Bio-Rad ChromLab Software User Manual

3.0

NGC™ Chromatography Systems

and ChromLab™ Software

User Guide

Version 3.0

NGC™ Chromatography

Systems and

ChromLab™ Software

User Guide

Version 3.0

Bio-Rad Technical Support Department

The Bio-Rad Technical Support department in the U.S. is open Monday through Friday, 5:00 AM to 5:00 PM, Pacific Time. Worldwide technical support is available on the Web at www.consult.bio-rad.com.

Phone: [phone], option 2

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Web: www.consult.bio-rad.com

Notice

No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage or retrieval system, without permission in writing from Bio-Rad.

Bio-Rad reserves the right to modify its products and services at any time. This user guide is subject to change without notice. Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors or omissions, or for any damage resulting from the application or use of this information.

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Copyright © 2014 by Bio-Rad Laboratories, Inc. All rights reserved.

Table of Contents

Chapter 1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

Main NGC Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

NGC Chromatography Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Finding Out More . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Chapter 2 The Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17

The Home Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

File Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Help Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

The System Control Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

The Method Editor Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

The Evaluation Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Instrument Control Touch Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Touch Screen Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Touch Screen Toolbar Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Chapter 3 System Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29

System Control Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

File Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

View Menu Commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Manual Menu Commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Tools Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Help Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Toolbar Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Context Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

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Chromatogram View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Changing Chromatogram View Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 Showing or Hiding Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Changing Trace Color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 Zooming In and Out. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 Changing the X-Axis Units and Scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Changing the Y-Scale Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Autoscaling the UV Trace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Annotating the Chromatogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 Showing and Hiding Events, Fractions, Errors, and Annotations . . . . . . . . . 44

Fluidic Scheme Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Modules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 Fluidic Scheme Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Working with Fluidic Schemes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Fluidic Scheme Mapping. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 Calibrations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Calibrating a Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Calibrating Flow Rate of Pumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Calibrating Pressure Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Verifying Plumbing with the Point-to-Plumb Feature . . . . . . . . . . . . . . . . . . . . . . 67 System Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Delay Volume Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Control Flow Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 Remote Access Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 Trace Settings Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 Device Input Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 Device Output Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78 Air Sensors Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 Email Notifications Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 System Name Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 System Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 General Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

Devices Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 Process Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

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Detector Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Single-Wavelength Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Multi-Wavelength Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Email Server Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Chapter 4 Performing a Manual Run. . . . . . . . . . . . . . . . . . . . . . . . . . 93

Preparing the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 Priming and Purging the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 Cleaning the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102 Running an Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103 Changing Module Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 Stopping a Manual Run. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 Clearing Run Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 Saving a Manual Run. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 Saving a Manual Run on the Touch Screen . . . . . . . . . . . . . . . . . . . . . . . . . . 110 Viewing Run Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

Chapter 5 Method Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

Before You Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114

Accessing Method Editor Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114

Opening a Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

Method Editor Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

File Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

Edit Menu Commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

View Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119

Help Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119

Toolbar Commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119

Phase Library Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

Adding a Phase to a Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

Method Outline Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Phase Parameters Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Method Steps Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123

Viewing Details of a Step in the Step Table . . . . . . . . . . . . . . . . . . . . . . . . . . 124

Adding, Modifying, and Deleting Steps in the Step Table. . . . . . . . . . . . . . . . 124

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Method Settings Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

Fluidic Scheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

Column Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

Detector Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

Unit Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

pH Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

Fraction Collection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133

Buffer Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133

Phase Controls and Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136

Standard Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

Sample Application Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

Column Wash Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

Elution Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144

System CIP (Clean in Place) — Storage Parameters . . . . . . . . . . . . . . . . . 145

Column Preparation/Activation Parameters . . . . . . . . . . . . . . . . . . . . . . . . 152

Column Performance Test Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

System Preparation Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154

Create New Phase Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155

Step Library Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156

Scout Parameters Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

Chapter 6 Creating a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

Standard Method Templates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160 Creating a Method from a Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 Creating a Method from Standard Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 Adding Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170 Editing Methods and Phases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170 Renaming Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 Rearranging Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 Deleting Phases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172 Opening a Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172

Running a Method and Collecting Fractions. . . . . . . . . . . . . . . . . . . . . . . . . . . . 173 Collecting Fractions Using the BioFrac Fraction Collector . . . . . . . . . . . . . 173 Collecting Fractions Using Outlet Valves . . . . . . . . . . . . . . . . . . . . . . . . . . 173

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Collecting Fractions in Run Queues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174 Collecting Fractions Using the BioFrac Fraction Collector . . . . . . . . . . . . . 174 Collecting Fractions Using Outlet Valves . . . . . . . . . . . . . . . . . . . . . . . . . . 174

Saving a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 Renaming a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 Deleting a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179 Scouting on Parameters within a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180 The Scouting Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 Page 1: Choose a Scouting Parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 Page 2: Select Method Steps to Scout . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182 Page 3: Generate Scout Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184 Using the Scouting Wizard to Scout Columns . . . . . . . . . . . . . . . . . . . . . . 185 Using the Scouting Wizard to Scout Samples . . . . . . . . . . . . . . . . . . . . . . 187 Creating a Scouting Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189 Special Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190 Viewing a Summary of the Scouting Method . . . . . . . . . . . . . . . . . . . . . . . . . 192 Running a Scouting Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192

Chapter 7 Evaluating Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195

Managing Analysis Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196 Evaluation Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198 File Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199 View Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201 Analysis Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201 Help Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202 Tab Toolbar Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202 Customizing the Chromatogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203 Displaying Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203 Selecting the Active Trace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204 Showing or Hiding a Trace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205 Changing the Axes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205 Controlling the Range of the Y-Scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205

Changing Trace Colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206 Zooming In and Out. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207 Obtaining Statistics of a Selected Region on the Chromatogram . . . . . . . . . 208

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Annotating the Chromatogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210 Copying the Chromatogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211 Customizing the Trace Table Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212

Changing Table Grouping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212 Sorting Table Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213 Ordering and Selecting Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213 Showing or Hiding Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213 Copying a Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214 Showing or Hiding Pre-Injection Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214 Manually Setting the Injection Point (x Alignment) . . . . . . . . . . . . . . . . . . . . . 215 Managing Runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216 Renaming a Single Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216 Deleting a Single Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216 Viewing Multiple Runs in Separate Tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217 Comparing Traces. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218 Viewing Multiple Runs in One Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219 Stacked View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219 Overlay View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221 Customizing the Trace Comparison Table . . . . . . . . . . . . . . . . . . . . . . . . . . . 222 Expanding or Collapsing Groups. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222 Hiding All Traces in a Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222 Showing All Traces in a Group . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222 Offsetting Traces — Overlay Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223 Managing Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224 Removing Runs from a Trace Comparison . . . . . . . . . . . . . . . . . . . . . . . . . . . 224 Saving a Trace Comparison Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224 Copying an Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225 Renaming an Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225 Deleting an Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226 Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226 Exporting Run Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226 Peak Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227

Automatic Peak Integration Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228 Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228 Baseline Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228

viii NGC Chromatography Systems and ChromLab Software

Table of Contents

Peak Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229 Peak Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229 Default Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229

Integrate and Delete . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230 Starting Peak Integration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230 Displaying Peak Results — the Chromatogram . . . . . . . . . . . . . . . . . . . . . . . 231 Changing Peak View Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232 Displaying Peak Results — the Peaks Table. . . . . . . . . . . . . . . . . . . . . . . . . . 233 Table Display Order and Column Selection . . . . . . . . . . . . . . . . . . . . . . . . 235 Showing or Hiding Columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235 Copying the Peaks Table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236 Grouping or Ungrouping the Peaks Table. . . . . . . . . . . . . . . . . . . . . . . . . . 236 Clearing Extinction Coefficient Values in the Peaks Table . . . . . . . . . . . . . 237 Adjusting Peaks Manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238 Saving Peak Integration Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240 Evaluating Fractions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241 Displaying Fraction Collection Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241 Displaying Fraction Collection Results — the Fractions Table . . . . . . . . . . . . 243 Calculating Protein Concentration for Fractions . . . . . . . . . . . . . . . . . . . . . 245 Viewing Fraction Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246 Pooling Fractions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246 Viewing Fraction Collection Results — the Heat Map. . . . . . . . . . . . . . . . . . . 248 Viewing Heat Map Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249 Column Performance Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251 Column Performance — Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251 Traces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252 Calculate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252 Analyzing Column Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 Resetting the Column Performance Properties. . . . . . . . . . . . . . . . . . . . . . 254 Deleting Column Performance Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254 Column Performance — Manual Adjustment . . . . . . . . . . . . . . . . . . . . . . . . . 255 Displaying Column Performance Results — the Chromatogram . . . . . . . . . . 255

Displaying Column Performance Results — the Column

Performance Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256

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Table of Contents

Chapter 8 Importing and Exporting Data . . . . . . . . . . . . . . . . . . . . . 259

Importing an NGC Method or Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259 Importing Unicorn Data Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261

Importing BioLogic DuoFlow Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263 Exporting Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264 Exporting Data as an NGC File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265 Exporting Run Data as a .csv File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269 Exporting Diagnostic Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271

Chapter 9 Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275

Producing a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276

Method Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277

Run Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277

Analysis Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278

Printing a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278

Saving a Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279

Appendix A Database Management . . . . . . . . . . . . . . . . . . . . . . . 281

Back Up the NGC Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282

Restore the NGC Database. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283

Appendix B Multicolumn Purifications . . . . . . . . . . . . . . . . . . . . . 285

Multicolumn Purification Method Templates. . . . . . . . . . . . . . . . . . . . . . . . . . . . 286 Multicolumn Sequential Purification Templates . . . . . . . . . . . . . . . . . . . . . . . 286 Multicolumn Tandem Purification Templates . . . . . . . . . . . . . . . . . . . . . . . . . 289 Performing Multicolumn Purification Chromatography . . . . . . . . . . . . . . . . . . . . 291 Plumbing the NGC System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291 Plumbing NGC Discover Pro Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291

Plumbing the NGC Discover Pro System to Use

Multicolumn Purification Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292 Priming the NGC System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294

Selecting and Saving a Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295 Running Multicolumn Purification Methods . . . . . . . . . . . . . . . . . . . . . . . . . . 296

x NGC Chromatography Systems and ChromLab Software

1 Introduction

NGC™ chromatography systems provide a general purpose purification platform for purifying all forms of biomolecules using a combination of chromatography techniques. The systems are also useful for developing and optimizing purification protocols. The systems can provide highly purified proteins, peptides, nucleic acids, monoclonal antibodies, and other small molecules.

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1 Introduction

ChromLab™ software enables you to set up and control an NGC instrument, run protein separations and other operations manually, program methods to automate purification runs, evaluate the results, and generate and print experiment reports. This user guide explains how to perform all these tasks.

Main NGC Features

NGC chromatography systems enable you to do the following:

Easily create purification and maintenance protocols from predefined method templates and protocol phases

Automate multicolumn purification processes using preprogrammed templates and multiple column switching valves

Automate multiple sample injections using either the sample inlet valve and the sample pump or the C-96 autosampler

Expand sample monitoring using the signal import module (SIM) to export digital signals to and import digital signals from external detectors

Collect large-volume fractions using multiple outlet valves while also collecting small-volume fractions using the BioFrac™ fraction collector

Automatically prepare buffers using preprogrammed buffer blending protocols

Analyze purification results through 1-click peak integration, determine protein concentration and calculate column performance

Automate purification protocol optimization using the scouting wizard

Easily locate fractions containing peaks of interest and view the protein concentration within each fraction

Extend the preconfigured systems with additional valves for buffers, samples, and columns

12 NGC Chromatography Systems and ChromLab Software

Main NGC Features

Organize the location of the modules to optimize separation performance based on method scale and complexity, and to minimize the system swept volume

Minimize errors when connecting tubing using the Point-to-Plumb™ feature in ChromLab software

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1 Introduction

NGC Chromatography Systems

All NGC chromatography systems include ChromLab software and the NGC touch screen.

NGC chromatography systems are available in several combinations. Each system is equipped with either two 10 ml system pumps (the 10 series) or two 100 ml system pumps (the 100 series).

The NGC Quest™ chromatography system includes the following:

Two system pumps

Mixer

Sample injection valve

Conductivity monitor with either a single-wavelength UV detector or a multi-wavelength UV/Vis detector (available on the Plus systems)

14 NGC Chromatography Systems and ChromLab Software

NGC Chromatography Systems

The NGC Scout™ chromatography system includes the following:

All modules on the Quest system

pH detector valve

Buffer blending valve

The NGC Discover™ chromatography system includes the following:

All modules on the Scout system

Column switching valve

Two buffer inlet valves

Sample pump

The NGC Discover Pro chromatography system includes the following:

All modules on the Discover system

Fourth expansion tier

Sample inlet valve

Outlet valve

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1 Introduction

Finding Out More

After you install NGC documentation from the NGC Chromatography Systems Documentation DVD, you can access installed NGC guides and tutorials on the Help menu in any ChromLab view.

More information about the NGC chromatography systems and ChromLab software is available from the following sources.

The NGC Chromatography Systems and ChromLab Software Installation Guide is available on your NGC Chromatography Systems Documentation DVD as a .pdf file. This guide explains how to set up your environment, set up and install the NGC instrument in the lab, install ChromLab software, and connect ChromLab to the NGC system.

The NGC Chromatography Systems and ChromLab Software Instrument Guide is available on your NGC Chromatography Systems Documentation DVD as a .pdf file. This illustrated guide details the modules that make up the NGC instrument and includes troubleshooting and maintenance information.

For ChromLab Help, clicking in dialog boxes accesses relevant information. Screen-level help is also available on the Help menu.

NGC video tutorials are available on the NGC Chromatography Systems Documentation DVD as .mp4 files.

Tip: You can click the Bio-Rad logo in the upper-left corner of any ChromLab window to launch the Bio-Rad website.

16 NGC Chromatography Systems and ChromLab Software

2 The Workspace

ChromLab™ software provides an intuitive interface for developing chromatography methods, operating an NGC™ instrument, and analyzing data from chromatography runs.

ChromLab software presents four primary workspaces.

The Home window

The System Control window

The Method Editor window

The Evaluation window

Each workspace is shown and described in this chapter. The NGC instrument touch screen is also described.

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2 The Workspace

The Home Window

ChromLab software opens with the Home window, which displays three panes and the System Control tab.

The three panes provide quick access to the system control, method editor, and evaluation workspaces. The status of connection to the NGC instrument is also displayed. Links to recently completed runs, recently created methods, and recently accessed or analyzed runs and analyses appear listed at the bottom of the window.

Tip: Clicking the Bio-Rad logo in the upper-right corner of any ChromLab window launches the Bio-Rad website.

18 NGC Chromatography Systems and ChromLab Software

The Home Window

Method Editor and Evaluation tabs become visible in the Home window when you

select tasks in the Method Editor and Evaluation panes.

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2 The Workspace

File Menu Commands

Connect to System — opens a dialog box that enables you to choose an NGC chromatography system to connect to. ChromLab detects the NGC systems available on the same subnetwork or those systems that are directly connected to the computer. Their system name, network name, and IP address appear in the table. To connect to a system, you can:

Select a name in the list of detected systems and click Connect.

Note: If your system does not appear in the list, click Detect. ChromLab searches the network for available NGC systems and refreshes the list.

Select the appropriate radio button, enter the system’s name or IP address, and click Connect.

Tip: To obtain the system’s name and IP address select System Information on the instrument touch screen dropdown menu.

Disconnect System — starting ChromLab connects you to the NGC system. This command enables you to disconnect ChromLab software from the system so you can work offline.

Manual Run — opens the System Control window in manual mode so you can perform a manual run or set up your system manually.

Calibrate — opens the Calibration dialog box, which displays instructions and options for selecting a module and calibrating it. See Calibrations on page 64 for details.

Open Template — opens the Template dialog box in which you can select a method template from template folders organized by technique.

Open Method — opens the Method dialog box in which you can select from a list of your saved methods.

New Method — opens the Method Editor window in which you can create a method using standard method phases and steps.

20 NGC Chromatography Systems and ChromLab Software

The Home Window

Import — displays links from which you can import the following:

NGC File — opens a dialog box in which you can import a method, a method with runs, or a run exported from ChromLab software running on another NGC system. See Importing an NGC Method or Run on page 259 for more information.

Unicorn Data — opens a dialog box in which you can import a Unicorn data file into the NGC database. See Importing Unicorn Data Files on page 261 for more information.

DuoFlow Data — opens a dialog box in which you can import a BioLogic DuoFlow™ data file into the NGC database. See Importing BioLogic DuoFlow Data Files on page 263 for more information.

Export — displays links from which you can export the following:

Methods/Method Runs — opens a dialog box in which you can export both single or multiple methods and single or multiple methods with associated runs.

Runs — opens a dialog box in which you can export single or multiple runs.

See Exporting Data as an NGC File on page 265 for more information.

Open Run/Analysis — opens a dialog box in which you can select a run or analysis to view or analyze.

Preferences — opens dialog boxes in which you can do the following:

Select pressure units for all system and software pressure values. This is a global setting.

Set up an SMTP server to receive email messages about system notifications from the ChromLab computer.

Exit — closes ChromLab.

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2 The Workspace

Help Menu Commands

Help — displays screen-level help topics and links to installed manuals.

Export Diagnostic Logs — opens the Export Diagnostic Logs dialog box in which you can export all critical information that Bio-Rad Technical Support requires to diagnose issues. The log files and data are zipped and saved to a location that you choose. See Exporting Diagnostic Logs on page 271 for more information.

About — displays ChromLab copyright and version information.

22 NGC Chromatography Systems and ChromLab Software

The System Control Window

The System Control Window

The System Control window enables you to run the instrument manually, monitor method runs while they are running, select fluidic schemes, calibrate pumps and detectors, and verify the accuracy of instrument plumbing. This window displays a chromatogram during a run. A fluidic scheme graphically depicts the flow path of all the modules on the system. A status panel appears above each module displaying its real-time status. In manual mode, clicking a module displays its controls and detailed settings. The Run Log documents each action that occurs during a run. The Run Queue lists all runs ready to be started.

System Control functionality is detailed in Chapter 3, System Control.

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2 The Workspace

The Method Editor Window

The Method Editor window enables you to create, open, review, edit, and run a method. You can also open and edit a method template to create a new template. Method Editor functionality is detailed in Chapter 5, Method Editor. See also Chapter 6, Creating a Method.

24 NGC Chromatography Systems and ChromLab Software

The Evaluation Window

The Evaluation Window

The Evaluation window enables you to view and compare run data, perform peak integration, and save run data as analyses. Evaluation functionality is detailed in Chapter 7, Evaluating Results.

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2 The Workspace

Instrument Control Touch Screen

In addition to ChromLab software running on a computer, the instrument is equipped with a touch screen that accesses system control functionality. You can use this touch screen to run, control, and monitor a run independent of ChromLab. See System Control on page 29 for more information.

Tip: When the NGC system has been inactive for two hours the LED display screens on the instrument turn off, the touch screen dims, and a dialog box appears on the touch screen informing you that the system is in standby mode. You can take the system out of standby mode by touching OK in the dialog box, starting the system pumps by initiating a manual or method run, or clicking on a module in the fluidic scheme that has an LED display.

26 NGC Chromatography Systems and ChromLab Software

Instrument Control Touch Screen

Touch Screen Menu Commands

Calibrate — opens the Calibration dialog box, which displays instructions and settings for selecting a module and calibrating it. See Calibrating a Module on page 64 for details.

Point-to-Plumb — starts the Point-to-Plumb™ feature and simultaneously turns off instrument LED lights so you can visually verify or change instrument plumbing. Displays the current fluidic scheme. See Verifying Plumbing with the Point-to-Plumb Feature on page 67 for details.

Change Fluidic Scheme — opens the Fluidic Scheme Selector dialog box in which you can edit the fluidic scheme or choose another one. See Fluidic Scheme Configurations on page 51 for details.

Map Fluidic Scheme — opens the Fluidic Scheme Mapping dialog box in which you can map devices on your instrument to their position in the fluidic scheme. See Fluidic Scheme Mapping on page 60 for details.

System Settings — opens the System Settings dialog box in which you can customize system settings. See System Settings on page 69 for more information about customizing your system.

System Information — opens the System Information dialog box, which lists the serial number and other general information about the NGC device as well as information about the system components, processes, and UV and UV/Vis detectors.

Service — for Bio-Rad technical service staff use only. Do not select this command.

Help — displays detailed information about touch screen menu commands.

About — displays ChromLab version and copyright information.

Shut Down — shuts down the NGC system, including the connected computer.

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2 The Workspace

Touch Screen Toolbar Commands

Save — saves in a data file the steps executed during a manual run.

Clear — deletes manual run data from the touch screen display.

Autoscale — automatically scales the chromatogram’s primary y-axis to the tallest peak height during the run. Autoscaling is enabled by default.

Reset Zoom — resets the view to show the full chromatogram.

Annotate — adds a note to the chromatogram at points on the x-axis during a run or after the run completes.

28 NGC Chromatography Systems and ChromLab Software