Perkinelmer Labchip GX II, Labchip GX User Manual

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 any person of such modifications.

Proper Equipment Operation

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 spécifiée par le fabricant, la protection fournie par l’appareil peut être entravée.

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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): [phone] Fax: [phone]

Email: [e-mail] 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): [phone]
Fax:	[phone]
Email:	[e-mail]

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: [phone]

Fax: [phone]

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Preface 4

FCC

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.

CE

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 expressément approuvé par l’entité responsable de la conformité peut annuler l’autorisation d’opérer l’appareil accordée à l’utilisateur.

Table of Symbols

Table 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 Description

Symbole 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.

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Table 1. Important Symbols (Continued)

Symbol Description

Symbole 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).

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Table 1. Important Symbols (Continued)
Symbol	Description
Symbole	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.
Equipment	Yellow	Caution, risk of danger
labels are color	Red	Stop
coded:	Blue	Mandatory action
Les étiquettes	Green Safe condition or information
de l’appareil	Jaune	Attention, danger potentiel
sont codées	Rouge	Arrêter
couleur:	Bleu	Intervention obligatoire
	Vert	Condition sûre ou informations de sécurité
	Helpful hints, additional information
	Conseils utiles, informations supplémentaires

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Instrument Safety

7

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.

WARNING

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.

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Instrument Safety

8

Chemical Safety

WARNING

Some chemicals used with the LabChip GX are potentially hazardous and can cause illness.

•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.

•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.

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Instrument Safety

9

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.

Class 1

Laser

Product

635 nm (visible red) laser source, 10 mW maximum continuous (CW)

WARNING

•Use of controls or adjustments or performance of procedures other than those specified herein may result in hazardous 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 shown below:

•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 removable 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.

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Instrument Safety 10

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.

WARNING

Danger of explosion if battery is incorrectly replaced. Replace only with the same or equivalent type recommended 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 5- 15R receptacle in the wall.

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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 mm2 conductor size (230 volt input). Power cord 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:

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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
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
Data Analysis ........................................................................................................	42
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

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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

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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

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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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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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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

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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.

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Introduction 19

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.

Figure 1. DNA/RNA Chip and Protein Chip Schematics

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.)

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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).

Figure 2. Electropherogram

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

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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.

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).

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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:

1Open the LabChip GX software. (See “Opening the LabChip GX Software” on page 23.)

2If necessary, create a new assay. (See “Creating a New Assay” on page 24)

3Clean the electrodes and the O-Rings as directed in the

LabChip GX/GXII Assay User Guide.

4If necessary, calibrate the optics (see page 41) and run Diagnostics (see page 291).

5Prepare the chip for the assay as directed in the LabChip GX/GXII Assay Quick Guide.

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6Prepare 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.)

7Run 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:

1Double-click on the LabChip GX icon on the Windows desktop.

2If 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.)

The LabChip GX Main Window opens.

3See “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:

1Right-click on the LabChip GX icon on the Windows desktop and click Copy.

2Right-click on the Windows desktop and click Paste. A copy of the LabChip GX icon is created on the desktop.

3Rename the icon as desired.

4Right-click on the new icon and click Properties.

5On the Shortcut tab, enter the following in the Target text box:

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•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:

1On the LabChip GX Main Window, select Tools Assay Editor. The Select Assay To Edit window opens.

2Select 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.

3Modify 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.)

4Click 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.

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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:

1Select Instrument Start Prime to start priming for a specific assay.

2Select 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:

1Click the Run button on the LabChip GX Main Window (see page 143) to open the Start Run Window.

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.

2Click the Run tab in the Start Run window.

3Select 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.)

4Type the operator's name in the Operator Name text box.

5Select 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.

6To read the plate barcode, select the Use Barcode check box. (The plate barcode can be used to name the data file if selected.)

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Running an Assay (Continued)

7On the Plate diagram, select the wells to be sampled.

•To select all wells and ladders on the plate, click the doublearrow 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.

8Select the desired sipping order for the selected wells, Rowwise, Column-wise, or File Order.

9Click the Output Tab in the Start Run window.

10To 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 cause loss of data if the network connection is slow or interrupted.

11If desired, select the Create Daily Sub-Directory check box to create a new sub-directory for data files each day.

12If 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.

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Running an Assay (Continued)

13To 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.

14To 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).

15Click the Advanced Tab in the Start Run window.

16To 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.

17To 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.

18To 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.

19To use a file to supply the sample names, click the Browse button next to Sample Names 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.

20To use a file to supply the Expected Peaks, click the Browse button next to Expected Peaks 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.)

21To use a file to supply the Excluded Peaks, click the Browse button next to Excluded Peaks File, 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.

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22Click 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.

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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:

1Select the check boxes next to the views to export. Selecting Export All selects all check boxes.

2For 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.

3If 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 well is exported to a separate CSV file.

4If Gel is selected:

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.

5If either Electropherogram or Gel is selected, choose the desired format for the image files.

6Click OK to save the Export settings. The specified files are exported at the end of the run.

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Monitoring the Run

The following occurs after a run is started in the LabChip GX software:

1The 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.

2After the run begins, the Start button on the LabChip GX main window changes to Stop.

3The 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.

4To 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.

5To stop the run before it is complete, see Stopping a Run.

6When the assay is complete, Run Successful displays in the Status line.

7If desired, remove the plate and/or remove the chip.

To save the analyzed data:

1Select File Save Workspace. The Save Workspace As Window opens with the default workspace name as the name of the data file.

2If 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.

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