PERKINELMER LAPCHIP GX TOUCH (01) PDF MANUAL


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PDF Content Summary: LabChip ® GX Touch/GXII Touch User Manual P/N CLS151164 Rev. C Publication Date: August 8, 2019 Preface 2 Preface Copyright This manual is published by PerkinElmer, Inc., 68 Elm Street, Hopkinton, MA 01748 USA. Copyright 2014 - 2019, PerkinElmer, 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 LabChip and PerkinElmer are registered trademarks of PerkinElmer, Inc. Protein Clear and ProteinEXact are trademarks of PerkinElmer, Inc. Microsoft and Windows are either registered trademarks or trademarks of Microsoft Corporation in the United States and/or other countries. All other 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. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preface 3 Contact Us If you have a question about a product that is not answered in this manual or online Help, or if you need assistance with this product, contact the PerkinElmer Technical Support Center from 8:00 A.M. to 8:00 P.M., Eastern Time, Monday through Friday: Phone: (US Toll Free): 800-762-4000 (Worldwide): +1 203-925-4602 Fax: +1 203-944-4904 Email: dxsupportamericas@perkinelmer.com Internet: http://www.perkinelmer.com Before you call, have the following information available for the technical representative: • Product serial number • Software version and firmware version (found by touching the Info View button in the lower right corner of the LabChip GX Touch software) • If applicable, the error number shown in the LabChip GX Touch 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. Phone: (US Toll Free): 800-762-4000 (Worldwide): +1 203-925-4602 Fax: +1 203-944-4904 Email: dxsupportamericas@perkinelmer.com Our programs can include such useful services as: • Preventive maintenance • Diagnostic servicing performed on-site by PerkinElmer field service engineers or remotely via Technical Support • Validation performed on-site by PerkinElmer field service engineers • Extended use of the PerkinElmer Technical Support Center • Software updates • Parts, labor, and travel expense coverage • Other customized services upon request Training For Your Product Contact the PerkinElmer Center for Training and Development for information about the availability of training courses for your product: Phone: (US Toll Free): 800-762-4000 (Worldwide): +1 203-925-4602 Fax: +1 203-944-4904 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. 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 applicable 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. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preface 5 Table of SymbolsTable 1 contains symbols that identify particularly important information and alert you to the presence of hazards. These symbols may appear in this manual and/or on the product it describes. Table 1. Important Symbols

Symbol Symbole Description Description

P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. 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. Refer to the User’s documentation. (ISO 7000-0434B) AVERTISSEMENT: Attention. 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. Hazardous voltage; risk of electric shock. (IEC 60417-6042) Tension dangereuse; risque de blessure par électrocution. Crush hazard. Risk of body parts, hair, jewelry, or clothing getting caught in a moving part. (ISO 3864) 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. (ISO 3864) Risque de blessure par piqûre. Risk of eye injury; wear safety glasses. Risque de lésion oculaire; porter des lunettes de sécurité. Risk of fire. (ISO 3864) Risque d’incendie. Risk of poison. (ISO 3864) Risque d’empoisonnement. Risk of explosion. (ISO 3864) Risque d’explosion. Hazardous fumes. Émanations dangereuses. Preface 6 Table 1. Important Symbols (Continued) Symbol Description Symbole Description Laser light; avoid exposure. Risk of eye injury. (ISO 3864) Rayonnement laser; éviter toute exposition. Risque de lésion oculaire. Lifting hazard. May result in injury. (ISO 3864) Levage dangereux. Peut entraîner des blessures. Temperature limit. (ISO 7000-0632) Limite de température. Use by date. (ISO 7000-2607) Utiliser par date. Protective ground symbol. (IEC 60417-5019) Symbole de terre de protection. Ground symbol. (IEC 60417-5017) Symbole de terre. Fuse. (IEC 60417-5016) Fusible. Alternating current. (IEC 60417-5032) Courant alternatif. On (power). |(IEC 60417-5007) Marche (alimentation). Off (power). (IEC 60417-5008) Arrêt (alimentation). CE compliance mark. Marque de conformité CE. Batch Code (ISO 7000-2492) Catalog number. (ISO 7000-2493) Numéro de catalogue. WEEE symbol (EN50419:2005). Do not dispose of as unsorted municipal waste. See the PerkinElmer website (www.perkinelmer.com) for more information. 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. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preface 7 Table 1. Important Symbols (Continued) Symbol Description Symbole Description Input. Entrée. Output. Sortie. Equipment labels are color coded: Les étiquettes de l’appareil sont codées couleur: P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Yellow Caution, risk of danger Red Stop Blue Mandatory action Green Safe condition or information Jaune Attention, danger potentiel Rouge Arrêter Bleu Intervention obligatoire Vert Condition sûre ou informations de sécurité Instrument Safety 8 Instrument Safety The following safety information about the LabChip GX Touch/GXII Touch is included in this documentation. Read and review all safety information before operating the LabChip GX Touch/GXII Touch. • Required Training • Chemical Safety on page 9 • Laser Safety on page 10 • Electrical Safety on page 11 • Mechanical Safety on page 13 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. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Instrument Safety 9 Chemical Safety WARNING Some chemicals used with the LabChip GX Touch/GXII Touch 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. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Instrument Safety 10 Laser Safety WARNING BRIGHT LIGHT HAZARD. LabChip GX /GXII Touch Instruments contain Class 3B laser diodes. The LabChip GX Touch/GXII Touch are 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. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Instrument Safety 11 Electrical Safety The LabChip GX Touch/GXII Touch 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 Touch/GXII Touch High Voltage circuitry is current-limited 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 Touch/GXII Touch 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 Touch/GXII Touch 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. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Instrument Safety 12 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 minimum flexible 0.75 cord - 1 must mm2 be conductor <HAR> Type size (230 H05VV-F, volt input). 3-conductor, 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 Touch/GXII Touch instruments contain two fuses. See Changing the Fuses on page 142 for fuse replacement instructions. Contact PerkinElmer Technical Support (see page 3) to order replacement fuses. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Instrument Safety 13 Mechanical Safety The LabChip GX Touch/GXII Touch instruments have a three axis robot that moves quickly and can be a pinch hazard. Keep the front door of the instrument closed and keep hands away from the plate loading position when the robot is moving. Keep hands away from the robot when not actively placing microplates in the instrument or changing the ladder and buffer tubes. Robot access areas are marked with the warning label below: P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Table of Contents 14 Table of Contents Preface ....................................................................................................................2 Instrument Safety ...................................................................................................8 Required Training................................................................................................8 Chemical Safety..................................................................................................9 Laser Safety...................................................................................................... 10 Electrical Safety ................................................................................................ 11 Mechanical Safety............................................................................................. 13 Introduction........................................................................................................... 18 Usage ............................................................................................................... 18 Assay User and Quick Guides........................................................................... 19 Principles of Operation ...................................................................................... 20 Preparing the Instrument to Run Samples .......................................................... 23 Opening the LabChip GX Touch Software ......................................................... 24 Purging the Pressure Lines ............................................................................... 24 Inserting the Chip .............................................................................................. 25 Calibrating the Instrument to Run Protein Clear HR Assays ..............................26 Priming the Chip Before the Run ....................................................................... 27 Placing the Barcode on the Plate ...................................................................... 28 Defining a New Plate Type ................................................................................ 29 Loading the Plate, Ladder Tube, and Buffer Tube .............................................31 Running an Assay................................................................................................. 32 Defining the Run Parameters ............................................................................ 33 Monitoring the Run............................................................................................ 37 Editing the Analysis Settings during a Run ........................................................ 38 Stopping a Run before the Run is Complete...................................................... 39 Continuing a Stopped Run ................................................................................ 40 Removing the Plate, Buffer Tube, and Ladder Tube ..........................................41 Removing the Chip............................................................................................ 41 Washing the Chip.............................................................................................. 42 Exporting Data ...................................................................................................... 43 Export Examples ............................................................................................... 44 Selecting the Auto Export Settings .................................................................... 46 Selecting the Exported Properties in the Well Table or Peak Table ...................47 Exporting Data in AIA Format for Use in Third-Party Analysis Software.............47 Exporting a Data File after a Run is Complete................................................... 48 Viewing the Data ................................................................................................... 49 Selecting the Well Data to View......................................................................... 49 Viewing Data in the Egram/Gel Tab................................................................... 50 Viewing Graphs in the Egram Tab ..................................................................... 52 Viewing Data in the Gel Tab.............................................................................. 52 Zoom In and Zoom Out ..................................................................................... 52 Viewing a Data File after a Run is Complete ..................................................... 53 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Table of Contents 15 Creating a Run File ...............................................................................................54 Using Sample Names Files...................................................................................55 Creating a Sample Names File.......................................................................... 56 Selecting Wells using a Sample Names File...................................................... 57 Using a Barcode to Specify the Sample Names File..........................................59 Editing Sample Names During a Run ................................................................ 60 Saving Data Files .................................................................................................. 61 Saving Data Files with LabChip GxP Option Installed........................................61 Organizing, Retrieving, and Backing Up Data Files ...........................................61 LabChip GxP Option............................................................................................. 62 Locking and Unlocking the Software..................................................................63 User Accounts................................................................................................... 64 Switching Users ................................................................................................ 64 Central Data Repository (CDR) ......................................................................... 65 CDR Security Suggestions ................................................................................ 65 Software Reference .............................................................................................. 66 CDR/Database Server Window ......................................................................... 67 Change Assay Folder Window........................................................................... 68 Change Password Window................................................................................ 69 LabChip GX Touch Main Window...................................................................... 70 Navigation Bar................................................................................................... 71 Home Window................................................................................................... 72 Login Window.................................................................................................... 74 Prime and Calibrate Window ............................................................................. 76 Prime Window ................................................................................................... 77 Run Window...................................................................................................... 78 Select Wells Tab.......................................................................................... 79 Setup Run Tab ............................................................................................ 81 Start Run Tab .............................................................................................. 84 Status Window .................................................................................................. 86 Tools Window.................................................................................................... 89 Export Setup Tab......................................................................................... 90 Diagnostics Tab........................................................................................... 95 Optics Normalization Tab............................................................................. 97 Plate Editor Tab........................................................................................... 98 Software IQ Tab......................................................................................... 100 Factory Access Tab ................................................................................... 102 Error Message Display............................................................................... 103 Unlock Application Window ............................................................................. 104 Views Window................................................................................................. 105 Select Wells to View Tab ........................................................................... 106 Egram/Gel Tab .......................................................................................... 108 EGram Tab ................................................................................................ 109 Gel Tab...................................................................................................... 113 Run Info Tab.............................................................................................. 116 EventLog Tab ............................................................................................ 119 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Table of Contents 16 Sample Names Tab ................................................................................... 120 Analysis Settings Tab ................................................................................ 122 Wash Window ................................................................................................. 124 LabChip GX Touch/GXII Touch Instrument Description ................................... 125 Front View....................................................................................................... 126 Rear Connectors ............................................................................................. 128 Side Connectors.............................................................................................. 129 Optics ............................................................................................................. 130 Chip Pressure System..................................................................................... 130 Barcode Reader .............................................................................................. 130 DNA, RNA, and Protein Chips ......................................................................... 131 Chip Interface.................................................................................................. 132 Microplate Carrier............................................................................................ 134 Specifications.................................................................................................. 135 Maintenance and Service ................................................................................... 137 Cleaning the Chip Interface ............................................................................. 138 Chip Interface Daily Cleaning .................................................................... 138 Chip Interface Monthly Cleaning ................................................................ 138 Calibrating the Optics...................................................................................... 139 Cleaning the Instrument Electrodes................................................................. 140 Cleaning the Microplate Carrier....................................................................... 140 Cleaning the Touch Screen ............................................................................. 140 Cleaning the Optics Lens ................................................................................ 140 Cleaning Test Chip C ...................................................................................... 141 Changing the Fuses ........................................................................................ 142 Running Software IQ ....................................................................................... 143 Running Operational Qualification (OQ) .......................................................... 144 Troubleshooting and Diagnostics...................................................................... 145 Searching for Events in the EventLog Tab....................................................... 145 Viewing Current Events in the EventLog Tab................................................... 146 Viewing Past Events in the EventLog Tab ....................................................... 146 Error Messages............................................................................................... 147 Device <Name> is Disconnected ............................................................... 148 Plate Carrier Motion Blocked ..................................................................... 148 Home Timeout ........................................................................................... 148 Move Timeout............................................................................................ 149 Pressure Leak Detected ............................................................................ 149 Focus Failed.............................................................................................. 149 Maximum Samples Exceeded.................................................................... 150 Chip Primed for Different Assay................................................................. 150 HV Check Failed........................................................................................ 150 Current Leakage Check Failed................................................................... 151 Chip Temperature Warning........................................................................ 151 GUI Cannot Connect to CFR Database...................................................... 151 Diagnostics ..................................................................................................... 152 Running Software IQ.................................................................................. 152 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Table of Contents 17 Running Operational Qualification (OQ)..................................................... 153 Running the Instrument Diagnostics Tests................................................. 153 Description of Instrument Diagnostic Tests ................................................ 154 Calibration Failures ......................................................................................... 160 Protein Clear HR Assay Failed Calibration................................................. 160 Protein Clear HR Assay Marginal Calibration............................................. 161 ProteinEXact Assay Failed Calibration....................................................... 162 Troubleshooting Assay Problems .................................................................... 162 Software Problems.......................................................................................... 163 Cannot Save a File .................................................................................... 163 Computer Software Lock-Ups .................................................................... 164 Cannot Connect to Remote CDR Server.................................................... 164 Zipping the Log Files....................................................................................... 165 Glossary of Terms .............................................................................................. 166 PerkinElmer Product Warranty .......................................................................... 178 PerkinElmer Software License Agreement........................................................ 180 Index.................................................................................................................... 184 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Introduction 18 Introduction This manual includes general instructions for using hardware with the LabChip GX Touch software. It includes general procedures for operating the system, maintaining the instrument, troubleshooting hardware and software problems, and using the LabChip GxP option to provide compatibility with 21 CFR Part 11 requirements. DNA, gDNA, RNA, Protein, Glycan, and Protein Charge Variant (CZE) Chip and Reagent Kits are available to run specific assays on the LabChip GX Touch/GXII Touch. 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 GXII Touch instruments. This section contains the following information: • Usage on page 18 • Assay User and Quick Guides on page 19 • Principles of Operation on page 20 Usage LabChip GX Touch software is for use with LabChip GX/GXII and GX Touch/GXII Touch instruments. LabChip GX/GXII and GX Touch/GXII Touch instruments are for research use only and not for use in diagnostic procedures. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Introduction 19 Assay User and Quick Guides Assay User Guides Assay User Guides provide information about a specific assay. Instructions for preparing the chip, the plate, the ladder tube, and the buffer tube are included in the LabChip GX Touch/GXII Touch 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 Touch/GXII Touch Assay User Guide for the specific assay that you are running. The current version of the Assay User Guides are available on the PerkinElmer web site at: http://www.perkinelmer.com. Assay Quick Guides Assay Quick Guides are included with each Assay Kit and include instructions for preparing the reagents and chip to run an assay. The current version of the Assay Quick Guides are available on the PerkinElmer web site at: http://www.perkinelmer.com. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Introduction 20 Principles of Operation The LabChip GX Touch 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. Examples of 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 seven electrodes in the electrode block that contact solutions in the chip wells when the front door 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. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Introduction 21 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 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 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Introduction 22 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. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preparing the Instrument to Run Samples 23 Preparing the Instrument to Run Samples This section includes general instructions for preparing the LabChip GX Touch instrument to run samples. For assay-specific information, see the LabChip GX Touch/GXII Touch Assay User Guide for the specific assay that you are preparing to run. For instructions on preparing the chip and plate, see the LabChip GX Touch/GXII Touch Assay Quick Guide for the specific assay. The current version of the Assay User Guides and Quick Guides are available on the PerkinElmer web site at: http://www.perkinelmer.com. To prepare the instrument to run samples: 1 Open the LabChip GX Touch software (see page 24). 2 Clean the electrodes and the O-Rings as directed in the LabChip GX Touch/GXII Touch Assay User Guide. 3 Purge the pressure lines (see page 24). 4 If necessary, calibrate the optics (see page 139) and run Diagnostics (see page 152). 5 Prepare the chip for the assay as directed in the LabChip GX Touch/GXII Touch Assay Quick Guide. 6 Insert the chip into the instrument (see page 25). 7 For Protein ClearTM HR chips, calibrate the instrument to run Protein Clear HR Assays (see page 26). 8 If desired, prime chips before the start of a run (not available for Protein Clear HR chips). See page 27. 9 Prepare the sample plate, ladder, and buffer for the assay as directed in the LabChip GX Touch/GXII Touch Assay Quick Guide. If your instrument is equipped with a barcode reader, see Placing the Barcode on the Plate on page 28 to use barcodes on the sample plates. 10 If desired, define a new plate type to use a plate other than the ones listed in the software (see page 29). 11 Load the Sample Plate, Ladder tube, and Buffer tube into the instrument (see page 31). P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preparing the Instrument to Run Samples 24 Opening the LabChip GX Touch Software To open the LabChip GX Touch software: 1 Touch the LabChip GX Touch icon on the Windows desktop. 2 If the LabChip GxP option is installed, the Unlock Application Window opens. Type a valid LabChip GX Touch user name and password into the text boxes and touch the Logon button. LabChip GX Touch user names are created in the LabChip GX Reviewer software. (For instructions on creating LabChip GX Touch user names, see the LabChip GX Reviewer User Manual.) 3 The LabChip GX Touch Main Window opens. The Navigation Bar displays on the left side of the LabChip GX Touch Main Window, and the Home Window displays in the center. Purging the Pressure Lines The LabChip GX Touch software provides a Purge Pressure Lines function to improve instrument performance. A positive pressure is applied to the lines and removes any potential liquid or debris out of the lines through the chip interface. Purge the pressure lines at the start of each day, before inserting a chip. To purge the pressure lines: 1 If a chip is already inserted into the instrument, remove the chip and close the chip door (see page 41). 2 Touch the Purge Pressure Lines button on the Home Window. The Status Window opens. The purge is complete when the Run Status displays “Purge successfully completed” and the instrument status returns to Idle. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preparing the Instrument to Run Samples 25 Inserting the Chip To insert the chip into the instrument: 1 Prepare the chip and reagents for the assay as directed in the Assay Quick Guide. Follow the instructions carefully to properly prepare the chip. 2 Touch the Home button on the Navigation Bar. 3 Touch the Unload Chip button on the Home Window. The chip door on the front of the instrument unlatches. 4 Lift the chip door up. 5 Place the chip into the cutout with the sipper through the hole in the chip holder. 6 Close the chip door and press down to latch the door. 7 If the chip supports multiple assays, a dialog prompts you to select the assay that the chip will be used for. Select the desired assay and touch the OK button. 8 If a Protein Clear HR chip is inserted into the instrument, calibrate the instrument to run Protein Clear HR assays (see page 26). 9 If any other chip is inserted into the instrument, the chip can be primed while preparing the first plate (see page 27). P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preparing the Instrument to Run Samples 26 Calibrating the Instrument to Run Protein Clear HR AssaysIf a Protein Clear HR chip is inserted into the instrument, the user must calibrate the instrument to run a Protein Clear HR assay before starting the run. Calibration is performed by processing a known protein sample, and uses the results to precisely set the electrode currents for that assay to obtain consistent chip-to-chip assay results. To calibrate the instrument to run Protein Clear HR assays: 1 Insert the Protein Clear HR chip (see page 25) OR Open the LabChip GX Touch software (see page 24) with the chip already inserted into the instrument. 2 Touch the Prime and Calibrate button on the Home Window. The Prime and Calibrate Window opens. 3 Select the plate type from the Select Plate Type drop-down list. 4 Select the assay from the Select Assay drop-down list. (To select the location of the assay file, touch the Change Assay Folder button and select the assay folder on the Change Assay Folder Window.) 5 Touch select the the well Select that Well contains Containing the VeriMAbStandard TM sample. Sample button to 6 Select the desired well from the full-size plate diagram and touch the Done button. 7 Touch the Prime and Calibrate button on the Prime and Calibrate Window. • If the calibration is successful, a dialog box opens indicating that the instrument is now calibrated for the Protein Clear HR assay. Touch the OK button. • If the calibration fails, a dialog box opens indicating that the calibration process failed and a Protein Clear HR assay run cannot be performed. Touch the OK button. Perform the recommended actions on page 160 and retry the calibration. • If the calibration is outside the % Purity target range or if dips from the Egrams could not be eliminated, a dialog box opens indicating that the calibration is marginal. Touch the Yes button to run the chip despite the issue displayed on the dialog box. Touch No to fix the issue. Perform the recommended actions on page 161 and retry the calibration. 8 To retry the calibration, select the Skip Prime Step check box on the Prime and Calibrate Window. The chip is calibrated but not primed. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preparing the Instrument to Run Samples 27 Priming the Chip Before the Run If a new chip that is not a Protein Clear HR chip has been inserted into the instrument, the chip is automatically primed at the start of the first run. Since priming is a lengthy process, the chip priming can be started before starting the run. (To save time, the sample plate can be prepared while the chip is priming.) To prime a chip before starting the run: 1 Insert the chip (see page 25). 2 Load the buffer tube (see page 31). If running a test ladder, load the ladder tube at the same time. 3 Touch the Home button on the Navigation Bar. 4 Touch the Prime button on the Home Window. The Prime Window opens. 5 On the Prime Window, select the assay for which to prime the chip on the Assay drop-down list. (To select the location of the assay file, touch the Change Assay Folder button and select the assay folder on the Change Assay Folder Window.) 6 If desired, select the Run Test Ladder after Prime check box to run one ladder after the prime is complete. 7 Touch the Prime button. The Prime Window displays the time left until the prime is complete. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preparing the Instrument to Run Samples 28 Placing the Barcode on the Plate For instruments equipped with a barcode reader, barcodes can be placed on the plate before loading the plate into the instrument. Figure 4 shows the size limits for the barcode label and the location on the microplate where the label should be placed. The barcode must be located on the short (portrait) end of the microplate, closest to well A1. If the barcode is not positioned properly, the barcode reader will not be able to read the barcode. Figure 4. Barcode Label Position P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preparing the Instrument to Run Samples 29 Defining a New Plate Type To use a plate other than the plates specified on the Setup Run Tab, create a new plate on the Plate Editor Tab. Use caution adding new plates. Entering wrong values on the Add Plate Window can result in damaged chips and broken sippers. It is best to use the plate specifications provided by the plate manufacturer. If the specifications are not available, measure the plate with a caliper. Many plates have a large variation in the Z-axis location of the well bottom. Make sure the Sip Height has enough margin to accommodate this variation: • Minimum Sip Height is 2.5mm. • Maximum Sip Height depends on the sample volume. • Sip Height of 4mm is probably safe. To add a new plate: 1 Touch the Tools button on the Navigation Bar. 2 Touch the Plate Editor button to open the Plate Editor Tab. 3 Touch the Custom Plates Tab. 4 Touch the Add Plate button to open the Add Plate Window. 5 Type the settings for the new plate. The diagram on the Add Plate window shows the location for each measurement. Acceptable plate parameters are: • PlateHeight: 0 to 16mm • WellDepth: 0 to 36mm • SipHeight: 2 to 36mm • (WellDepth – SipHeight) <= PlateHeight 6 Touch the OK button. 7 Perform a Punch Test from the Plate Editor Tab to verify the new plate settings are acceptable: • Cover the corner wells on the plate with a piece of the tape provided by PerkinElmer. • Use an old, expired chip with a good sipper. • On the Plate Editor Tab, select the new plate name and touch the Verify Plate button. • Follow the onscreen instructions. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preparing the Instrument to Run Samples 30 Defining a New Plate Type (Continued) • The instrument will move to the specified number of wells in each corner of the plate, punching holes in the tape. • The Punch test is acceptable if the punched hole is >0.5mm from the edge of the well. • Holes may not be perfectly centered. Possible sources of errors: • Sipper splay • Plate tolerances • Robot alignment error • If all holes are too close to the edge (<0.5mm) in the same direction, adjust the X-Margin or Y-Margin values on the Add Plate window. 8 Select the new plate name on the Setup Run Tab when starting the run. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Preparing the Instrument to Run Samples 31 Loading the Plate, Ladder Tube, and Buffer Tube To load the Sample Plate, Ladder tube, and Buffer tube into the instrument: 1 Prepare the samples and load the samples into the plate as instructed in the Assay Quick Guide. Follow the instructions carefully to properly prepare the plate. 2 Fill the Ladder and Buffer tubes as instructed in the Assay Quick Guide. 3 Touch the Home button on the Navigation Bar. WARNING Pinch Hazard. Keep hands away from plate carrier when carrier is moving. 4 Touch the Unload Plate button on the Home Window. The plate carrier on the left side of the instrument moves out to the loading position. 5 Place the sample plate onto the plate carrier. Place the Ladder tube and Buffer tube into the plate carrier. 6 Touch the Load Plate button. The plate carrier retracts into the instrument. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 32 Running an Assay This section includes general instructions for using the LabChip GX Touch hardware and software to run an assay: To run an assay: 1 Complete the steps in the Preparing the Instrument to Run Samples section. 2 Define the parameters of the assay run (see page 33). 3 Monitor the run (see page 37). 4 If desired, edit the analysis parameters during the run (see page 38). 5 If necessary, stop the run before it completes (see page 39) and continue the stopped run if desired (see page 40). 6 Remove the Plate, Buffer Tube, and Ladder Tube (see page 41). 7 Unload the chip (see page 41). Store the chip according to the instructions in the Assay User Guide. 8 If necessary, wash the chip (see page 42) immediately before running the chip again. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 33 Defining the Run Parameters To define the run parameters: 1 Touch the Home button and then touch the Run button. If the maximum number of samples for the chip have already been run, a message displays instructions for resolving the problem. The Select Wells Tab opens. 2 Select the assay to run in the Select Assay drop-down list. If the desired assay is not displayed, touch the Change Assay Folder button and select the assay folder in the Change Assay Folder Window. 3 Select the plate type in the Select Plate Type drop-down list. To use a plate that is not listed in the Plate Name list, see Defining a New Plate Type on page 29. 4 To use an existing run file to specify the run settings, touch the Import Run File button, navigate to the run file, select the desired file, and touch the Open button. The settings specified in the run file display in the Select Wells Tab and Setup Run Tab. To use the settings in the run file, touch the Next button twice and skip to step 26. For more information about run files, see page 54. 5 To sample the wells in the order in which the wells are selected in the plate diagram, select the Selection Sip Order check box before selecting the wells. 6 On the Plate diagram, select the wells to be sampled. • If desired, touch the Full Size button to enlarge the Plate diagram to better view and select the desired wells. • To select or clear all rows on the plate, touch the Select All Rows button at the top left corner of the plate. • To select or clear all wells in a row, touch the row letter on the left side of the plate. (Clear a selected row by touching the row letter.) • To select or clear a single column, touch the column number at the top of the plate. (Clear a selected column by touching the column number.) • To select or clear all wells in a quadrant, touch the 1, 2, 3, or 4 button. • To select or clear single wells, touch the well. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 34 Defining the Run Parameters (Continued) • To select or clear adjacent wells, touch and drag over the desired wells. • To use a Sample Names file to select the wells, see Selecting Wells using a Sample Names File on page 57. 7 If desired, select the Column-wise check box to sample the plate in column order. If not selected, the plate is sampled in row order. 8 If desired, select the Advanced Settings check box. • To repeatedly run the selected wells and combine the data into one data file, touch the + or - button under Sample Sips to select the number of times to sample the selected wells. • To perform the assay multiple times on the same plate, touch the + or - button under Plate Cycles to select number of times to run the assay. • To randomly sample a specific percent of the selected wells, touch the + or - button under Random Select% to specify the percent of wells to sample during the run. 9 Touch the Next button . The Setup Run Tab opens. 10 If desired, type the name of the operator in the Operator text box. (If the LabChip GxP option is installed, the name of the current user is automatically displayed and cannot be edited.) 11 For ProteinEXact chips that have been primed before the run (see page 27), select the Skip Warm and Skip Prime check boxes to avoid repeating the priming and warming process. 12 To read the plate barcode (if your instrument is equipped with a barcode reader), select the Read Plate Barcode check box. (The plate barcode can be used as part of the data file name if selected.) 13 To change the Data Path, touch the Browse button, select the desired location for the data file in the Browse for Folder window, and touch the OK button. If the LabChip GxP option is installed, the data file must be located in the CDR. To restore the default path, touch the Default button. 14 Select the Copy to check box to automatically create a copy of the data files. Touch the Browse button, select the desired location for the data files in the Browse for Folder window, and touch the OK button. To restore the default path, touch the Default button. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 35 Defining the Run Parameters (Continued) NOTE If the LabChip GxP option is not installed, 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. If the LabChip GxP option is installed and the network connection is interrupted, data files are archived in a local folder and copied to the CDR when the network connection is restored. For more information about the GxP option, see page 62. 15 If desired, select the Create Daily Sub-Directory check box to create a new sub-directory for data files each day. 16 To automatically export data tables, graphs, or gels, select the Auto Export check box. (See Selecting the Auto Export Settings on page 46 for more information about selecting data to export.) 17 To automatically print the exported data to a PDF file after the run is complete, select the Auto Print check box. 18 To export all data at the end of the run rather than as each well is completed, select the Defer Export to Plate Completion check box. 19 To add the File Prefix, Project Name, Computer 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. 20 To use a Sample Names file to supply the sample names: a Select the Sample Names file check box. b Touch the Browse button next to Sample Names file. c Select the name of the CSV file that contains the sample names, and touch the Open button. The path and name of the file displays in the text box. (See Sample Names File on page 177 for more information.) P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 36 Defining the Run Parameters (Continued) 21 To use the Sample Names file to select the wells to read, select the Use Sample Names File for Sample Selection check box. (For details, see page 57). 22 To use a file to supply the Expected Peaks: a Select the Expected Peaks File check box. b Touch the Browse button next to Expected Peaks File. c Select the name of the GEP file that contains the expected peaks, and touch the Open button. The path and name of the file displays in the text box. (See Expected Peak File on page 170 for more information.) 23 To use a file to supply the Excluded Peaks: a Select the Excluded Peaks File check box. b Touch the Browse button next to Excluded Peaks File. c Select the name of the GEP file that contains the excluded peaks, and touch the Open button. The path and name of the file displays in the text box. (See Excluded Peak File on page 170 for more information.) 24 Touch the Next button . The Start Run Tab opens. 25 For ProteinEXact runs, type the Total Ladder Concentration of the reagent into the text box. 26 Review the selections displayed. To change any selections, use the Back and Next buttons to make the desired changes. 27 Touch the Start button to start the assay. The Status Window displays the status of the run. 28 After the run has started, you can: • Change the exported properties in the Well Table or Peak Table (see page 47). • Edit the sample names (see page 60). • Edit the analysis settings (see page 38). • View the raw data from the run (see page 49) P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 37 Monitoring the Run After a run is started in the LabChip GX Touch software: 1 The priming and warming steps are performed. • The priming step fills the channels of the chip with reagent. (Only performed if the chip holder has been opened since the last run and the chip has not been primed.) • The warming step allows the heater plate in the chip holder to regulate chip temperature to 30°C. • Data collection begins after the priming and chip warming steps are completed. 2 For ProteinEXact chips, the calibration steps are performed. 3 The Status Window displays the Chip and Run Status, the plate diagram, and an electropherogram and gel of the well currently being read. 4 For ProteinEXact chips, the Status Window displays the calibration status of the calibration step currently being performed instead of the plate diagram (see page 37). Figure 5. ProteinEXact Status Window P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 38 Monitoring the Run (Continued) NOTE If the ProteinEXact calibration steps do not display, restart the software and prime the chip. 5 Data is saved to a GX Touch data file (*.gxd) with the name shown in the Setup Run Tab after each well is completed. 6 To view the results for individual wells as data is acquired or after the run is finished, see page 49. 7 If analysis settings are changed during the run (see page 38), the analyzed data uses the current analysis settings if Perform Sample Analysis is selected on the Select Wells Tab. 8 To stop the run before it is complete, see page 39. 9 When the assay is complete, Successfully Completed displays in the Status line on the Status Window. 10 Remove the plate (see page 41) and/or remove the chip (see page 41) as necessary. Editing the Analysis Settings during a Run Specific analysis settings can be adjusted in the LabChip GX Touch software while a plate is running. If Auto Export is selected on the Setup Run Tab, the Analysis Settings cannot be changed unless the Defer Export to Run Completion check box is selected. After a run is complete, the analysis settings can be changed to view the data, but the analysis settings cannot be saved. To adjust the analysis settings: 1 After the run is started, touch the Views button and then the Analysis Settings button. The Analysis Settings Tab opens. 2 Change the Analysis Settings as desired. Press Enter or Tab, or move to another text box, to enable the Apply and Cancel buttons. (See Analysis Settings Tab for a description of each analysis setting.) 3 Click the Apply button to apply the settings to the current run. The initial analysis settings are saved as Version 0. If changes are made during the run, the analysis settings at the end of the run are saved as Version 1. Use LabChip Reviewer to view the analysis settings versions. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 39 Stopping a Run before the Run is Complete The run is completed automatically after reading the last selected well. If you need to stop the run before it is complete, touch the Stop button on the Navigation Bar. The run stops immediately. If a well is in progress, the data for that well is not saved. A message box confirms that you want to stop the run in progress. Figure 6. Stop Run Message Touch Yes to stop the run. The Status line on the Status Window displays stopped by user as shown in Figure 7. Figure 7. Stopped by User Data for any completed wells displays in the Views Window. To continue to read wells from an aborted run, see Continuing a Stopped Run. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 40 Continuing a Stopped Run If a run is stopped before it is complete, you can start a new run to read the remaining unread wells in the plate. When selecting the wells for the assay, select only the wells that were not read so that the run starts with the well that was not completed. The data is saved in a new data file. It is not added to the data file from the original run. To continue a run: 1 Touch the Run button on the Home Window. 2 On the Select Wells Tab, select the wells that were not read in the previous run, beginning with the well that was in progress when the run was stopped. 3 On the Setup Run Tab, select the same options for this run as were selected for the stopped run. 4 On the Start Run Tab, touch the Start button to begin. The new run starts with the well that was not completed in the previous run. A separate data file is created for the current run. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 41 Removing the Plate, Buffer Tube, and Ladder Tube To remove the plate, Buffer tube, and Ladder tube from the instrument when the run is complete: 1 Touch the Home button on the Navigation Bar. WARNING Pinch Hazard. Keep hands away from plate carrier when carrier is moving. 2 Touch the Unload Plate button on the Home Window. Wait until the plate carrier is fully extended. 3 Remove the plate from the plate carrier. 4 If necessary, clean the plate carrier with DI water or 70%- isopropanol solution. 5 Remove the Buffer and Ladder tubes if necessary. WARNING Pinch Hazard. Keep hands away from plate carrier when carrier is moving. 6 Touch the Load Plate button on the Home window to retract the plate carrier. Removing the Chip To remove the chip from the instrument: 1 Touch the Home button on the Navigation Bar. 2 Touch the Unload Chip button on the Home Window. The chip door on the front of the instrument unlatches. 3 Lift the chip door up. 4 Remove the chip from the chip holder. 5 Close the chip door and press down to latch the door. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Running an Assay 42 Washing the Chip Some protein samples may have components which produce data with extra peaks, spikes or other artifacts. When these artifacts are present, washing protein chips on the LabChip GXII Touch immediately before the next use can often restore data quality. 1 Prepare the chip and buffer tube as instructed in the Assay User Guide. 2 Insert the prepared chip and buffer tube into the instrument (see page 25). 3 Touch the Home button on the Navigation Bar. 4 Touch the Wash button on the Home Window. 5 When the wash is complete, follow the instructions in the Assay User Guide to run the chip. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Exporting Data 43 Exporting Data The Peak Table, Well Table, Gel, Graph, or raw data can be exported automatically at the end of a run or after each well is read. Select the desired settings in the Export Settings Tab (see page 47) and then select the Auto Export check box on the Export Setup Tab. After the run has started, change the exported properties in the Well Table or Peak Tables if desired (see page 47). Data can also be exported after a run is complete (see page 48). Peak Tables and Well Tables are exported to either CSV files or XML such files. as MicrosoftCSV files ® Excel. can be imported into a spreadsheet program Raw Data can be exported to a CSV file, an XML file, or to an AIA file format (a CDF file) which is used by some graphical analysis software tools. Gel and Graph data is exported to the selected image format (i.e., BMP, GIF, JPEG, PNG, TIFF, WMF, or EMF). This section includes the following information for using the GX Touch software to export Peak Tables, Well Tables, Gels, Graphs, or raw data: • Export Examples on page 44 • Selecting the Auto Export Settings on page 46 • Selecting the Exported Properties in the Well Table or Peak Table on page 47 • Exporting Data in AIA Format for Use in Third-Party Analysis Software on page 47 • Exporting a Data File after a Run is Complete on page 48 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Exporting Data 44 Export Examples This section shows export examples for the following data: • Peak Table • Raw Data • Gel on page 45 Peak Table Either a CSV file (ASCII text file in a comma-separated format) or an XML file that contains the data in all columns in the Peak Table. The peak table can be viewed in the LabChip GX Reviewer software. Figure 8 is an example of part of a Peak Table CSV file exported from a DNA assay (data truncated for this example): Figure 8. Exported Peak Table Excluded Peaks are not exported and are missing in the exported file. is exported For example, into Microsoftif peaks ® 3, Excel, 5, and peaks 7 are 3, excluded, 5, and 7 are when not the data included. Raw Data Either a CSV file (ASCII text file), an XML file, or an AIA Format file that contains the signal data from the run as one file per well or multiple wells in the same file. Exported data has been smoothed using the polynomial filter. Raw data can be exported in a Chromatography Data Interchange Format (formerly AIA format), which is used by some graphical analysis software tools. The Include Size Data and Export Single Table options are not available with Chromatography Data Interchange Format. In addition to exporting time and value information, you can choose to export Size information. This information is determined based on aligned data and is used to correlate the peaks from one row to another. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Exporting Data 45 Export Examples (Continued) Below is an example of part of a raw data CSV file, including size data, exported from a DNA assay. In this example, the header is not included and data is truncated. DATA Time,Value,Size 0.000,-1.097,0 0.017,-1.512,0 0.033,-1.913,0 ...12.933,19.774,14 12.950,19.836,16 12.967,20.165,19 12.983,20.761,21 13.000,21.384,23 13.017,21.498,25 ...Gel Exports the gels in the selected image format. Options are available to export all gels into the same image file or into a separate file for each gel. The Height selector on the Export tab determines the height, in pixels, of the exported graphic. Figure 9 shows all gels exported to one image file. Figure 9. Exported Gels P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Exporting Data 46 Selecting the Auto Export Settings The Auto export settings specify the data to automatically export at the end of each run and specify the format for each type of data. The settings in the export tab are only used if the Auto export check box is selected in the Setup Run Tab. To select the data to export: 1 Touch the Tools button on the Navigation Bar and then touch the Export Setup button to open the Export Setup Tab. 2 Touch the Export Settings Tab. 3 To export the files to a location other than the data folder, touch the Browse button and select the desired location for the data files. To reset the location to the default, touch the Default button. 4 Select the desired check boxes under Export Selections: • Select the Export All check box to select all check boxes. • To export all views of the same type to a single data file, the Export All check box and select the Export as Single File check box. If selected, the gels for all wells are included in a single graphic file and the Raw Data for all wells is included in a single AIA, CSV, or XML file. • If Gel is selected, touch the + or - buttons next to Height (Pixels) to specify the desired height of the exported gel graphic. • If Raw Data is selected, touch the AIA Format check box to export in Chromatography Data Interchange Format or clear the check box to export in CSV or XML format. • 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 Raw data file. (Not available for CZE assays or if the AIA Format check box is selected.) • If Peak Table, Well Table, or Raw Data is selected for export, choose the desired format for the exported data files. • If either Electropherogram or Gel is selected, choose the desired format for the exported image files. 5 Touch Save to save the Export settings. 6 Start the Run (see Running an Assay on page 32). 7 After the run has started, change the exported properties in the Well Table or Peak Table if desired (see page 47). P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Exporting Data 47 Selecting the Exported Properties in the Well Table or Peak Table The properties that are included in the Exported Peak Table or Well Table files can only be selected after the run is started. NOTE The desired properties should be selected during the Warm or Load step to ensure that all properties are exported for all wells if Single File is selected. To change the exported data: 1 Touch the Tools button on the Navigation Bar. 2 Touch the Export Setup button to open the Export Setup Tab. 3 To change the Peak Table or Well Table export properties: a Touch the Peak Properties Tab or Well Properties Tab. b Move the desired properties into the exported list by selecting the properties and using the Left or Right arrow buttons to move the properties into the desired list. 4 The changes take effect with the next file that is exported. Exporting Data in AIA Format for Use in Third- Party Analysis Software To export data in AIA format for use in third-party analysis software: 1 Touch the Tools button on the Navigation Bar and then touch the Export Setup button to open the Export Setup Tab. 2 Touch the Export Settings Tab. 3 To export the files to a location other than the data folder, touch the Browse button and select the desired location for the data files. To reset the location to the default, touch the Default button. 4 Select the Raw Data check box under Export Selections. 5 Select the AIA Format check box under Raw Data Options. 6 Touch Save to save the Export settings. 7 Start the Run (see Running an Assay on page 32). P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Exporting Data 48 Exporting a Data File after a Run is Complete To export a data file after a run is complete: 1 If the data file is not open, open the data file (see page 53). 2 Touch the Views button on the Navigation Bar. 3 Touch the Select Wells button to open the Select Wells to View Tab. 4 Touch the Export Plate button to export a data file to using the settings in the Export Settings Tab on the Views Window. If Peak Table or Well Table are selected for export, the exported table columns are selected in the Export Setup Tab on the Tools Window. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Viewing the Data 49 Viewing the Data Data can be viewed in the Status Window or in the Views Window. View data for the current run while the run is in progress, or after the run is complete. The Status Window displays the raw data from the run. The Egram/Gel Tab, EGram Tab, and Gel Tab on the Views Window can display either analyzed or raw data. This section includes the following procedures for viewing data in the LabChip GX Touch software during a run: • Selecting the Well Data to View on page 49 • Viewing Data in the Egram/Gel Tab on page 50 • Viewing Graphs in the Egram Tab on page 52 • Viewing Data in the Gel Tab on page 52 • Zoom In and Zoom Out on page 52 • Viewing a Data File after a Run is Complete on page 53 NOTE After a run is complete, use the LabChip GX Reviewer software to view and analyze the plate data. The LabChip GX Reviewer software can open multiple data files in the same workspace to compare data from different plates or different runs. Selecting the Well Data to View To select the well data to view in the graphs on the EGram/Gel tab and the EGram tab: 1 Touch the Views button on the Navigation Bar. 2 Touch the Select Wells button to open the Select Wells to View Tab. 3 To view data from a single well: a Clear the Overlay check box. b Touch the well in the plate diagram. Only one well can be selected at a time. 4 To view data from multiple wells overlaid on the same graph: a Select the Overlay check box. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Viewing the Data 50 b Touch each well to view in the overlay graphs. Multiple wells can be selected at the same time. Touch a well again to deselect the well. 5 To display the analyzed data on the Egram/Gel Tab, EGram Tab and Gel Tab, select the Perform Sample Analysis check box. To display the raw data only, clear the Perform Sample Analysis check box. 6 Use the gels in the Gel Tab or the Egram/Gel Tab to select the wells if there are multiple cycles. Touching a well in the Select Wells to View Tab selects the well data from the last plate cycle. 7 To view the data in the Egram/Gel Tab, see page 50. 8 To view the graphs in the EGram Tab, see page 52. 9 To view the data in the Gel Tab, see page 52. 10 See Zoom In and Zoom Out on page 52 for details on zooming graph and gel views. Viewing Data in the Egram/Gel Tab The Egram/Gel Tab displays a graph at the top of the tab and the gels of all the well data at the bottom of the window. The graph at the top of the window can display a single well or multiple wells overlaid in the same graph. Gels for all wells in the run display at the bottom of the window. The wells selected on the Select Wells to View Tab display in the Egram/Gel Tab. The wells to view can also be selected using the gels on the bottom of the Egram/Gel tab: 1 Select or clear the Overlay check box. 2 Touch a gel at the bottom of the tab to add the graph to the overlay. If the overlay check box is selected, the most recently added well displays at the top of the overlay graph. If the Overlay check box is not selected, only one well can be selected. 3 To change the graph display options, select the desired options in the Graph Settings on the EGram Tab. 4 To change the gel display options, select the desired options in the Gel Settings on the Gel Tab. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Viewing the Data 51 Graph Overlay The graph in the Egram/Gel Tab can display multiple wells overlaid in the same graph for visual comparison. Each well is shown in a different color and line style with a legend at the top of the window. Figure 10 shows the electropherograms of two wells in the same graph. Figure 10. Graph with Multiple wells To remove a specific sample from the graph, touch the sample that you want to remove in the Select Wells to View Tab or Egram/Gel Tab. To display only one sample in the graph, clear the Overlay check box and touch one sample in the Select Wells to View Tab or Egram/Gel Tab. Overlay Offset Use the Overlay Offset text box on the Graph Settings to offset each of the graphs by the RFU value specified. Figure 11 shows the electropherograms of two wells in the same graph, offset by 50 RFU. Figure 11. Overlay Offset P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Viewing the Data 52 Viewing Graphs in the Egram Tab The EGram Tab displays a graph containing the data from one or more completed wells. Data from multiple wells can be displayed in the same graph for visual comparison. The data file name and well name display at the top of the graph. To navigate through the wells on a plate, touch the Left, Right, Up, and Down buttons. The Select Wells to View Tab and the Egram/Gel Tab update to display the current well. Select the Scale to Sample Peaks check box to scale the view to the minimum and maximum X values of the current sample peaks. Marker and/or system peaks are ignored. (If Overlay is selected, the view scales to the sample peaks in the most recently selected well.) Clear the Scale to Sample Peaks check box to scale the view to the minimum and maximum X values of all peaks, including marker peaks and system peaks. To change the graph view options, select the Graph Settings check box and select the desired options in the Graph Settings. Viewing Data in the Gel Tab To compare the gels of all wells, view the gels in the Gel Tab. The color, width, and contrast of the gels can be changed using the Gel Settings. Select the Overlay check box to select multiple gels. The selected wells display in the graphs in the Egram/Gel Tab and the Gel Tab. Zoom In and Zoom Out You can zoom in and out on data displayed in the Egram/Gel Tab, Gel Tab, and EGram Tab. The Graph and the Gel on the Egram/Gel tab both zoom to the same levels when either view is zoomed in. All tabs also zoom to the same levels. To zoom in: • Touch and drag on a graph or gel to enclose the region of interest. The selected area enlarges to fill the view. In the Gel tab, all lanes zoom to the same level. In a Gel, drag straight up or down in a single gel lane to zoom in. Dragging horizontally pans the view of the gels. • You can continue zooming in until you reach the maximum magnification (the graph will not zoom in any closer). P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Viewing the Data 53 To zoom out: • In the EGram tab, touch the Unzoom button to zoom out to the previous zoom level. Touch the Unzoom All button to zoom out to the default view. • In the Gel tab or the Egram/Gel tab, double-tap a gel header to zoom out to the previous zoom level. • In the Egram/Gel tab or the EGram tab, double-tap the graph to zoom out to the previous zoom level. Viewing a Data File after a Run is Complete To view a data file after a run is complete: 1 Touch the Views button on the Navigation Bar. 2 Touch the Select Wells button to open the Select Wells to View Tab. 3 Touch the Review Plate button to open a data file to view the data. If a data file is already open, touch the OK button in the Review Plate window to clear the current plate data. Select the desired data file to open in the Select a Data File window and then touch the Open button. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Creating a Run File 54 Creating a Run File A Run File contains all of the settings required to run a plate, including all the tab settings on the Run Window. Importing a Run File on the Select Wells Tab changes the settings on all tabs. To create a run file if desired: 1 If the run will include auto export data, touch Tools, touch the Export Setup Tab, and then select the desired data to export. See Selecting the Auto Export Settings on page 46 for details. 2 Touch the Home button and then touch the Run button. 3 Select the desired assay, plate and sampling options and select the wells to sample on the Select Wells Tab. See Running an Assay on page 32 for details. 4 Touch the Next button to open the Setup Run Tab. 5 Select the desired run options on the Setup Run Tab. 6 Touch the Next button to open the Start Run Tab. 7 Touch the Export button . The Save Run Parameters to File window opens. 8 Type the desired name for the run file, select the file location, and touch the Save button to save the run file. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Using Sample Names Files 55 Using Sample Names Files If desired, Sample Names files can be used to select wells to read. Sample Names files are also used to import sample names into a data file as the data file is created. This section includes general instructions for using Sample Names files in the LabChip GX Touch software: • Creating a Sample Names File on page 56 • Selecting Wells using a Sample Names File on page 57 • Using a Barcode to Specify the Sample Names File on page 59 • Editing Sample Names During a Run on page 60 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Using Sample Names Files 56 Creating a Sample Names File Sample Names Files created in the LabChip GX Touch software can be used to specify the desired sample names for each well in a plate. The Sip order can also be specified to match the order of wells in the Sample Names file. Sample Names Files created in the LabChip GX Touch software do not contain Expected Peaks. Existing Sample Names files can also be edited in the LabChip GX Touch software by importing the existing file, editing the sample names and User Comments, and then exporting the edited file. To create a new Sample Names file: 1 When a plate is not running, touch the Views button on the Navigation Bar. 2 Touch the Sample Names button to open the Sample Names Tab. 3 Touch the Blank 96 Wells or Blank 384 Wells button to open a blank Sample Names file with 96 or 384 rows. The default Sample Names for each well are the same as the well label. Or, to open an existing Sample Names file, click the Import button and select the desired Sample Names file (*.csv). 4 Double-tap a sample name and edit the sample name as desired. The Well Labels cannot be changed and rows cannot be added or deleted. If desired, the wells can be displayed in Row Order or Column Order using the Row Order and Column Order option buttons. Select the By Quadrant check box to display the wells by quadrants. 5 If desired, type comments for the samples in the User Comments column. 6 To save the Sample Names file, touch the Export button and specify the desired location and file name. The wells are saved in the same order as they are displayed in the table. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Using Sample Names Files 57 Selecting Wells using a Sample Names File The wells to be sampled during the run can be selected using a Sample Names file. When using a Sample Names file to select the wells, only wells with an entry in the Sample Names file are selected for sampling. Use the LabChip GX Touch software, LabChip GX Reviewer software, Excel, or a LIMS to create the Sample Names file. The format must match the file format described in the LabChip GX Reviewer User Manual if the file is created with Excel or a LIMS. Sample Names files that are created in LabChip GX Touch software (see page 56) always contain all 96 or 384 wells on the plate. Existing Sample Names files containing less than 96 or 384 wells can be edited but not created in the LabChip GX Touch software. The Sample Names file used to select the samples is a .csv file that contains one row for each well to be sampled, and does not contain rows for wells that are not sampled. Using the Sample Names file in Figure 12 to select the wells in the run will select wells A1, A5, A11, A12, B1, B2, F5, and F6 for sampling. Figure 12 shows the wells selected in the Select Wells Tab. Figure 12. Sample Names file for Selecting Samples P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Using Sample Names Files 58 Selecting Wells using a Sample Names File (Continued) Figure 13. Selected Wells on Run Window This Sample Names file cannot be created in the Sample Names Editor window in the LabChip GX Reviewer software because the files created in the Sample Names Editor window always contain one row for each well in the plate. The Sample Names files for selecting Microsoft® wells Excel are and typically are saved created as a by *.csv a LIMS file. or can be created in To select the wells using a Sample Names file: 1 Create the Sample Names file with one row for each well to be sampled. 2 Touch the Home button and then touch the Run button. 3 Select the desired run settings on the Select Wells Tab. 4 Select at least one well in the plate diagram. It does not matter which well is selected. The Next button is not enabled unless at least one well is selected. 5 Touch the Next button or the Setup Run Tab. 6 Select the Sample Names file check box. 7 Touch the Browse button next to the Sample Names text box, select the Sample Names file (*.csv), and touch the Open button. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Using Sample Names Files 59 Selecting Wells using a Sample Names File (Continued) 8 Select the Use Sample Names file for Sample Selection check box. 9 Select the desired options on the Setup Run Tab. 10 Touch the Select Wells button. 11 Select or clear the desired sipping order options: Column-wise and File Sip Order. 12 Select any other run parameters as desired, and then start the run. Using a Barcode to Specify the Sample Names File If your instrument is equipped with a barcode reader, the desired Sample Names file can be specified by using the plate barcode in the name of the Sample Names file. At run-time, the plate barcode is read and then the barcode is used to read the corresponding Sample Names file. To use the plate barcode to specify the Sample Names file: 1 Decide on a location and file name format for the Sample Names files. For example, the Sample Names files can be named “Sample Names” followed immediately by the barcode on the plate. 2 Create a temporary CSV file, using “%barcode%” as a placeholder for the barcode string. For example, create a temporary file named “Sample Names%barcode%.csv” and save it in the location where the actual Sample Names files for the runs will be saved. 3 On the Select Wells Tab, select the desired run parameters. 4 On the Setup Run Tab, touch the Browse button next to Sample Names file, and select the CSV file that contains the %barcode% wildcard. The Use Sample Names file for Sample Selection check box is automatically selected when the Sample Names file contains the string %barcode%. 5 In the Select Wells tab, select the desired Sipping Order options: Column-wise and/or File Order. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Using Sample Names Files 60 Using a Barcode to Specify the Sample Names File (Continued) 6 Touch the Start Run button. The Start Run Tab opens. 7 Touch the Export button and save the Run file. The Run File can be imported to run multiple plates with the same settings. 8 To start the run, touch the Start button. 9 When the run is started, the plate barcode is read and the Sample Names file with the corresponding barcode is used to select the wells to sample. In the example above, if the plate barcode is 12345, then the file named “Sample Names12345.csv” will be used to select the wells in the run. Editing Sample Names During a Run The default Sample Names assigned during a run can be edited after the run starts, but before the sample well read is complete. (After the well has been read, the data is saved in the data file, and the sample name can no longer be changed.) same names assigned using a sample names file can also be edited before the well has been read. 1 After a run is started, touch the Views button on the Navigation Bar. 2 Touch the Sample Names button to open the Sample Names Tab. If a sample names file was specified, the names from the Sample Names File display. Otherwise, the well labels are used as the default sample names. 3 Edit the sample names as desired. (If a well has already been read, the Sample Names and Comment fields are disabled for the well and cannot be edited.) 4 Add comments to the Comment fields as desired. 5 Touch the Apply button to save the changes. You must touch Apply before the well read is complete. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Saving Data Files 61 Saving Data Files While running an assay, the raw time series data received from the instrument is automatically saved to the data file (.gxd), one well at a time as each well is completed. The Analysis settings from the assay are also saved in the data file. If a run is stopped before it is complete, the data for all completed wells is saved in the data file. The name and location of the data file is specified in the Setup Run Tab. This section includes general instructions for saving data files in the LabChip GX Touch software: • Saving Data Files with LabChip GxP Option Installed • Organizing, Retrieving, and Backing Up Data Files Saving Data Files with LabChip GxP Option Installed If the LabChip GxP option is installed, the raw time series data received from the instrument is saved to the CDR, one well at a time as each well is completed. If the connection to a remote CDR server is lost after a run is started, the data is saved to a local folder and copied to the CDR when the network connection is restored. Organizing, Retrieving, and Backing Up Data Files As you work in the LabChip GX Touch software, it is a good practice to organize the LabChip GX Touch data files. • Create a folder in which to save the data files. If desired, each user can save data files to their own subfolder to organize the data files. • Review the files periodically, even if only one person uses the LabChip GX Touch software. If you are not using the LabChip GxP option, archive files you are no longer using but want to save by copying to a backup disk, and then delete unneeded files. Verify there is enough free space on the hard drive to save new plate data files. If you are using the LabChip GxP option, see LabChip GxP Option on page 62 for backup options. • Each user in the laboratory can specify a particular data file prefix to easily differentiate data files. A new folder can be created each day to store the data from all runs. To automatically create the folders, select the Create Daily Sub-Directory check box on the Setup Run Tab. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. LabChip GxP Option 62 LabChip GxP Option A LabChip GxP option is available for the LabChip GX Touch software. This option contains built-in technical controls and features specifically designed to provide compatibility with 21 CFR Part 11 requirements. Users are responsible for establishing policies and standard operating procedures that complement the capabilities provided by the software in order to ensure complete compliance to the rule. NOTE Using the LabChip GxP compatibility option alone does not ensure 21 CFR Part 11 compliance. Laboratory processes and procedures must comply with 21 CFR Part 11 regulations. The LabChip GxP option ensures that assays, output data, analysis settings, event data, and backup data files are not available for editing or tampering. Data is stored in a secure folder on the local computer user accounts, or on Microsofta network ® server. SQL ServerTo manage ® 2014 LabChip Express GX is provided Touch with the LabChip GxP option. The LabChip GxP option requires an internal USB Key (dongle) installed inside the instrument cover. The USB Key is only to be installed by trained PerkinElmer Service personnel. The following procedures are included in this section: • Locking and Unlocking the Software on page 63 • User Accounts on page 64 — Switching Users on page 64 • Central Data Repository (CDR) on page 65 — CDR Security Suggestions on page 65 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. LabChip GxP Option 63 Locking and Unlocking the Software The LabChip GX Touch software with the LabChip GxP option installed allows you to lock the LabChip GX Touch software. The software also locks after it has been left unattended for an amount of time specified by the LabChip GX Touch Administrator. Locking the LabChip GX Touch software prevents unauthorized users from accessing the software while you are away from the computer. After the software is locked, only the logged in user or a LabChip GX Touch Administrator can unlock the software. To lock the LabChip GX Touch software: 1 On the Home Window, touch the User button in the lower right corner. The Unlock Application Window opens on top of the LabChip GX Touch Main Window and displays the User name of the current user. Figure 14. Login Window 2 Touch the Lock button. The Unlock Application Window opens and the software is locked until unlocked by the current user or an administrator. NOTE If a run is in progress, the run continues and the data is logged under the user name of the user that was logged in at the beginning of the run, even if another user logs in during the run. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. LabChip GxP Option 64 Locking and Unlocking the Software (Continued) To unlock the LabChip GX Touch software: 1 On the Unlock Application Window, type the password for the logged in user in the Password text box and touch the Logon button. 2 If the password for the current user is not available, type a LabChip GX Touch Administrator user name and password in the Unlock Application Window and touch the Logon button. The Administrator is logged into the LabChip GX Touch software and the previous user is logged out. User Accounts Access to the LabChip GX Touch software is controlled by user accounts when the LabChip GxP option is installed. Each user must sign into the LabChip GX Touch software from the Unlock Application Window. User accounts are managed in the LabChip GX Reviewer software. See the LabChip GX Reviewer User Manual for information on creating and managing user accounts. Switching Users The LabChip GX Touch software with the LabChip GxP option installed allows you to switch users during operation. To switch users: 1 On the Unlock Application Window, touch the Switch User button. 2 Type the user name and password of the new user and touch the Logon button. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. LabChip GxP Option 65 Central Data Repository (CDR) The Central Data Repository (CDR) is a protected folder located on the local computer or on a network server. All data files (.gxd) are saved in the CDR folder. The CDR folder is protected from changes by unauthorized users. The CDR is only used when the LabChip GxP option is installed. The data files can be organized into virtual folders in the CDR using the folder options in the Setup Run Tab. The folders are not actually created in the CDR folder, but are displayed in the LabChip GX Reviewer and LabChip GX Touch software to organize the data files. The LabChip GX Reviewer software enables you to create new folders, rename existing folder, and delete empty folders. CDR Security Suggestions To ensure proper security of data files, the LabChip GX Touch Administrator should: 1 Change the administrator password. Make sure to keep a copy of the password in a safe place. This password cannot be reset if forgotten. To change the administrator password: a Log into the LabChip GX Touch software as the administrator. b On the Home Window, touch the User button in the lower right corner. The Unlock Application Window opens. c Touch the Change Password button. The Change Password Window opens. d Type the current password in the Old Password text box. e Type the new password in both the New Password and Confirm Password text boxes. NOTE Write down the administrator password and keep a copy in a safe place. The administrator password cannot be reset or recovered if forgotten or lost. f Touch the OK button. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 66 Software Reference This section describes the windows in the LabChip GX Touch software. Each topic describes the options and buttons on the window, and how to open the window. • CDR/Database Server Window on page 67 • Change Assay Folder Window on page 68 • Change Password Window on page 69 • LabChip GX Touch Main Window on page 70 — Navigation Bar on page 71 — Home Window on page 72 • Login Window on page 74 • Prime and Calibrate Window on page 76 • Prime Window on page 77 • Run Window on page 78 — Select Wells Tab on page 79 — Setup Run Tab on page 81 — Start Run Tab on page 84 • Status Window on page 86 • Tools Window on page 89 — Export Setup Tab on page 90 — Diagnostics Tab on page 95 — Optics Normalization Tab on page 97 — Plate Editor Tab on page 98 — Software IQ Tab on page 100 — Factory Access Tab on page 102 — Error Message Display on page 103 • Unlock Application Window on page 104 • Views Window on page 105 — Select Wells to View Tab on page 106 — Egram/Gel Tab on page 108 — EGram Tab on page 109 — Gel Tab on page 113 — Run Info Tab on page 116 — EventLog Tab on page 119 — Sample Names Tab on page 120 — Analysis Settings Tab on page 122 • Wash Window on page 124 P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 67 CDR/Database Server Window Use the CDR/Database Server Window to specify the location of the CDR folder or to view the current location of the CDR folder when the LabChip GxP option is installed. Figure 15. CDR/Database Server Window The CDR/Database Server Window contains the following options: Server Name / IP Address - The server name or IP address of the computer where the CDR is installed. Apply button - Connects to the CDR on the specified computer or server. If the CDR cannot be contacted due to network problems or because the CDR is not installed yet, an error message displays. Cancel button - Closes the window without connecting to the remote CDR Server. If the LabChip GX Touch software is not connected to the CDR, assays cannot be run until the CDR is connected. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 68 Change Assay Folder Window The Change Assay Folder window is used to select the Assay Folder when priming a chip or running a plate. To open the Change Assay Folder window, touch the Change Assay Folder button on the Prime Window or on the Select Wells Tab. Figure 16. Change Assay Folder Window The Change Assay Folder window contains the following options: New Folder button - Enables you to create new assay folders. Rename button - Enables you to rename the current assay folder. Use the LabChip GX Reviewer software to create new assay folders. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 69 Change Password Window Use the Change Password Window to change the password for the current user. This window is only available if the LabChip GxP option is installed with the LabChip GX Touch software. To open the Change Password Window, touch the User button on the Home Window and then touch the Change Password button. Figure 17. Change Password Window The Change Password Window contains the following options: Old Password - The current password for the current user. New Password - The new password for the current user. Confirm Password - The new password for the current user. OK button - Saves the new password and closes the window. Cancel button - Closes the window without saving changes to the password. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 70 LabChip GX Touch Main Window Use the LabChip GX Touch main window to access the Navigation Bar and Home Window. The LabChip GX Touch Main Window opens when the software is opened. Figure 18. LabChip GX Touch Main Window P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 71 Navigation Bar The Navigation Bar on the left side of the LabChip GX Touch Main Window provides access to the main functions of the LabChip GX Touch software. Touching a navigation button opens the corresponding window. The Navigation bar contains the following buttons: Home button - Opens the Home Window to start a prime, calibration, pressure line purge, run, or wash operation or to load/unload plates or chips. Status button - Opens the Status Window to view the current status of the instrument, chip, and run. For Protein Clear HR and ProteinEXact assays, the status of prime/calibration displays. Views button - Opens the Views Window to view data from the last completed run. After a new run is started or the software is closed, data from a completed run is no longer available in the LabChip GX Touch software. Use the LabChip GX Reviewer software to view or analyze data from previous runs. Tools button - Opens the Tools Window to add plates, run software and hardware diagnostics, select Auto export options, calibrate the optics, or access PerkinElmer service engineer software functions. Exit button - Closes the LabChip GX Touch software. Error button - Only displays if an error has occurred. Opens the Current Events Tab to view the error details and to clear the error. Warning button - Only displays if a Warning has occurred. Opens the Current Events Tab to view the warning details and to clear the warning. Stop button - Stops the current operation in progress. If running a plate, the run stops immediately and the current well does not finish reading. Any data collected from the current well is discarded. If priming or washing a chip, the prime or wash stops immediately. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 72 Home Window The Home Window displays to the right of the Navigation Bar and is used to prime a chip, calibrate a chip, wash a chip, run a plate, or purge the instrument’s pressure lines. Also used to load and unload plates and chips in the instrument. The status of the instrument and user information also display. If the LabChip GxP option is installed, the Home Window displays the CDR Server status and provides access to the Login window. To open the Home window, touch the Home button on the Navigation Bar. Figure 19. Home Window The Home window contains the following buttons: Prime - Opens the Prime Window to prime the chip (not available for Protein Clear HR chips). Prime and Calibrate - Opens the Prime and Calibrate Window to calibrate the instrument to run Protein Clear HR assays (only for Protein Clear HR chips). P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 73 Home Window (Continued) Run - Opens the Run Window to run an assay. See the Assay User Guide for chip preparation instructions. While an assay is running, the Exit button on the Navigation Bar changes to a Stop button to stop the run in progress. Assays that have been stopped cannot automatically be resumed. See Continuing a Stopped Run on page 40 for details on restarting a stopped assay. Wash - Opens the Wash Window and immediately begins washing the chip. See the Assay User Guide for chip preparation instructions. Unload/Load Plate - Ejects or retracts the microplate carrier to access the microplate, buffer tube, and ladder tube. Purge Pressure Lines - Forces any potential liquid or debris out of the pressure lines to improve instrument performance. Unload Chip - Unlatches the front door to access the chip. Manually close the door to load the chip. Instrument Status - Displays the current status of the LabChip GX Touch instrument: • Calibrating - The GX Touch software is calibrating the instrument to run a Protein Clear HR or ProteinEXact assay. • Connecting - The GX Touch software is connecting to the instrument. • Eject Plate - The GX Touch is ejecting a plate carriage. • Idle - The GX Touch is not active. • Open Door - The GX Touch is opening the front door to access the chip. • Logon - A user has not yet logged into the software. • Priming - The GX Touch is priming a chip. • Purging - The GX Touch is purging the pressure lines. • Retract Plate - The GX Touch is retracting a plate carriage. • Startup - The GX Touch software is initiating communication with the instrument. • Running - The GX Touch is running an assay. • Warming - The GX Touch is warming a chip. • Washing - The GX Touch is washing a chip. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 74 Home Window (Continued) Server Status - Only displays if the LabChip GxP option is installed. Displays the current status of the CDR/Database server connection: • Connected to server - The software is connected to the server. Touch the button to open the CDR/Database Server Window. • Mapping Server - The software is locating the server name or IP address of the computer where the CDR is installed. • Locked by Timeout - Displays if the software has been left unattended for an amount of time specified by the LabChip GX Touch Administrator. • Locked by User - Displays if the software has been locked by the user. • Server is Not available - The software is not connected to the server. • Server not mapped - The software has not been mapped to a CDR server. User button - Only displays if the LabChip GxP option is installed. Opens the Unlock Application Window to log into the software, lock the software, switch users, or change the password of the current user. Information (i) button - Opens the InfoView window to access information about LabChip GX Touch software, the LabChip GX Touch online help, and the Log Zipper function. Login Window Use the Login Window to log in to the LabChip GX Touch software, lock the software, switch users, or change passwords when the LabChip GxP option is installed. The LabChip GX Touch software will not start until a valid user name and password are entered. The Login Window opens when you start the LabChip GX Touch software with the LabChip GxP option installed. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 75 Login Window (Continued) Figure 20. Login Window The Login Window contains the following options: Username text box - The user name to log into the LabChip GX Touch software. Each user should have a unique user name. Password text box - The password assigned to the Username. All passwords must be at least 5 characters long and must contain at least one uppercase letter and at least one number. The User Account Policies specify additional password requirements. NOTE The Switch User, Change Password, and Lock buttons are only available if a user is already logged into the LabChip GX Touch software. Switch User button - Enables the User Name and Password text boxes to enable a new user to log in. The current user is automatically logged out. Change Password Button - Opens the Change Password Window to change the password for the current user. Logon button - Logs in the user and closes the Login Window. Lock button - Opens the Unlock Application Window and locks the LabChip GX Touch software. Only the current user or an administrator can unlock the software. Cancel button - Closes the Login Window without logging the user into the software. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 76 Prime and Calibrate Window Use the Prime and Calibrate window to calibrate the instrument to run a Protein Clear HR assay. To open the Prime and Calibrate window, touch the Prime and Calibrate button on the Home Window. Figure 21. Prime and Calibrate Window The Prime and Calibrate window contains the following options: Change Assay Folder button - Touch to select the folder that contains the desired assays. Select Assay drop-down list - Touch to select the assay to run. A1 button - Touch to enlarge the plate diagram to select the well containing the VeriMAb sample. Skip Prime step check box - Only displays if a Protein Clear HR chip has already been calibrated. If selected, the chip is calibrated without a second prime. Select Plate Type drop-down list - Select the desired plate type to be used during the run. Prime and Calibrate button - Starts the calibration process. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 77 Prime Window Use the Prime window to prime chips that do not support Protein Clear HR assays. The chip must be primed for the same assay (or assay family) as the assay that will run on the chip. To use the chip for a different assay, wash and reprime the chip by selecting the correct assay and using the appropriate reagents. Load the buffer tube and the chip before opening the Prime window. To open the Prime window, touch the Prime button on the Home Window. Figure 22. Prime Window The Prime window contains the following options and buttons: Change Assay Folder button - Touch to select the folder that contains the desired assays. Assay - Specifies the assay for which to prime the chip. The selections available depend on the chip type and the assay type that was selected when the chip was inserted. Run Test Ladder after Prime check box - If selected, runs one ladder well after priming is complete. Prime button - Starts priming the chip and displays the status of the priming step. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 78 Run WindowUse the Run Window to define the assay run parameters. To open the Run Window, touch the Run button on the Home Window. The Run Window contains the following tabs: • Select Wells Tab • Setup Run Tab • Start Run Tab P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 79 Select Wells Tab Use the Select Wells tab to select the assay, plate type, wells to read, and advanced run options. See the Assay User Guide for chip and sample prep instructions. To open the Select Wells tab, touch the Run button on the Home Window or touch the Select Wells tab on top of the Run Window. Figure 23. Select Wells Tab The Select Wells tab contains the following options and buttons: Change Assay Folder button - Touch to select the folder that contains the desired assays. Select Assay drop-down list - Select the type of assay to run. The assay types available depend on the chip that is loaded in the instrument. The instrument automatically identifies the chip type when the chip is loaded in the instrument. Select Plate Type drop-down list - Choose the type of plate that will be used in the run. Import Run File button - Opens the Import Run Parameters from XML File window to select a run file to import. See Creating a Run File on page 54 for details on run files. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc. Software Reference 80 Select Wells Tab (Continued) Plate Diagram - Select the wells to read during the run. Selected wells are blue, unselected wells are white. • To select all rows on the plate, touch the Select All Rows button at the top left corner of the plate diagram. • To select a row, touch the row letter on the left side of the plate. • To select a column, touch the column number at the top of the plate. • Clear a single well by touching the selected well. Full Size button - Enlarges the Plate Diagram to full screen to enable easier selection of wells, especially when selecting wells on 384-well plates. Touch the Done button in the upper right corner to return to the Select Wells tab. Quadrants - Touch the 1, 2, 3, or 4 buttons to select or clear all wells in each quadrant. Any wells that are already selected are not changed unless the wells are in the specified quadrant. Column-wise check box - Specifies the order in which the wells are sampled during the assay: • If selected, the wells in each column are sampled from top to bottom before proceeding to the next column (A1, B1, C1... A2, B2, C2...). Ladders are sipped every 12 wells, so some columns will include a ladder in the column. • If cleared, the wells in each row are sampled from left to right before proceeding to the next row (A1, A2, A3... B1, B2, B3...). Ladders are sipped every 12 wells. Selection Sip Order check box - If selected, the wells are sipped in the order in which the wells are selected. Selecting a rectangular region orders the wells from the start of the selection region to the end of the selection region, either row-wise or column-wise. If not selected, the wells are sipped in row or column order. Advanced Settings - If selected, uses the Advanced Run Settings: • Sample Sips - Specifies the number of times to run the selected wells. Each well is sampled once, and then the entire run repeats. The data from all wells is combined in one data file. • Plate Cycles - Specifies how many times to repeat the assay on the plate. • Random Select% - Specifies the percent of wells to randomly sample from the selected wells. For example, if 10 wells are selected, and the Random Select% is set to 50%, five wells, selected at random, will be sampled during the run. Next button - Opens the Setup Run Tab. P/N CLS151164 Rev. C LabChip GX Touch/GXII Touch User Manual PerkinElmer, Inc.


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