on the right side of the Gel View to
open the Gel View Properties.
2 Select the Show Expected Peaks Legend check box.
Figure 27. Expe cted Peaks Legend

Viewing the EFs/EPs/EGs in the Well Table

A column is added to the Well Table for each Expected Peak entered in the Expected Fragments/Proteins/Glycans Tab. The column displays the property selected in the Property Displayed in
Well Table list in the Assay Analysis Window.

Viewing the EFs/EPs/EGs in the Peak Table

Expected Fragments, Expected Proteins, and Expected Glycans are identified in the Peak Table with the peak name
displayed in the Type column.
Data Analysis 71
Figure 28. DNA Assay Peak Table

Modifying Analysis Parameters

Some analysis parameters can be changed in the software to modify the data evaluation for sample analysis. The following procedures are included in this section:
• “Changing the Peak Find Parameters” on page 73
• “Adding a Peak” on page 74
• “Splitting a Peak” on page 75
• “Excluding a Peak” on page 74
• “Merging Two Peaks” on page 75
• “Adjusting the Peak Baseline” on page 76
• “Setting the Baseline for a Range of Peaks” on page 76
• “Selecting a Default Ladder” on page 77
• “Using the Default Ladder for Alignment” on page 79
• “Exporting the Default Ladder in an Assay” on page 79
• “Clearing the Default Ladder in a Plate” on page 79
• “Changing the Time Window for Analysis” on page 80
Data Analysis 72
• Aligning or Unaligning the Marker Peaks
These settings can be changed after the run is complete or when reanalyzing a previously saved data file.

Changing the Peak Find Parameters

After data filtering, the peak find algorithm locates the peaks and calculates the local peak baselines. The algorithm begins by finding all the peaks above the noise threshold to determine the baseline, after which any peaks below the noise threshold are rejected. A local baseline is calculated for each peak to allow for baseline drift.
The following Peak Find parameters can be changed:
•Min Peak Height
•Min Peak Width
•Slope Threshold
• Inflection Threshold
•Start Time
•End Time
•Filter Width
• Baseline Plateau
Data Analysis 73
To change the Peak Find parameters for all wells:
1 Select Analysis Analysis Settings to open the Assay
Analysis Window, and then click the Peak Find Tab.
2 Change the parameters as necessary at the top of the window. 3 Click the OK button to save the setting, reanalyze the data, and
close the window. Click the Apply button to apply the changes and reanalyze the data, but keep the Assay Analysis window open. Click the Apply Global button the apply the settings to all plates in the workspace and reanalyze the data, but keep the Assay Analysis window open.
To change peak find settings for individual wells:
1 Select Analysis Analysis Settings to open the Assay
Analysis Window, and then click the Peak Find Tab.
2 In the Well drop-down list, select the well number that you want
to change the settings for.
3 Change the settings at the bottom of the window under Well
Peak Find Settings to change the settings for the selected well.
4 Click the OK button to save the setting, reanalyze the data, and
close the window. Click the Apply button to apply the changes and reanalyze the data, but keep the Assay Analysis window open.

Adding a Peak

You can manually add a peak in a region where a peak has not been identified.
1 In the Graph View, right-click at the top of the area where the
peak is to be added. The area must be outside any previously identified peak and the cursor must be an up arrow.
2 Select Add Manual Peak from the shortcut menu. A new peak
centered at the selected location is created.
3 If necessary, adjust the Peak Baseline.

Excluding a Peak

You can exclude any peak or fragment from being used in the analysis.
To exclude a peak:
Data Analysis 74
1 In the Peak Table View, right-click on the peak to be excluded. 2 Select Exclude Peak from the shortcut menu. The Type for the
peak changes to X (excluded), and the value is not used in the analysis.
3 Right-click on an Excluded Peak in the peak table and select
Include Peak to include the peak in the data analysis.
OR
1 In the Graph View, right-click near the top of the peak to be
excluded.
2 Select Exclude Peak from the shortcut menu. The Type for the
peak changes to X (excluded), and the value is not used in the analysis.
3 Right-click on an Excluded Peak in the Graph view and select
Include Peak to include the peak in the data analysis.

Splitting a Peak

If two poorly resolved peaks have been identified as a single peak, you can split the single peak into two separate peaks.
1 In the Graph View, zoom in as necessary to view the single
2 Position the cursor inside the peak at the horizontal location
Data Analysis 75
peak.
where you want to split the peak. (The Split Peak option is not available if the cursor is an up arrow. Move the cursor until the peak is not selected.)
Figure 29. Splitting a Peak
3 Right-click on the graph and select Split Pea k on the shortcut
menu. A new Manual Peak is created abutting the original peak.

Merging Two Peaks

If the analysis has defined two separate peaks, the two distinct adjacent peaks can now be merged into one peak. This will include the area of both peaks in the total concentration and %purity calculations.
To merge two adjacent peaks: 1 Exclude one of the peaks from the analysis, following the
procedure “Excluding a Peak” on page 74.
2 Verify that Show Peak Baselines is selected in the Graph View
Properties.
3 Click and drag the baseline of the remaining peak to include the
area under the excluded peak.

Adjusting the Peak Baseline

The Peak Baseline can be manually adjusted in the Graph View. 1 In the Graph View, zoom in on the peak baseline. (If the peak
baselines are not displayed, select Show Peak Baselines in the
Graph View Properties to display the baseline for each peak.)
2 Click the triangle at one end of the peak baseline and drag to
the desired location.
To reset the baseline to the original position, right-click near the baseline end point and choose Reset to Defaults.

Setting the Baseline for a Range of Peaks

A straight line can be drawn under multiple peaks to create a single baseline for all peaks above the straight line.
To draw a single baseline:
Data Analysis 76
1 In the Graph View, zoom in on the peaks. (If the peak baselines
are not displayed, select Show Peak Baselines in the Graph
View Properties to display the baseline for each peak.)
2 Holding the SHIFT key, click at the point where the baseline will
begin and drag to the desired end point of the baseline.
3 Release the mouse at the end of the baseline. The baselines for
peaks that are entirely contained within the baseline span are adjusted to the new baseline.
To draw multiple baselines using Manual Baseline mode: 1 In the Graph View, zoom in on the peaks. (If the peak baselines
are not displayed, select Show Peak Baselines in the Graph
View Properties to display the baseline for each peak.)
2 Right-click on the graph, away from a peak, and select Manual
Baseline on the shortcut menu.
3 Click and drag in the graph to draw manual baselines.
Note: Clicking and dragging in the graph does not zoom in while
Manual Baseline mode is on. Clicking and dragging in the Gel
View still zooms in when Manual Baseline mode is on.
4 To turn off Manual Baseline mode, right-click on the graph, away
from a peak, and select Manual Baseline again.

Removing a Manual Baseline

To reset a manual baseline back to the original analyzed baseline:
1 Right-click on one end of the manual baseline and select Reset
to Analyzed Base from the shortcut menu.
To reset all manual baselines:
1 Right-click on one end of a manual baseline and select Reset
All Peak Bases.
2 Click OK in the Reset All Peak Bases window.

Selecting a Default Ladder

For DNA, gDNA, and RNA assays, a ladder in an assay can be defined as the default ladder. The default ladder can be used as the ladder for wells on the plate, can be applied to all of the plates in the open collection, or can be saved as the default ladder in a new assay.
Data Analysis 77
To set a specific ladder on a plate as the default ladder for the plate:
1 With the plate data file open, select Analysis Analysis
Settings to open the Assay Analysis Window, and then click the
Peak Find Tab.
2 Under Well Peak Find Settings, in the Well drop-down list,
select the ladder that will be defined as the default ladder.
3 Click the Save as Default Ladder button. (The Save as Default
Ladder button only displays when a ladder is selected.)
4 Click the Apply button to save the default ladder settings. The
Analysis Tab displays the ladder data in the Default Ladder table
and the Markers table (see Figure 30 on page 78).
Selecting a Default Ladder (Continued)
Figure 30. Default Ladder Settings
Data Analysis 78
5 The Ladder Peak Time and Area settings can be changed in the
Default Ladder table, but default ladder peaks cannot be added or deleted and the ladder peak sizes cannot be changed.
6 The Marker Time, Height and Area can be changed in the
Markers table.
7 Click the Apply button at the bottom of the window to save the
changes to the active plate. Click the Apply Global button to apply the default ladder settings to all open data files in the collection. (This allows you to import the default ladder into a plate that does not include any good ladders on the plate.)
8 See “Using the Default Ladder for Alignment” on page 79 to
align wells in the plate using the default ladder.

Using the Default Ladder for Alignment

For DNA, gDNA, and RNA assays, after the default ladder is selected for a data file, the default ladder must be assigned to the desired wells in the plate.
1 With the plate data file open, select Analysis Analysis
Settings to open the Assay Analysis Window, and then click the
Alignment Tab.
2 Select the Align Well Groups to Specified Ladder option. 3 For each group of wells under Align Well Group, select Default
Ladder in the To Ladder column.
4 Click the Apply button to apply the changes to the active data
file or click the Apply Global button to apply the changes to all data files in the current collection.

Exporting the Default Ladder in an Assay

Data Analysis 79
The default ladder in a data file is included in the analysis settings for a new assay when the settings are exported as an assay. Exporting the assay enables you to use the default ladder in future runs.
1 After clicking the Apply or Apply Global button in the Assay
Analysis Window, the Export as Assay button displays.
2 Click the Export as Assay button. The Export Assay Settings
from Plate to Assay File window opens.
3 Select the desired location for the assay file, type the desired
name for the assay file, and click the Save button.
4 Select the new assay in the Run Tab on the Start Run Window.
The new data file will include the default ladder.

Clearing the Default Ladder in a Plate

To delete the default ladder for a plate and return the alignment to the ladder settings for the assay type:
1 With the plate data file open, select Analysis Analysis
Settings to open the Assay Analysis Window, and then click the
Analysis Tab.
2 Click the Clear Default Ladder button at the bottom of the
Default Ladder table.

Changing the Time Window for Analysis

The Start Ti me and End Time parameters in the Peak Find tab define the time window within which peaks are found.
To change the Start Time and End Time parameters for all wells in the open assay:
1 Select Analysis Analysis Settings to open the Assay
Analysis Window, and then click the Peak Find Tab.
2 Change the parameters as necessary. 3 Click the OK button to save the setting, reanalyze the data, and
close the window. Click the Apply button to apply the changes and reanalyze the data, but keep the Assay Analysis window open.

Aligning or Unaligning the Marker Peaks

To perform data analysis for DNA, Protein, RNA, and Glycan assays, the LabChip GX software aligns marker peaks included in the sample wells with markers from the ladder.
• To view the unaligned data (spike rejected, filtered and baseline corrected), choose Analysis Turn Off Analysis.
• To re-enable analysis, choose Analysis Turn On Analysis.
Data Analysis 80
The default setting for this function is enabled. Turning off the analysis displays the data without aligning the markers in the wells and the ladders.
Figure 31. Data Before and After Alignment
Data Analysis 81
Upper and Lower Marker Peaks for DNA Assays
For each DNA sample, the upper and lower marker peaks are assigned first and then the data is aligned so that the well markers match the ladder markers in time, allowing the size and concentration of the sample peaks to be determined.
For DNA assays, the first peak is assigned to be the lower marker and is then offset to match the lower marker in the ladder. The upper marker is then assigned to the last peak in the sample well or to the peak nearest the ladder’s upper marker. The Upper Marker and Lower Marker are aligned to the ladder markers by resampling the well data in a linear stretch or compression using a point-to­point fit.
If the sample marker peaks are either more than twice as far apart or less than half as far apart as the ladder markers, they are assumed to be the wrong peaks, and analysis of the well stops, producing the error Marker peaks n ot detected.
In DNA assays, the height of marker peaks is assay dependent. Ladder peaks are analyzed to calculate a marker peak threshold that is used to locate the marker peaks in the sample wells. If the marker peaks found using this calculated method fail to align with those of a sample, the LabChip GX software will use the minimum peak height threshold setting instead (if this value is lower than the value for the marker peak). For example, the calculated threshold might be too high to find the sample's markers if they happen to be very small for some reason. Either no markers will be found or the wrong peaks will be assumed to be markers and these may not align with the ladder markers. Consequently, the software attempts to use the minimum peak height threshold that, if it is set low enough, will catch the real markers, allowing the sample to align.
If you get unexpected peaks in the ladder analysis or the markers have been set incorrectly, you can manually exclude peaks or set a peak to be used as a marker.
NOTES
• Excluding a peak or manually setting a peak to be an upper or lower marker for a DNA assay can cause errors with analysis.
• You can move the boundary between the Peak Table and the Graph view up or down to increase or decrease the size of the Peak Table, making it possible to see all of the results at once.
Right-clicking in the Peak Table View of a well of a DNA assay opens a shortcut menu with the following commands:
Data Analysis 82
• Include Peak (only for peak type “?”)
• Exclude Peak
• Force Lower Marker
• Force Upper Marker
• Add Expected Peak
NOTE
You can also right-click on a peak in the Graph View to view the same menu.
Lower Marker Peaks in Protein or RNA Assays
For each protein or RNA sample, the first peak in the sample is designated as the Lower Marker. After all lower markers are assigned, the data is aligned so that the well markers match the ladder markers in time, allowing the size and concentration of the sample peaks to be determined.
If there are unexpected peaks in the ladder analysis or if the marker has been set incorrectly, you can manually exclude peaks or set a peak to be used as a marker.
NOTES
• Excluding a peak or manually setting a peak to be the lower marker can cause analysis errors.
• You can move the boundary between the Peak Table and the Graph view up or down to increase or decrease the size of the Peak Table, making it possible to see all of the results at once.
Right-clicking in the Peak Table View of a well of a Protein or RNA assay opens a shortcut menu with the following commands:
• Include Peak (only for peak type “Xsys” or “?”)
• Exclude Peak
• Force Lower Marker
• Force Expected Peak
Data Analysis 83
Lower Marker Peaks in Glycan Assays
For each Glycan sample, the lower marker is added to the samples and ladders. The lower marker is identified because the concentration is much higher than the sample or ladder. After all lower markers are assigned, the data is aligned so that the well markers match the ladder markers in time, allowing the size and corrected area of the sample peaks to be determined.
If there are unexpected peaks in the ladder analysis or if the marker has been set incorrectly, you can manually exclude peaks or set a peak to be used as a marker.
NOTES
• Excluding a peak or manually setting a peak to be the lower marker can cause analysis errors.
• You can move the boundary between the Peak Table and the Graph view up or down to increase or decrease the size of the Peak Table, making it possible to see all of the results at once.
Right-clicking in the Peak Table View of a well of a Glycan assay opens a shortcut menu with the following commands:
• Include Peak (only for peak type “Xsys” or “?”)
• Exclude Peak
• Force Lower Marker
• Force Expected Peak

Saving and Exporting Assays

Assays are created by PerkinElmer and are included with the LabChip GX software. The instrument and software settings used to run each plate and to analyze the plate are contained in an assay (.asy or .asyx) file, which is selected at the start of the run in the
Start Run Window. After each well is complete, the data is analyzed
using the analysis settings in the assay file. If the default analysis settings often need to be modified for more optimal analysis, a new assay file can be created with the modified settings to be used on subsequent runs.
To save a modified assay:
1 Run a plate with the original assay file. 2 Modify the analysis settings for the plate as needed. 3 Right-click on the plate title in the Plate View or Plate List, select
Export Assay, specify a name and location for the assay file,
and click the Save button.
-- OR -­On the Assay Analysis Window, click the Export as Assay button, specify a name and location for the assay file, and click the Save button.
Data Analysis 84
4 When running the next plate, select the new assay file in the
Start Run window.
The procedure above can also be used to automatically include a set of expected peaks in the assay.

Changing the View of the Data

The views in the LabChip GX Main Window can be customized to display data according to the preferences of the user. These options do not change the raw data but provide different means of displaying the data.
To change the view in the main window, see:
• “Viewing Gels” on page 85
• “Viewing Zero Baselines ” on page 86
• “Adjust Pane Widths” on page 87
• “Show or Hide Views” on page 87
• “Zoom In and Zoom Out” on page 88
• “Viewing Graphs in the Overlay Electropherograms Tab” on
page 89
• “Viewing Graphs in the Electropherograms Tab” on page 90
• “Viewing Analysis Errors and Warnings” on page 92
Data Analysis 85
• “Viewing Multiple Properties in the Well Table View” on page 93
• “Exporting Data Manually” on page 105

Viewing Gels

To compare the gels generated by the instrument, view the gels in the Gel View.
Figure 32. Gel View
The color, width, and contrast of the gels can be changed using the
Gel View Properties.
To rearrange gels, click on the column header (well name) and drag the well to the desired location. To hide a well, select the well and then click the (X) button on the column header, or right-click on the well in the Plate View or Plate List and select Remove Well.

Viewing Zero Baselines

All electropherograms produced with the instrument show some amount of background fluorescence. By default, the LabChip GX software enables the zero baseline function. To remove the zeroing, select Analysis Analysis Settings to open the Assay Analysis
Window, click the Peak Find Tab, and select the None check box
under Baseline Algorithm.
Data Analysis 86
Figure 33. Zero Bas eline On
Figure 34. Zero Basel ine Off

Adjust Pane Widths

The LabChip GX Main Window displays several different views of the data files open in the workspace. You can change the height and width of the views to make the views smaller or larger.
To adjust panes: 1 Place the cursor over the edge of the pane that you want to
adjust. The cursor changes to a line with arrows on each end.
2 Click and drag up, down, left, or right. The pane is resized after
you release the mouse button. The layout setting is saved as part of the collection.
3 To save the setting, save the workspace. To create new
collections with the same settings, the collection can be saved as a collection template (see “Collection Menu” on page 146).

Show or Hide Views

Data Analysis 87
The views displayed in the LabChip GX Main Window can be hidden to maximize other views in the main window.
To hide a view: 1 Select Collection Layout on the LabChip GX Main window.
The Layout Options Window opens.
2 Click on the location that is selected for the view to clear the
selection. The view is hidden.
3 If a location (Left, Right, or Bottom) does not contain any views,
the pane closes and the remaining panes enlarge to fill the space.
Note: The Gel View is always displayed and cannot be hidden.
To display a hidden view: 1 Select Collection Layout on the LabChip GX Main window.
The Layout Options Window opens.
2 Click on the desired location for the hidden view (Left, Right, or
Bottom). If multiple views are displayed in the same location, use the tabs at the top of the location to switch between views.

Zoom In and Zoom Out

You can zoom in and out on data displayed in the Gel View and the
Graph View. The Graph View and the Gel view both zoom to the
same levels when either view is zoomed in.
To z o om i n:
• Click and drag to enclose the region of interest. When you release the mouse button, the selected area enlarges to fill the view. In the Gel view, all lanes in the collection zoom to the same level.
• You can continue zooming in until you reach the maximum magnification (the graph will not zoom in any closer).
• Use the horizontal scroll bar under the graph to pan from left to right.
To z o om o ut :
• Right-click in the Graph view or Gel view and select Unzoom to go to the previous zoom setting or select Unzoom All to zoom out to the default view.
Data Analysis 88
For more information, see Viewing Graphs in the Overlay
Electropherograms Tab and Viewing Graphs in the Electropherograms Tab.
Data Analysis 89

Viewing Graphs in the Overlay Electropherograms Tab

If the Overlay Electropherograms Tab is not open, select Collection
Layout on the LabChip GX Main Window, select the location where you want to display the Overlay Electropherograms tab, and click the Apply button. The Overlay Electropherograms tab opens.
Figure 35. Overlay Electro pherograms Tab with Multiple
Graphs
Data from multiple wells can be overlaid in the same graph for visual comparison. Click on one well, then hold down the CTRL key and click on the additional wells to view in the graph. Each peak graph is shown in a different color and line style with a legend at the top of the window. You can remove wells from the overlay by CTRL + clicking the corresponding wells (the bounding box disappears).
Use the Overlay Offset text box on the Graph View Properties to offset each of the graphs by the RFU value specified.
Figure 36. Ove rlay Offset
Data Analysis 90
To add samples to the Overlay Electropherograms Tab, Ctrl + click on the sample that you want to add in the Plate View or Plate
List, Gel View, Well Table View, or Peak Table View. Selected wells
are identified by: dashed outlines around the selected gel lanes in the Gel view, light blue wells in the Plate view, and dark gray rows in the Well Table view and Peak Table view.
To remove a specific sample from the graph, Ctrl + click on the sample that you want to remove in the Plate View or Plate List, Gel
View, Well Table View, or Peak Table View.
T o display onl y one sample in the Overlay Electropherograms tab, click on one sample in the Plate View or Plate List, Gel View, Well
Table View, or Peak Table View.
To view the point coordinates and size of the position of the cursor, hold down the CTRL or Shift key and move the cursor over
the graph. To view the point coordinates and slope of a point on the trace,
hold down the ALT key and the CTRL key and move the cursor over the trace.

Viewing Graphs in the Electropherograms Tab

If the Electropherograms Tab is not open, select Collection Layout on the LabChip GX Main Window, select the location where
you want to display the Electropherograms tab, and click the Apply button. The Electropherograms tab opens.
Figure 37. Electro pherograms Tab with Multiple Graphs
Data Analysis 91
Data from multiple wells can be displayed in the same tab for visual comparison. A separate graph for each well in the collection is displayed in the Electropherograms tab. The data file name and well name display at the top of each graph. If all of the wells are not visible, use the scroll bar on the tab to scroll through the wells in the collection.
Zooming in or out on one graph zooms all of the graphs in the tab to the same zoom level.
To only display the wells selected in the Gel View or Well Table
View, select the Graph Selected Gels Only check box in the Graph View Properties.
To move the graphs in the tab, in the Gel View click and drag the well to the desired position.
To change the number of graphs displayed in the tab, select the desired number of Rows and Columns of graphs to display in the
Graph View Properties. Selecting 8 Rows by 12 Columns displays
an entire 96-well plate.
To view the point coordinates and size of the position of the cursor, hold down the CTRL or Shift key and move the cursor over
the graph. To view the point coordinates and slope of a point on the trace,
hold down the ALT key and the CTRL key and move the cursor over the trace.

Viewing Analysis Errors and Warnings

Analysis errors and warnings are indicated by red or yellow exclamation points in the wells in the Plate View or below the headers in the Gel View. The details of the error or warning can be displayed in the Well Table View. After the Analysis Error column is added to the Well Table, the analysis error text can be displayed in the Electropherograms Tab or the Overlay Electropherograms Tab.
Viewing Analysis Errors and Warnings in the Well Table
To view the details of an analysis error or warning, display the Analysis Error in the Well Table View.
1 Click the Well Table tab. 2 Right-click in the table header. The Select Well Table Columns
Window opens.
3 In the Available Columns list, select Analysis Error.
Data Analysis 92
4 Click the Right Arrow button to move Analysis Error to the
Selected Columns list.
5 If desired, click and drag Analysis Error to the desired column
location. (The top column in the list is the first column in the table.)
6 Click the Save button.
Viewing Analysis Errors and Warnings on the Graphs
The text of analysis errors and warnings can be displayed on the graphs in the Electropherograms Tab or the Overlay
Electropherograms Tab. The Analysis Error columns must be
displayed in the Well Table to be available for selection in the Graph
View Properties.
1 Click the Electropherograms Tab or the Overlay
Electropherograms Tab.
2 Click the Properties tab on the right side of the graph. The
Graph View Properties tab opens.
3 Select Analysis Error in the Well Annotation drop-down list. 4 If desired, click the Well Annotation Location button to change
the location.
5 Click off of the Graph View Properties tab to close the tab.

Viewing Multiple Properties in the Well Table View

Properties for Expected Peaks and Smears display in the Well
Table View. When entering the settings in the Expected Fragments/Proteins/Glycans Tab or the Smear Analysis Tab on the Assay Analysis Window, the property to display in the well table is
specified in the Property Displayed in Well Table column.
To display multiple properties for the same Expected Peak or Smear in the Well Table:
1 In the Expected Fragments/Proteins/Glycans tab, or the Smear
Analysis tab, enter the properties for the expected peak or smear, selecting one of the desired properties in the Property
Displayed in Well Table column.
2 Click in the next row and type the same name as an existing EP
or smear in the Name field of the table. The row will automatically update with the same entries as the original row. The only field that can be changed is the Property Displayed in Well Tabl e column.
Data Analysis 93
3 Change the Property to the desired selection. 4 Repeat until all desired properties have been added to the table. 5 Click the Apply button to display the new columns in the Well
Table. Duplicate properties in the table will be removed when the settings are applied to the plate.

Copying Information

The Edit menu and some of the right-click pop-up menus offer the following choices for copying information from the LabChip GX software for use with other applications, depending on the selection:
•Copy Gel
• Copy Lane
•Copy Graph
• Copy Rows to Clipboard
• Copy Column to Clipboard
Choosing any of these commands places a copy of the selected item on the computer's clipboard. You can then paste the item into a word processing, graphics, or other program.
Choosing Copy Gel copies all of the wells displayed in the Gel View with the labels as part of the graphic. To copy a gel, right-click in the
Gel View and choose Copy Gel.
Data Analysis 94
Choosing Copy Lane copies the selected well in the Gel View with the labels as part of the graphic. To copy a gel, right-click in the Gel
View and choose Copy Lane.
Choosing Copy Graph copies the graph displayed in the Graph
View. The size of the image that is placed on the clipboard when
copying a graph is the same size as the graph displayed in the software.
Copying rows from the Peak Table View or the Well Table View places ASCII information from the selected row or rows on the clipboard. To copy a row or multiple rows, select the desired rows in
the table, right-click on one of the selected rows, and select Copy Rows to Clipboard.
Copying columns from the Well Table View is only available for certain columns in the table. To copy a column, select a single cell in the column, right-click on the cell, and select Copy Column to Clipboard.

Reanalyzing a Data File

Occasionally you may need to open and view or reanalyze a data file that was run and saved previously. The raw data values are saved in the plate data file, along with the original analysis settings that were chosen for the run and any changed analysis settings. This enables you to reanalyze the data with new settings or to view previously saved settings.
The following analysis parameters can be changed:
• Plate peak find settings and Well peak find settings (see
“Changing the Peak Find Parameters” on page 73)
• Sample names and comments (see “Using Sample Names
Files” on page 63)
• Add a Peak (see “Adding a Peak” on page 74)
• Exclude peaks from analysis (see “Excluding a Peak” on
page 74)
• Reassign upper/lower markers (see “Upper and Lower Marker
Peaks for DNA Assays” on page 81 or “Lower Marker Peaks in Protein or RNA Assays” on page 82)
Data Analysis 95
• Alignment or no alignment with ladder peaks (see “Aligning or
Unaligning the Marker Peaks” on page 80)
• Assay - you can save the changed settings under a new assay name, if desired (see “Saving and Exporting Assays” on
page 84)
To reanalyze a data file:
1 Open the workspace that contains the plate data (see page 59). 2 Change the analysis parameters (see list above) as needed. 3 When you click the Apply, Apply Global, or OK buttons in the
Assay Analysis Window, the data is automatically re-analyzed
and the updated information is displayed.
4 To view previous analysis settings, click the Restore Plate
button at the bottom of the Assay Analysis window and select the version to view.

Printing Workspace Information

Choosing File Print opens the Print Window to select the information to print from the open workspace. The selected information can be printed to a printer or to a PDF file. If the
workspace contains multiple collections, information from the active (selected) collection is printed.
The header of each printout contains the workspace name, the collection name, and the page number. The footer of each printout contains information about the LabChip GX software, data file, assay, and instrument. If the 21 CFR Part 11 option is installed, the footer also includes the data file version, signed state, and lock state.
The following information can be printed for the open workspace:
• Print All
• “Gel” on page 97
• “Electropherogram” on page 97
• “Overlay Electropherogram” on page 98
Data Analysis 96
• “Well Table” on page 99
• “Peak Table” on page 100
• “Multiple Electropherogram” on page 101
See below for descriptions of each option.
Print All
This option prints the results of the assay in all of the available formats. The page layout depends on the options selected in Print Settings.
Data Analysis 97
Gel
This option prints a gel image with the lanes marked by the sample name.
Figure 38. Printed Gel
Electropherogram
Choosing this option prints an individual electropherogram of each of the selected wells.
Figure 39. Pri nted Electrophe rogram
Data Analysis 98
Overlay Electropherogram
Choosing this option prints one graph with the electropherograms for all of the selected wells overlaid onto a single graph.
Figure 40. Pri nted Overlay Electrop herogram
Data Analysis 99
Well Table
Choosing this option prints the columns displayed in the Well Table
View. To change the columns that are printed or the order of the
columns, change the columns in the Well Table View.
• Selecting the Add Border check box prints the table with a border around each cell in the table.
• Selecting the Add Well Name as Header check box prints the well name, well label, and sample name at the top of the page.
• Selecting both the Well Table and the Peak Table prints each well on a separate page with the Well Table row at the top of the page and the Peak Table for the well below it.
Figure 41. Prin ted Well Table
Data Analysis 100
Peak Table
Choosing this option prints the columns displayed in the Peak Table
View. To change the columns that are printed or the order of the
columns, change the columns in the Peak Table View.
• Selecting the Exclude Marker check box removes all markers from the printout.
• Selecting the Add Border check box prints the table with a border around each cell in the table.
• Selecting the Add Well Name as Header check box prints a well header (plate name, well name, and sample name) before the peaks in each well.
• Selecting the Per Page or Per Well option for the Column Header specifies whether the Peak Table column headers are printed only at the top of each page (default), or if the headers are also printed at the beginning of each new well table.
• Selecting both the Well Table and the Peak Table prints each well on a separate page with the Well Table row at the top of the page and the Peak Table for the well below it.
Figure 42. Pri nted Peak Table
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