Agilent Technologies 2100 Maintenance And Troubleshooting Manual
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Agilent Technologies 2100 Maintenance And Troubleshooting Manual

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  • Page 1 Agilent 2100 Bioanalyzer System Maintenance and Troubleshooting Guide Agilent Technologies...

  • Page 2: Safety Notices

    Notices Warranty © Agilent Technologies, Inc. 2011-2016, receive no greater than Restricted Rights as 2017 defined in FAR 52.227-19(c)(1-2) (June The material contained in this docu- 1987). U.S. Government users will receive No part of this manual may be reproduced ment is provided “as is,”...
  • Page 3 This manual is based on the 2100 Expert Software revision B.02.08. Other software revisions may have an impact on results. Maintenance and Troubleshooting...

  • Page 4: Table Of Contents

    2 Troubleshooting the Instrument Communication Verify the Instrument Communication Troubleshooting Communication Issues Changing COM Port Settings USB to Serial Adapter 3 Troubleshooting the 2100 Expert Software Run Installation Qualification Test 4 Hardware Diagnostics Overview Diagnostic Test Procedure 5 Troubleshooting the DNA Application...
  • Page 5 Cleaning the Syringe Adapter Replacing the Syringe Adapter Replacing the Gasket Checking the Chip Priming Station for Proper Performance - Seal Test 10 Maintenance of the Agilent 2100 Bioanalyzer instrument Overview Cleaning the Lens Changing the Fuses 11 Maintenance of the Vortexer...
  • Page 6 Contents Maintenance and Troubleshooting...

  • Page 7: Essential Measurement Practices

    Maintenance and Troubleshooting Essential Measurement Practices Overview Tools and Handling Chip Priming Station Reagents and Reagent Mixes Gel and Gel-Dye Mix Samples Chips Agilent 2100 Bioanalyzer System Agilent Technologies...

  • Page 8: Overview

    Essential Measurement Practices Overview Overview This section lists all user relevant hints on handling tools, chips, reagents and the Agilent 2100 Bioanalyzer system. For the latest information on assay-related hints, go to the Agilent web site at: www.agilent.com/genomics/bioanalyzer Maintenance and Troubleshooting...

  • Page 9: Tools And Handling

    Essential Measurement Practices Tools and Handling Tools and Handling • Always follow the GLP-rules established in the laboratory. • Always wear gloves when handling chips to prevent contamination. • When pipetting sample, use non-filter pipette tips that are of adequate size. Pipette tips that are too large will lead to poor quantitation accuracy.

  • Page 10: Chip Priming Station

    Essential Measurement Practices Chip Priming Station Chip Priming Station • Refer to the appropriate Kit Guide for the correct position of the syringe clip and base plate. • Replace the syringe with each new kit. • Check the performance of the chip priming station by applying the seal test on a monthly basis.

  • Page 11: Reagents And Reagent Mixes

    Essential Measurement Practices Reagents and Reagent Mixes Reagents and Reagent Mixes • Handle and store all reagents according to the instructions given in the specific Kit Guide. • Keep all reagents and reagent mixes (for example, the gel-dye mix) refrigerated at 4°C when not in use for more than 1 hour. Reagents left at room temperature may decompose, leading to poor measurement results.

  • Page 12: Samples

    Essential Measurement Practices Samples Samples • Refer to the assay specific Kit Guides for maximum allowed sample and salt concentration. • For RNA assays: Heat denature all RNA samples and RNA ladder for 2 minutes at 70°C before use. • For protein assays: Use 0.5 mL tubes for denaturation. Using larger tubes will lead to poor results.

  • Page 13: Chips

    Essential Measurement Practices Chips Chips • Prepared chips must be used within 5 minutes. Reagents may evaporate, leading to poor results. • For DNA and RNA assays, vortex chips for 1 minute. Inappropriate and insufficient vortexing will lead to poor results. Use only the IKA vortexer for chip vortexing.

  • Page 14: Agilent 2100 Bioanalyzer System

    Essential Measurement Practices Agilent 2100 Bioanalyzer System Agilent 2100 Bioanalyzer System • Do not touch the 2100 Bioanalyzer instrument during a run and never place it on a vibrating surface or near air-circulating instruments (for example, temperature cyclers). • Do not force the chip to fit in the 2100 Bioanalyzer instrument. The electrode cartridge may be damaged when the lid is closed.

  • Page 15: Troubleshooting The Instrument Communication

    Maintenance and Troubleshooting Troubleshooting the Instrument Communication Verify the Instrument Communication Troubleshooting Communication Issues Overview Troubleshooting Communication Issue Flow Chart Changing COM Port Settings USB to Serial Adapter How to create a Support Package Agilent Technologies...

  • Page 16: Verify The Instrument Communication

    Troubleshooting the Instrument Communication Verify the Instrument Communication Verify the Instrument Communication To check whether your PC communicates with the Agilent 2100 Bioanalyzer instrument: 1 Start the instrument. The power switch is located at the rear where the power cable plugs in.
  • Page 17 Troubleshooting the Instrument Communication Verify the Instrument Communication If the instrument is connected successfully, additional hardware information (serial number, cartridge type,...) is displayed on top of the screen, see Figure on page 17. If the icon does not change, the instrument is not connected successfully. For solutions, see “Overview”...

  • Page 18: Troubleshooting Communication Issues

    • Check if license keys have been registered with the software. Go to Help > Registration > Add Licenses. Ensure that 2 licenses have been entered: the instrument control license and the electrophoresis license. • Check the COM port settings in the 2100 Expert Software, see “Changing COM Port Settings”...

  • Page 19: Troubleshooting Communication Issue Flow Chart

    Troubleshooting the Instrument Communication Troubleshooting Communication Issues Troubleshooting Communication Issue Flow Chart www.agilent.com/genomics/contact “How to create a Support Package” on page 22 “USB to Serial Adapter” on page 21 Maintenance and Troubleshooting...

  • Page 20: Changing Com Port Settings

    2 Under COM Port choose a different port number from the drop down list. 3 Check the icon of the 2100 Bioanalyzer instrument on the screen. If it is no longer dimmed, communication between the 2100 Bioanalyzer instrument and PC is working properly.

  • Page 21: Usb To Serial Adapter

    USB-Serial Adapter cable is plugged into the USB port of your PC. For off-line systems, please install the driver from the Agilent 2100 Expert Software CD by clicking on the executable file found in SupportDriver/88-8031CDM20824.exe. If a CD is not available, download the driver.

  • Page 22: How To Create A Support Package

    (via email) to Agilent support. In order to create a Support Package, in the 2100 Expert software, open Help > Create support package. In the pop-up window, a list of tasks is presented.
  • Page 23 Alternatively: N O T E • In the Windows Start menu, open All Programs > Agilent 2100 Bioanalyzer > Utilities > Create support package. In the pop-up window, a list of tasks is presented. • Make sure all tasks are selected, then click collect to proceed.
  • Page 24 Troubleshooting the Instrument Communication How to create a Support Package Maintenance and Troubleshooting...
  • Page 25 Maintenance and Troubleshooting Troubleshooting the 2100 Expert Software Run Installation Qualification Test Agilent Technologies...

  • Page 26: Troubleshooting The 2100 Expert Software Run Installation Qualification Test

    Troubleshooting the 2100 Expert Software Run Installation Qualification Test Run Installation Qualification Test If it is suspected that the 2100 Expert Software is not working properly, check for corrupted or missing files. 1 Start the 2100 Expert Software and select the Validation (Verification) context.
  • Page 27 7 The result of the installation qualification test depends on whether the software installation is complete and no files are corrupted. To review the results, switch to the Results tab: 8 If the test passes and the 2100 Bioanalyzer system still does not function properly, see “Verify the Instrument Communication”...
  • Page 28 Troubleshooting the 2100 Expert Software Run Installation Qualification Test Maintenance and Troubleshooting...
  • Page 29 Maintenance and Troubleshooting Hardware Diagnostics Overview Diagnostic Test Procedure Agilent Technologies...
  • Page 30 Hardware Diagnostics Overview Overview Several tests are provided for the 2100 Bioanalyzer system to check the functionality of the hardware. These tests should be performed on a regular basis, or if incorrect measurements or error messages occur. Table 2 page 30 provides an overview of the available test chips.

  • Page 31: Hardware Diagnostics Overview

    Stepper motor test Checks for proper movement of the stepper motor. Electrode/Diode test Checks photodiode and current versus voltage performance of the 2100 Bioanalyzer instrument. Electrode/Diode test chip required. High voltage stability test Checks the accuracy and stability of all 16 high voltage power supplies. Unused chip (DNA, RNA or protein) required.

  • Page 32: Diagnostic Test Procedure

    For details on the test procedure, please refer to the documentation included with the test chip kits. Diagnostic tests cannot be run while the 2100 Expert Software is performing a chip run. N O T E 1 Start the 2100 Expert Software.
  • Page 33 7 If there are failures, repeat the failed tests. 8 If failures persist, contact Agilent Technologies at www.agilent.com/genomics/contact. The results of diagnostic tests are stored as .xdy files in Agilent\2100 bioanalyzer\2100 expert\diagnosis. If tests fail, send the .xdy files to Agilent Technical Support.
  • Page 34 Hardware Diagnostics Diagnostic Test Procedure Maintenance and Troubleshooting...

  • Page 35: Troubleshooting The Dna Application

    Missing Upper Marker Broad Peaks Baseline Dips Baseline Noise Baseline Jumps Wavy Baseline Late Migration Peak Tailing Unexpected Run Time Error Message: No data received since 5 seconds Symptoms (High Sensitivity DNA) Artefact Peaks Split Peaks Baseline Negative Dips Agilent Technologies...

  • Page 36: Overview

    Run Log for the data file. Select the Log Book tab in the Data and Assay context. The Run Log lists all the actions and errors that occurred during the run. In rare cases, results generated by the 2100 Bioanalyzer system might not be as expected. To help find the reason for the discrepancy, see “Symptoms...

  • Page 37: Symptoms (Dna)

    Troubleshooting the DNA Application Symptoms (DNA) Symptoms (DNA) Click to go straight to the troubleshooting hints. • “Residual Gel in Spin Filter after Centrifugation” on page 38 • “Too High Quantitation Results” on page 38 • “Too Low Quantitation Results” on page 39 •...

  • Page 38: Symptoms (Dna)

    Troubleshooting the DNA Application Symptoms (DNA) Residual Gel in Spin Filter after Centrifugation Most probable causes Solution Gel was filtered at insufficient g-value. Refer to the Kit Guide for proper centrifuge settings. Cooled centrifuge was used for gel Repeat centrifugation step at room temperature. filtration.

  • Page 39: Too Low Quantitation Results

    Troubleshooting the DNA Application Symptoms (DNA) Too Low Quantitation Results Most probable causes Solution Pipetting error during preparation of Check dilution procedure and calibration of pipette. reagent mixes. Chip pipetting error. Prepare new chip. Always insert the pipette tip to the bottom of the well when dispensing the liquid.

  • Page 40: Wrong Sizing Result

    Prepare a new chip. Least probable causes Solution Vibration of 2100 Bioanalyzer Do not touch 2100 Bioanalyzer instrument during a run. instrument. Remove vibration devices, such as vortexers and vacuum pumps, from bench. Changes of ambient temperature of Place 2100 Bioanalyzer instrument in thermally stable environment.

  • Page 41: Run Aborted

    30 minutes prior to use. Store chips at room temperature. Least probable causes Solution High voltage power supply Check high voltage power supply using the “Overview” on page 30. If the power supply is defective. defective, contact Agilent Technologies at www.agilent.com/genomics/contact. Maintenance and Troubleshooting...

  • Page 42: Chip Not Detected

    Least probable causes Solution High voltage power supply defective. Check high voltage power supply using the “Overview” on page 30. If the power supply is defective, contact Agilent Technologies at www.agilent.com/genomics/contact. Back to “Symptoms (DNA)” on page 37 Maintenance and Troubleshooting...

  • Page 43: Additional Sample Or Ladder Peaks

    Check if clip and base plate of priming station are in the correct position (see Kit Guide). Vibration of 2100 Do not touch 2100 Bioanalyzer instrument during a run. Remove vibration devices, such as Bioanalyzer instrument. vortexers and vacuum pumps, from bench.

  • Page 44: Spikes

    Spikes Most probable causes Solution Vibration of 2100 Bioanalyzer instrument. Do not touch 2100 Bioanalyzer instrument during a run. Remove vibration devices, such as vortexers and vacuum pumps, from bench. Chip or gel-dye mix contaminated with particles. Prepare new chip with new gel-dye mix: Wear powder-free gloves only.

  • Page 45: Low Signal Intensity

    Troubleshooting the DNA Application Symptoms (DNA) Low Signal Intensity Most probable causes Solution Dye concentration too low. Use dye concentration according to the Kit Guide. Let the dye warm up to room temperature for 30 minutes before preparing the gel-dye mix. Protect the dye from light during this time.
  • Page 46 Clean the electrodes. Load the chip immediately after taking it out of its sealed bag. Vibration of 2100 Bioanalyzer instrument. Do not touch 2100 Bioanalyzer instrument during a run. Remove vibration devices, such as vortexers and vacuum pumps, from bench. Autofocus failure.

  • Page 47: Missing Peaks

    Autofocus failure or high voltage Check autofocus and high voltage power supply by means of the “Hardware power supply defective Diagnostics” on page 29. If a diagnostic test fails, contact Agilent Technologies at www.agilent.com/genomics/contact. Back to “Symptoms (DNA)” on page 37...

  • Page 48: Missing Upper Marker

    Troubleshooting the DNA Application Symptoms (DNA) Missing Upper Marker Most probable causes Solution Alignment of upper marker not set Manually assign upper marker. Follow instructions for “Manual Marker properly. Assignment” on page 58 Upper marker digested by restriction Inactivate restriction enzymes by adding EDTA or heat according to the enzymes.

  • Page 49: Broad Peaks

    Troubleshooting the DNA Application Symptoms (DNA) Broad Peaks Most probable causes Solution Leak currents due to contaminated Clean electrodes with analysis-grade water and a toothbrush, see “How to Clean electrodes. the Pin Set of the Electrode Cartridge” on page 126. Chip not properly primed.

  • Page 50: Baseline Dips

    Least probable causes Solution Autofocus failure. Check autofocus by means of the “Overview” on page 30. If the diagnostic test fails, contact Agilent Technologies at www.agilent.com/genomics/contact. Back to “Symptoms (DNA)” on page 37 Maintenance and Troubleshooting...

  • Page 51: Baseline Noise

    Autofocus failure or high voltage Check autofocus and high voltage power supply by means of the “Hardware power supply defective. Diagnostics” on page 29. If tests fail, contact Agilent Technologies at www.agilent.com/genomics/contact. Back to “Symptoms (DNA)” on page 37 Maintenance and Troubleshooting...

  • Page 52: Baseline Jumps

    Solution Vibration of 2100 Bioanalyzer Remove vibration devices, such as vortexers and vacuum pumps, from bench. instrument. Instrument lid was touched during the Do not touch the 2100 Bioanalyzer instrument during a run. run. Least probable causes Solution Laser defective.

  • Page 53: Wavy Baseline

    Ensure the humidity in the room is below 70% at 15 – 27 °C (59 – 81 °F). Least probable causes Solution Changes in ambient temperature of more Place the 2100 Bioanalyzer instrument in a thermally stable environment. than 5°C during the run. High voltage power supply defective. Check high voltage power supply using the “Overview”...

  • Page 54: Late Migration

    Troubleshooting the DNA Application Symptoms (DNA) Late Migration Most probable causes Solution Chip not properly primed. Clogged chip Prepare a new chip. Check chip priming station as described in “Checking the priming station or wrong priming Chip Priming Station for Proper Performance - Seal Test” on page 139.
  • Page 55 Replace vortex adapter as described in “Maintenance of the Vortexer” page 149. Changes in ambient temperature of Place the 2100 Bioanalyzer instrument in a thermally stable environment. more than 5°C during the run. Back to “Symptoms (DNA)” on page 37...

  • Page 56: Peak Tailing

    Troubleshooting the DNA Application Symptoms (DNA) Peak Tailing Most probable causes Solution Sample salt concentration is too high. Refer to the maximum sample buffer salt limits as specified in the Kit Guide. Dilute samples with deionized DNase free water, if necessary. Back to “Symptoms (DNA)”...

  • Page 57: Unexpected Run Time

    Troubleshooting the DNA Application Symptoms (DNA) Unexpected Run Time Unexpected Run Time Most probable causes Solution Lower and/or upper markers are called Turn off alignment and check which bands are the correct lower and upper incorrectly. markers. For more details, see “Manual Marker Assignment”...
  • Page 58 Troubleshooting the DNA Application Symptoms (DNA) Manual Marker Assignment 1 Turn alignment off . Check the gel-like image to identify which bands are the correct lower and upper markers. 2 Turn the alignment back on . Check the electropherogram of each sample.
  • Page 59 Troubleshooting the DNA Application Symptoms (DNA) 3 To adjust the lower marker, right click on the correct peak, and choose Manually Set Lower Marker. 4 To adjust the upper marker, right click on the correct peak, and choose Manually Set Upper Marker. Maintenance and Troubleshooting...
  • Page 60 Troubleshooting the DNA Application Symptoms (DNA) The data is properly aligned after the markers are called correctly. Maintenance and Troubleshooting...

  • Page 61: Error Message: No Data Received Since 5 Seconds

    Ensure the Agilent USB-Serial Adapter cable, black cable (5188-8031) for 2100 Expert Software version B.02.08 and greater is used to connect the 2100 Bioanalyzer instrument to the computer through a USB port. See “USB to Serial Adapter”...

  • Page 62: Symptoms (High Sensitivity Dna)

    Troubleshooting the DNA Application Symptoms (High Sensitivity DNA) Symptoms (High Sensitivity DNA) Follow protocols appropriate for the Next Generation Sequencing or targeted-enrichment N O T E system used. Additional inquiries should be directed to the manufacturer of those products. Click to go straight to the troubleshooting hints. •...

  • Page 63: Artefact Peaks

    Troubleshooting the DNA Application Symptoms (High Sensitivity DNA) Artefact Peaks Most probable causes Solution Samples are in water. Refer to the Kit Guide for sample buffer specifications. For optimal results, samples should be dissolved in 10 mM Tris and 1 mM EDTA. Probable causes Solution Chip, gel-dye mix, or samples are...

  • Page 64: Split Peaks

    Troubleshooting the DNA Application Symptoms (High Sensitivity DNA) Split Peaks Most probable causes Solution Sample concentration is too high. Prepare a new chip. Follow guidelines in the Kit Guide for the amount of sample to be loaded. Back to “Symptoms (High Sensitivity DNA)” on page 62 Maintenance and Troubleshooting...

  • Page 65: Baseline Negative Dips

    Troubleshooting the DNA Application Symptoms (High Sensitivity DNA) Baseline Negative Dips Most probable causes Solution Residual RNase ZAP and/or SDS Only use RNaseZAP when decontaminating the contamination on the electrode pins. pins according to “How to Clean the Pin Set of the Electrode Cartridge”...
  • Page 66 Troubleshooting the DNA Application Symptoms (High Sensitivity DNA) Maintenance and Troubleshooting...

  • Page 67: Troubleshooting The Rna Application

    Additional Sample or Ladder Peaks Additional Saturating Bands Degraded RNA Ladder and/or Samples Spikes Low Signal Intensity Baseline Noise Broad Peaks Missing Peaks Missing RNA Fragment Wavy Baseline Late Migration Error Message: No data received since 5 seconds Agilent Technologies...

  • Page 68: Overview

    Select the Log Book tab in the Data and Assay context. The Run Log lists all the actions and errors that occurred during the run. In rare cases, results generated by the 2100 Bioanalyzer system might not be as expected. To help find the reason for the discrepancy, see “Symptoms...

  • Page 69: Symptoms (Rna)

    Troubleshooting the RNA Application Symptoms (RNA) Symptoms (RNA) Click to go straight to the troubleshooting hints. • “Residual Gel in Spin Filter after Centrifugation” on page 70 • “Too High Quantitation Results” on page 70 • “Too Low Quantitation Results” on page 71 •...

  • Page 70: Residual Gel In Spin Filter After Centrifugation

    Troubleshooting the RNA Application Symptoms (RNA) Residual Gel in Spin Filter after Centrifugation Most probable causes Solution Gel was filtered at insufficient g-value. Refer to the Kit Guide for proper centrifuge settings. Cooled centrifuge was used for gel Repeat centrifugation step at room temperature. filtration.

  • Page 71: Too Low Quantitation Results

    Troubleshooting the RNA Application Symptoms (RNA) Too Low Quantitation Results Most probable causes Solution Reference measurement (e.g. UV Purify sample prior to measurement. absorption) was elevated due to contaminants in sample. Pipetting error during preparation of Use appropriate calibrated pipette and tips. ladder, samples, or reagent mixes.

  • Page 72: Chip Not Detected

    Least probable causes Solution High voltage power supply defective. Check high voltage power supply using the “Overview” on page 30. If the power supply is defective, contact Agilent Technologies at www.agilent.com/genomics/contact. Back to “Symptoms (RNA)” on page 69 Maintenance and Troubleshooting...
  • Page 73 30 minutes prior to use. Store chips at room temperature. Least probable causes Solution High voltage power supply defective. Check high voltage power supply using the “Overview” on page 30. If the power supply is defective, contact Agilent Technologies at www.agilent.com/genomics/contact. Maintenance and Troubleshooting...

  • Page 74: Additional Sample Or Ladder Peaks

    After centrifugation, the freshly prepared gel-dye mix should be taken up from the top of the tube. Vibration of 2100 Bioanalyzer Do not touch the 2100 Bioanalyzer instrument during a run. instrument Remove vibration devices, such as vortexers and vacuum pumps, from the bench.
  • Page 75 Troubleshooting the RNA Application Symptoms (RNA) Additional Saturating Bands Only present in RNA 6000 Pico or Small RNA assays. N O T E Most probable causes Solution Residual RNaseZAP on electrode pins. A dedicated electrode cassette for the use of RNA 6000 Pico and Small RNA assays.
  • Page 76 Troubleshooting the RNA Application Symptoms (RNA) Degraded RNA Ladder and/or Samples Most probable causes Solution RNase contamination of the pin set. Decontaminate pin set. Follow decontamination procedure, see “How to Clean the Pin Set of the Electrode Cartridge” on page 126. Decontaminate pipettes and work space.

  • Page 77: Spikes

    Symptoms (RNA) Spikes Most probable causes Solution Vibration of 2100 Bioanalyzer Do not touch the 2100 Bioanalyzer instrument during a run. instrument. Remove vibration devices, such as vortexers and vacuum pumps, from the bench. Particles in tubes. For reagent preparation, use tubes that are supplied with the kit. Do not use autoclaved tubes.

  • Page 78: Low Signal Intensity

    Vortex chip for 1 minute. Only use IKA vortexer. Adjust speed to set-point . Least probable causes Solution Autofocus or laser failure. Check autofocus and laser using the “Overview” on page 30. If laser stability diagnostic tests fail, contact Agilent Technologies at www.agilent.com/genomics/contact. Back to “Symptoms (RNA)” on page 69 Maintenance and Troubleshooting...
  • Page 79 Clean the electrodes. Load the chip immediately after taking it out of its sealed bag. Vibration of 2100 Bioanalyzer Do not touch the 2100 Bioanalyzer instrument during a run. instrument. Remove vibration devices, such as vortexers and vacuum pumps, from the bench.
  • Page 80 Troubleshooting the RNA Application Symptoms (RNA) Broad Peaks Most probable causes Solution Sample contaminated with genomic Check RNA isolation protocol. To remove genomic DNA, perform DNase DNA. treatment. Leak currents due to contaminated pin Clean the pin set of the electrode cartridge. Follow cleaning procedure, see “How set.

  • Page 81: Missing Peaks

    Laser broken. Perform Laser, optics, and autofocus tests as described in “Hardware Diagnostics” on page 29. If tests fail, contact Agilent Technologies at www.agilent.com/genomics/contact. Autofocus failure or high voltage Check autofocus and high voltage power supply by means of the “Hardware...
  • Page 82 Troubleshooting the RNA Application Symptoms (RNA) Missing RNA Fragment Most probable causes Solution Sample salt concentration is too high. Refer to the maximum sample buffer salt limits as specified in the Kit Guide. Dilute samples with deionized RNase free water, if necessary, Probable causes Solution RNase contamination of electrodes or...
  • Page 83 Troubleshooting the RNA Application Symptoms (RNA) Wavy Baseline Most probable causes Solution Contamination with genomic DNA. Check RNA isolation protocol. To remove genomic DNA, perform DNase treatment. Leak currents due to contaminated Clean the electrode cartridge as described in “How to Clean the Pin Set of the electrodes.
  • Page 84 Symptoms (RNA) Least probable causes Solution Changes in ambient temperature of Place the 2100 Bioanalyzer instrument in a thermally stable environment. more than 5°C during the run. Autofocus failure or high voltage Check autofocus and high voltage power using the “Overview”...

  • Page 85: Troubleshooting The Dna Application

    Troubleshooting the RNA Application Symptoms (RNA) Late Migration Most probable causes Solution Chip not properly primed. Clogged chip Check chip priming station as described in “Checking the Chip Priming Station priming station or wrong priming for Proper Performance - Seal Test” on page 139.

  • Page 86: Symptoms (Rna)

    Ensure the Agilent USB-Serial Adapter cable, black cable (5188-8031) for 2100 Expert Software version B.02.08 and greater is used to connect the 2100 Bioanalyzer instrument to the computer through a USB port. See “USB to Serial Adapter”...

  • Page 87: Troubleshooting The Protein Application

    Low Signal Intensity Low Ladder Peaks Broad Peaks Baseline Dips Late Migration Error Message: No data received since 5 seconds Symptoms (High Sensitivity Protein) Saturation of Lower Marker or Sample Peaks – Optical Signal too High Low Signal Intensity Agilent Technologies...

  • Page 88: Overview

    Run Log for the data file. Select the Log Book tab in the Data and Assay context. The Run Log lists all the actions and errors that occurred during the run. In rare cases, results generated by the 2100 Bioanalyzer system might not be as expected. To help find the reason for the discrepancy, see “Symptoms...

  • Page 89: Symptoms (Protein)

    Troubleshooting the Protein Application Symptoms (Protein) Symptoms (Protein) Click to go straight to the troubleshooting hints. • “Residual Gel in Spin Filter after Centrifugation” on page 90 • “Too High Quantitation Results” on page 90 • “Too Low Quantitation Results” on page 91 •...

  • Page 90: Residual Gel In Spin Filter After Centrifugation

    Troubleshooting the Protein Application Symptoms (Protein) Residual Gel in Spin Filter after Centrifugation Most probable causes Solution Gel was filtered at insufficient g-value. Refer to the Kit Guide for proper centrifuge settings. Cooled centrifuge was used for gel Repeat centrifugation step at room temperature. filtration.

  • Page 91: Too Low Quantitation Results

    Troubleshooting the Protein Application Symptoms (Protein) Too Low Quantitation Results Most probable causes Solution Alignment of upper marker not set Manually set upper marker. Follow instructions for “Manual Marker properly. Assignment” on page 96. Pipetting error during preparation of Refer to the Kit Guide for proper preparation of reagents. reagent mixes or chip.
  • Page 92 Troubleshooting the Protein Application Symptoms (Protein) Wrong Sizing Result Most probable causes Solution Incorrect assignment of ladder peaks. Check assignment of ladder peaks. For details, please refer to the Online Help or Users Guide. Incorrect assignment of upper and/or Store sample buffer and denaturing solution according to the instructions given lower marker.

  • Page 93: Chip Not Detected

    Least probable causes Solution High voltage power supply defective. Check high voltage power supply using the “Overview” on page 30. If the power supply is defective, contact Agilent Technologies at www.agilent.com/genomics/contact. Back to “Symptoms (Protein)” on page 89 Maintenance and Troubleshooting...

  • Page 94: Run Aborted

    30 minutes prior to use. Store chips at room temperature. Least probable causes Solution High voltage power supply Check high voltage power supply using the “Overview” on page 30. If the power defective. supply is defective, contact Agilent Technologies at www.agilent.com/genomics/contact. Maintenance and Troubleshooting...
  • Page 95 Troubleshooting the Protein Application Symptoms (Protein) Unexpected Run Time Unexpected Run Time Most probable causes Solution Lower and/or upper markers are called Turn off alignment and check which bands are the correct lower and upper incorrectly. markers. For more details see “Manual Marker Assignment”...
  • Page 96 Troubleshooting the Protein Application Symptoms (Protein) Manual Marker Assignment 1 Turn alignment off . Check the gel-like image to identify which bands are the correct lower and upper markers. 2 Turn the alignment back on . Check the electropherogram of each sample.
  • Page 97 Troubleshooting the Protein Application Symptoms (Protein) 3 To adjust the lower marker, right click on the correct peak, and choose Manually Set Lower Marker. 4 To adjust the upper marker, right click on the correct peak, and choose Manually Set Upper Marker. The data is properly aligned after the markers are called correctly.
  • Page 98 Troubleshooting the Protein Application Symptoms (Protein) Maintenance and Troubleshooting...

  • Page 99: Additional Sample Or Ladder Peaks

    Troubleshooting the Protein Application Symptoms (Protein) Additional Sample or Ladder Peaks Most probable causes Solution Sample or ladder not denatured properly. Prepare fresh sample aliquot. Heat sample or denaturing solution and ladder for 5 minutes at 100°C Improper tubes used for denaturing samples. Use 0.5 mL tubes for denaturing sample or denaturing solution.
  • Page 100 After centrifugation, the gel-dye mix should be taken up from the top of the tube. Vibration of 2100 Bioanalyzer instrument. Do not touch the 2100 Bioanalyzer instrument during a run. Remove vibration devices, such as vortexers and vacuum pumps, from bench.
  • Page 101 Troubleshooting the Protein Application Symptoms (Protein) Missing Upper Marker Most probable causes Solution Upper marker was called incorrectly. Check upper marker assignment. Follow instructions for “Manual Marker Assignment” on page 96. Improper preparation of sample buffer Refer to the Kit Guide for instructions on storage and preparation of the sample or denaturing solution.
  • Page 102 Troubleshooting the Protein Application Symptoms (Protein) Broad Variability of the Lower Marker If the lower marker is detected, the assay performance is not affected by lower marker or N O T E system peak variability. Most probable causes Solution Buffer components of the sample , e.g. Ionic strength of the sample buffer may affect the lower marker intensity.
  • Page 103 Agilent Technologies at www.agilent.com/genomics/contact. High voltage power supply defective. Check high voltage stability using the “Overview” on page 30. If the high voltage stability test fails, contact Agilent Technologies at www.agilent.com/genomics/contact. Back to “Symptoms (Protein)” on page 89 Maintenance and Troubleshooting...

  • Page 104: Spikes

    Protect the dye from light during this time. Probable Causes Solution Vibration of 2100 Bioanalyzer Do not touch the 2100 Bioanalyzer instrument during a run. instrument. Remove vibration devices, such as vortexers and vacuum pumps, from the bench.
  • Page 105 Troubleshooting the Protein Application Symptoms (Protein) Poor Reproducibility Most probable causes Solution Wrong peak alignment. Check lower and upper marker assignment. Follow instructions for “Manual Marker Assignment” on page 96. Improper denaturation of sample(s). Use fresh sample aliquot. Heat samples with denaturing solution for 5 minutes at 100°C Use 0.5 mL tubes for denaturing samples.

  • Page 106: Low Signal Intensity

    Troubleshooting the Protein Application Symptoms (Protein) Low Signal Intensity Most Probable Causes Solution Protein concentration is too low. Follow specifications given in the Kit Guide. Sample salt concentration is too Salt concentration strongly affects the sensitivity of the assay. If necessary dilute, high.
  • Page 107 Troubleshooting the Protein Application Symptoms (Protein) Low Ladder Peaks Most probable causes Solution Ladder degraded. Refer to the Kit Guide for proper ladder storage. Optional: Prepare ladder aliquots and use a new aliquot. Ladder not diluted after denaturing. Refer to Kit Guide for proper chip preparation. Probable causes Solution Improper denaturation of ladder.

  • Page 108: Broad Peaks

    Troubleshooting the Protein Application Symptoms (Protein) Broad Peaks Most probable causes Solution Lower and/or upper markers are called Turn off alignment and check which bands are the correct lower and upper incorrectly. markers. For more details see “Manual Marker Assignment” on page 96.
  • Page 109 Troubleshooting the Protein Application Symptoms (Protein) Baseline Dips If the lower marker is detected, the assay performance is not affected by dips. N O T E Most probable causes Solution Sample contains additional detergents See Kit Guide for a list of compatible buffers and buffer compounds. For an and dyes.

  • Page 110: Late Migration

    Least probable causes Solution Defective heater plate. Run the temperature test by using the “Overview” on page 30. If the heater plate is defective, contact Agilent Technologies at www.agilent.com/genomics/contact. Back to “Symptoms (Protein)” on page 89 Maintenance and Troubleshooting...
  • Page 111 Ensure the Agilent USB-Serial Adapter cable, black cable (5188-8031) for 2100 Expert Software version B.02.08 and greater is used to connect the 2100 Bioanalyzer instrument to the computer through a USB port. See “USB to Serial Adapter”...

  • Page 112: Symptoms (High Sensitivity Protein)

    Troubleshooting the Protein Application Symptoms (High Sensitivity Protein) Symptoms (High Sensitivity Protein) Click to go straight to the troubleshooting hints. • “Saturation of Lower Marker or Sample Peaks – Optical Signal too High” on page 113 • “Low Signal Intensity” on page 114 Maintenance and Troubleshooting...
  • Page 113 Troubleshooting the Protein Application Symptoms (High Sensitivity Protein) Saturation of Lower Marker or Sample Peaks – Optical Signal too High Most probable causes Solution Insufficient dilution of Follow instructions in the Kit Guide. Dilution of the labeling reaction by 1:200 is recommended. ladder or samples.
  • Page 114 Troubleshooting the Protein Application Symptoms (High Sensitivity Protein) Low Signal Intensity Most probable causes Solution Insufficient labeling of ladder or Follow instructions in the Kit Guide. samples. Labeling occurs between pH 8-9. Proteins must contain lysines for labeling reaction. Check buffer compatibility in the “Compatibility List for the Labeling Reaction” in the Kit Guide.

  • Page 115: Maintenance Of The Electrode Cartridge

    Cleaning the Electrodes before each RNA Pico or Small RNA Assay Cleaning the Electrodes after each RNA Pico or Small RNA Assay RNase Decontamination of the Pin Set How to Clean the Pin Set of the Electrode Cartridge Agilent Technologies...

  • Page 116: Overview

    Maintenance of the Electrode Cartridge Overview Overview The cleaning procedure of the electrode cartridge depends on the assay that is run on the 2100 Bioanalyzer system. For details see “How to Clean the Pin Set of the Electrode Cartridge” on page 126.

  • Page 117: Dna And Protein Assays

    Maintenance of the Electrode Cartridge DNA and Protein Assays DNA and Protein Assays Assay Before each run After each run Monthly or after liquid spill: Pin set cleaning DNA and Optional: Electrode cleaner: With brush: Protein Electrode cleaner: • deionized H O for 10 seconds.

  • Page 118: Cleaning The Electrodes After Each Dna And Protein Assays

    1 Slowly fill one of the wells of the electrode cleaner with 350 μL deionized analysis-grade water. 2 Open the lid and place electrode cleaner in the 2100 Bioanalyzer instrument. 3 Close the lid and leave it closed for about 10 seconds.

  • Page 119: Rna Nano Assay

    Maintenance of the Electrode Cartridge RNA Nano Assay RNA Nano Assay Assay Before each run After each run Monthly or after liquid spill: Pin set cleaning RNA Nano Electrode cleaner: Electrode cleaner: RNase decontamination with • RNase ZAP for 60 seconds. •...

  • Page 120: Cleaning The Electrodes Before Each Rna Nano Assay

    Never fill more than 350 µL of water in the electrode cleaner. 1 Slowly fill one of the wells of an electrode cleaner with 350 μL RNaseZAP. 2 Open the lid and place electrode cleaner in the 2100 Bioanalyzer instrument.

  • Page 121: Cleaning The Electrodes After Each Rna Nano Assay

    RNA Nano Assay Cleaning the Electrodes after each RNA Nano Assay When the assay is complete, immediately remove the used chip from the 2100 Bioanalyzer instrument and dispose of it according to good laboratory practice. Then perform the following procedure to ensure that the electrodes are clean and no residues are left over from the previous assay.

  • Page 122: Rnase Decontamination Of The Pin Set

    Maintenance of the Electrode Cartridge RNA Nano Assay RNase Decontamination of the Pin Set When the pin set of the electrode cartridge is suspected to be contaminated with RNases follow the instructions described in “How to Clean the Pin Set of the Electrode Cartridge”...

  • Page 123: Rna Pico Or Small Rna Assay

    Maintenance of the Electrode Cartridge RNA Pico or Small RNA Assay RNA Pico or Small RNA Assay Assay Before each run After each run Monthly or after liquid spill: pin set cleaning RNA Pico or Electrode cleaner: Electrode cleaner: RNase decontamination with Small RNA •...

  • Page 124: Cleaning The Electrodes Before Each Rna Pico Or Small Rna Assay

    1 Slowly fill one of the wells of an electrode cleaner with 350 μL RNase-free water. 2 Open the lid and place electrode cleaner in the 2100 Bioanalyzer instrument. 3 Close the lid and leave it closed for 5 minutes.

  • Page 125: Cleaning The Electrodes After Each Rna Pico Or Small Rna Assay

    RNA Pico or Small RNA Assay Cleaning the Electrodes after each RNA Pico or Small RNA Assay When the assay is complete, immediately remove the used chip out of the 2100 Bioanalyzer instrument and dispose of it according to good laboratory practice.

  • Page 126: How To Clean The Pin Set Of The Electrode Cartridge

    Do not touch the electrodes while the cartridge is in the 2100 Bioanalyzer instrument, this could damage the electrodes and high voltage power supply. 1 Turn off line power to the 2100 Bioanalyzer instrument. The line switch is located at the rear of the instrument.
  • Page 127 Maintenance of the Electrode Cartridge How to Clean the Pin Set of the Electrode Cartridge 2 Open the lid and pull the metal lever on the inside left of the lid to the vertical position as shown in Figure 1 on page 127.
  • Page 128 Maintenance of the Electrode Cartridge How to Clean the Pin Set of the Electrode Cartridge 4 Open the bayonet socket of the pin set by turning the plastic lever to the left, see Figure 2 on page 128. Plastic lever Bayonet socket Figure 2 Bayonet socket of the electrode pin set...
  • Page 129 Maintenance of the Electrode Cartridge How to Clean the Pin Set of the Electrode Cartridge 5 Remove the cover of the bayonet socket by gently pulling the plastic lever. The pin set may stick to the electrode base. Remove it by carefully pulling it off, see Figure 3 on page 129.
  • Page 130 11 Lock the pin set to the electrode base by turning the plastic lever of the bayonet cover to the right, see Figure 2 on page 128. 12 Slide the electrode cartridge with the pin set into the 2100 Bioanalyzer instrument lid as shown in Figure 1 on page 127 and move the metal lever to the flat (closed) position.

  • Page 131: Maintenance Of The Chip Priming Station

    Maintenance and Troubleshooting Maintenance of the Chip Priming Station Overview Replacing the Syringe Cleaning the Syringe Adapter Replacing the Syringe Adapter Replacing the Gasket Checking the Chip Priming Station for Proper Performance - Seal Test Agilent Technologies...

  • Page 132: Overview

    Maintenance of the Chip Priming Station Overview Overview Regular cleaning procedures are necessary to maintain the performance of the chip priming station. The table below gives an overview on the different maintenance procedures. Procedure Time interval Or if... Replacing the syringe With each new kit ...syringe is broken, see “Replacing the...

  • Page 133: Replacing The Syringe

    Maintenance of the Chip Priming Station Replacing the Syringe Replacing the Syringe When Quarterly or whenever it is clogged. Parts required Description Syringe kit that comes with each DNA, RNA and Protein kit Deionized water 1 Unscrew the old syringe from the top of the chip priming station. 2 Remove clip from the old syringe.

  • Page 134: Cleaning The Syringe Adapter

    Maintenance of the Chip Priming Station Cleaning the Syringe Adapter Cleaning the Syringe Adapter When Quarterly or whenever it is clogged. Parts required Description Syringe kit that comes with each DNA, RNA and Protein kit Deionized water 1 Open the priming station. 2 Move the mounting ring holding the adapter in place to the left as shown in Figure 4 on page 134.
  • Page 135 Maintenance of the Chip Priming Station Cleaning the Syringe Adapter 3 Press the syringe adapter out of its mount as shown in Figure 5 on page 135. Figure 5 Removing/replacing the syringe adapter 4 Remove dried gel at the opening of the adapter with a needle. 5 Screw on syringe and flush water through the adapter several times.

  • Page 136: Replacing The Syringe Adapter

    Maintenance of the Chip Priming Station Replacing the Syringe Adapter Replacing the Syringe Adapter When If significantly clogged and unable to clean thoroughly. Parts required Description G2938-68716 Gasket kit 1 Follow the steps described in “Cleaning the Syringe Adapter” on page 134 to remove the syringe adapter.

  • Page 137: Replacing The Gasket

    Maintenance of the Chip Priming Station Replacing the Gasket Replacing the Gasket The silicone gasket, see Figure 6 on page 137, ensures a tight connetion between the chip and syringe adapter. Gasket Syringe adapter Figure 6 Syringe adapter with gasket When Quarterly or when it is torn.
  • Page 138 Maintenance of the Chip Priming Station Replacing the Gasket 2 Pull out the old silicone gasket with your fingers or tweezers. See Figure 7 on page 138 for a disassembled adapter. Figure 7 Syringe adapter with disassembled gasket 3 Insert a new silicone gasket and gently push into place. 4 Insert the syringe adapter into the chip priming station as described in “Replacing the Syringe Adapter”...

  • Page 139: Checking The Chip Priming Station For Proper Performance - Seal Test

    Maintenance of the Chip Priming Station Checking the Chip Priming Station for Proper Performance - Seal Test Checking the Chip Priming Station for Proper Performance - Seal Test When Every month or whenever a component of the priming station (syringe, adapter or gasket) was replaced.
  • Page 140 Maintenance of the Chip Priming Station Checking the Chip Priming Station for Proper Performance - Seal Test 6 Wait for 5 seconds and lower latch of the clip to release the plunger as shown in Figure 9 on page 140. Syringe clip Lower latch Figure 9...

  • Page 141: Maintenance Of The Agilent 2100 Bioanalyzer Instrument

    Maintenance and Troubleshooting Maintenance of the Agilent 2100 Bioanalyzer instrument Overview Cleaning the Lens Changing the Fuses Agilent Technologies...

  • Page 142: Overview

    The 2100 Bioanalyzer instrument should be kept clean. Cleaning should be done with a damp lint-free cloth. Do not use an excessively damp cloth allowing liquid to drip into the 2100 Bioanalyzer instrument.

  • Page 143: Cleaning The Lens

    Description Reagent-grade isopropanol Lens tissue 1 Switch off the instrument. The line switch is located at the rear of the 2100 Bioanalyzer instrument. 2 Open the lid of the instrument. 3 Dampen a lens tissue with isopropanol and gently swab the surface of the lens.

  • Page 144: Changing The Fuses

    C AU T I O N ➔ Use Agilent recommended fuses only. 1 Switch off the instrument. The line switch is located at the rear of the 2100 Bioanalyzer instrument. 2 Disconnect the power cable from the power input socket.
  • Page 145 Maintenance of the Agilent 2100 Bioanalyzer instrument Changing the Fuses 3 To access the fuse drawer, gently lift the outer plastic housing of the power inlet socket using a screw driver, see Figure 10 on page 145. Figure 10 Remove power inlet housing...
  • Page 146 Maintenance of the Agilent 2100 Bioanalyzer instrument Changing the Fuses 5 Replace the two fuses. Perform this procedure with care. N O T E 6 Slide in the fuse drawer and push till it fits tightly as shown in Figure 12 page 146.
  • Page 147 Maintenance of the Agilent 2100 Bioanalyzer instrument Changing the Fuses 7 Close the fuse drawer housing (see Figure 13 on page 147), reconnect the instrument to the power line and switch it on. Figure 13 Close fuse drawer housing Maintenance and Troubleshooting...
  • Page 148 Maintenance of the Agilent 2100 Bioanalyzer instrument Changing the Fuses Maintenance and Troubleshooting...
  • Page 149 Maintenance and Troubleshooting Maintenance of the Vortexer Changing the Adapter Agilent Technologies...

  • Page 150: Maintenance Of The Vortexer Changing The Adapter

    Maintenance of the Vortexer Changing the Adapter Changing the Adapter When Whenever the vortex adapter is damaged. Tools required Description Screw driver Parts required Description 5065-9966 IKA vortex mixer adapter (for MS 2 vortexers) IKA 3617036 IKA vortex mixer adapter (for MS 3 vortexers) NOTE: This part must be purchased directly from IKA.

  • Page 151: Spare Parts And Accessories

    Maintenance and Troubleshooting Spare Parts and Accessories Overview Agilent Technologies...

  • Page 152: Overview

    Overview Overview “Overview” on page 152 provides a list of spare parts and accessories that are available for the 2100 Bioanalyzer system. To buy parts, please refer to the Agilent Online Store: www.agilent.com/genomics/bioanalyzer Reorder number Part Description 5185-5990 Filters for gel matrix Extra filters for gel matrix.
  • Page 153 Index Index chips gel-dye 2100 expert software degraded RNA demo port reagents diagnostic test samples additional peaks hardware diagnostics symptoms head adapter troubleshooting protein high sensitivity DNA high sensitivity protein artefact peaks high sensitivity DNA electrode cartridge electrode cleaner installation qualification...
  • Page 154 Index reproducibility protein protein mounting ring RNA fragment split peaks high sensitivity DNA RNA pico status indicator next generation sequencing symptoms syringe adapter 134, 136, troubleshooting syringe clip RNAse contamination 122, syringe optical signal RS232 cable protein run aborted 41, 73, run log test chips run time...
  • Page 155 Spare Parts and Accessories Index Maintenance and Troubleshooting...
  • Page 156 This manual is based on the 2100 Expert Software revision B.02.08. Other software revisions may have an impact on results. ©...

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