SCIEX C100HT Operator's Manual
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SCIEX C100HT Operator's Manual

SCIEX C100HT Operator's Manual

Biologics analyzer system
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C100
Biologics Analyzer System
HT
Operator Guide
RUO-IDV-05-3828-A
June 2018

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Summary of Contents for SCIEX C100HT

  • Page 1 C100 Biologics Analyzer System Operator Guide RUO-IDV-05-3828-A June 2018...
  • Page 2 SCIEX warranties are limited to those express warranties provided at the time of sale or license of its products and are SCIEX s sole and exclusive representations, warranties, and obligations.

  • Page 3: Table Of Contents

    Contents 1 Operational Precautions and Limitations....................6 General Safety Information..............................6 Regulatory Compliance..............................6 Australia and New Zealand............................6 Canada..................................7 Europe..................................7 United States................................7 International................................8 Electrical Precautions.................................8 AC Mains Supply................................8 Protective Earth Conductor............................9 Chemical Precautions.................................9 Environmental Precautions..............................10 Electromagnetic Environment............................10 Decommissioning and Disposal..........................11 Equipment Use and Modification.............................11 Qualified Personnel................................12 Contact Us..................................12 Technical Support................................12...
  • Page 4 Manually Integrate the Data............................60 View Reports..................................64 View the Data Report..............................64 View the Plate Report..............................67 Analyze the Data Manually..............................70 Analyze the Data from the C100HT Software......................70 Open a Plate................................71 7 Routine Maintenance..........................73 Clean the Surfaces................................73 Replace the Fuse................................73 Test the Detector................................74 Test the Filter...................................74...
  • Page 5 Controller and Monitor Specifications..........................91 B Reagents and Accessories........................93 Order Parts..................................93 Reagents and Accessories..............................93 C100HT Glycan Labeling and Analysis Kit........................93 C Hazardous Substance Information.......................95 D Start a Run as a Routine User.......................97 E Additional Functions in the Data Trace Tab..................103 New Trace Properties Dialog............................103 Open Data File Dialog..............................104...

  • Page 6: Operational Precautions And Limitations

    Operational Precautions and Limitations Note: Before operating the system, carefully read all of the sections of this guide. This section contains general safety-related information and provides regulatory compliance information. It also describes potential hazards and associated warnings for the system and the precautions that should be taken to minimize the hazards.

  • Page 7: Canada

    Operational Precautions and Limitations Canada • Electromagnetic Interference (EMI): CAN/CSA CISPR11. This ISM device complies with Canadian ICES-001. Refer to Electromagnetic Interference. • Safety: • CAN/CSA C22.2 No. 61010-1 • CAN/CSA 222.2 No. 60101-2-081 Europe • Electromagnetic Compatibility (EMC): Electromagnetic Compatibility directive 2014/30/EU as implemented in these standards: •...

  • Page 8: International

    The covers need not be removed for routine maintenance, inspection, or adjustment. Contact a SCIEX Field Service Employee (FSE) for repairs that require the covers to be removed. • Follow required electrical safe work practices.

  • Page 9: Protective Earth Conductor

    • Determine which chemicals have been used in the system prior to service and regular maintenance. Refer to the Safety Data Sheets for the health and safety precautions that must be followed with chemicals. SCIEX Safety Data Sheets can be found at sciex.com/tech-regulatory.

  • Page 10: Environmental Precautions

    Operational Precautions and Limitations Environmental Precautions Use qualified personnel for the installation of electrical mains, heating, ventilation, and plumbing supplies and fixtures. Make sure that all of the installations comply with local bylaws and biohazard regulations. For information about the required environmental conditions for the system, refer to the Site Planning Guide. Allow access space around the equipment when setting up the system.

  • Page 11: Decommissioning And Disposal

    When removing the system from service, separate and recycle different materials according to national and local environmental regulations. Note: SCIEX will not accept any system returns without a completed Decontamination Form. Contact an FSE to obtain a copy of the form.

  • Page 12: Qualified Personnel

    Qualified Personnel Only qualified SCIEX personnel shall install, inspect, and service the equipment. After installing the system, the Field Service Employee (FSE) uses the Installation Qualification to orient the customer on system operation, cleaning, and basic maintenance.

  • Page 13: Documentation Symbols And Conventions

    Operational Precautions and Limitations Documentation Symbols and Conventions The following symbols and conventions are used throughout the guide. DANGER! Danger signifies an action which leads to severe injury or death. WARNING! Warning signifies an action that could cause personal injury if precautions are not followed.

  • Page 14: Introduction

    The system includes the following components: • The C100 Biologics Analyzer capillary electrophoresis system • A SCIEX-supplied controller consisting of a computer and a monitor. Pre-installed on the controller are: • C100 software • DataReviewer software...

  • Page 15: Hardware Overview

    Introduction Hardware Overview Figure 2-1 Front and Side Panel Item Description Service door Cartridge door Sample door LED power indicator; green when the system is on, blue when it is off. Operator Guide C100 Biologics Analyzer System RUO-IDV-05-3828-A 15 / 122...
  • Page 16 Introduction Figure 2-2 Back Panel Item Description Name plate FCC Compliance label Waste Electrical and Electronic Equipment label No User-serviceable Parts label For Research Use only label RoHS label RS-232 connector Voltage switch Power switch, mains supply connection, and fuse holder High Voltage label C100 Biologics Analyzer System...

  • Page 17: Cartridge

    Introduction Cartridge Note: Always allow the cartridge to stand in the cartridge stand at room temperature for at least 20 minutes before use. Figure 2-3 Cartridge in Cartridge Stand Item Description Gel reservoir Cartridge purge port Cartridge data key Capillary windows Cartridge stand Operator Guide C100...

  • Page 18: Theory Of Operation

    Introduction Theory of Operation The C100 Biologics Analyzer system uses capillary electrophoresis to enable high resolution and sensitive separation of glycan samples. This 12-channel capillary electrophoresis instrument uses multiple-use cartridges for cost-effective analysis of up to 96 samples in as little as 2 hours and 50 minutes. The cartridge can be used for 1000 separations.

  • Page 19: Prepare The Samples

    Prepare the Samples Safety Refer to the Safety Data Sheets (SDS), available at sciex.com/tech-regulatory, for information about the proper handling of materials and reagents. Always follow standard laboratory safety guidelines. Overview The SCIEX C100 Glycan Labeling and Analysis kit provides reagents and supplies required to label, separate, and identify reducing carbohydrates for 1000 samples using the C100 Biologics Analyzer System.

  • Page 20: Equipment And Materials Required

    Prepare the Samples Equipment and Materials Required Note: Unless a manufacturer name is specified, part numbers are for items available from SCIEX. For information about the contents of the kit, refer to C100 Glycan Labeling and Analysis Kit. Customer-Supplied Equipment and Supplies •...

  • Page 21: Prepare The Reagents, Stock Solutions, And Master Mixes

    Prepare the Samples • Double-deionized (DDI) water (MS-grade water filtered through a 0.2 μm filter and with resistance above 18 M ) Prepare the Reagents, Stock Solutions, and Master Mixes Reconstitute the Bracketing Standard (BST-10) 1. Add 200 µL of DDI water to the BST-10 vial and then vortex for at least 20 sec to mix. 2.

  • Page 22: Prepare The Digestion Solution

    Prepare the Samples 1. Reconstitute the D1 reagent. a. Add 500 µL of DDI water to the D1 vial. b. Vortex the vial to mix. Each vial of D1 is enough for 500 samples. The reconstituted D1 reagent can be stored at 4 °C for up to 24 hours.

  • Page 23: Prepare The Labeling Solution

    Prepare the Samples Reagent For 1 Sample For up to 24 For up to 100 Samples Samples 12 µL 290 µL 1200 µL PNGase F enzyme 1 µL 25 µL 100 µL • From New England Biolabs 2 µL 50 µL 200 µL •...

  • Page 24: Denature The Proteins

    Prepare the Samples Reagent For 1 Sample For up to 24 For up to 100 Samples Samples Reconstituted IST 1 µL 25 µL 100 µL Double-deionized (DDI) water (MS-grade water 8 µL 192 µL 800 µL filtered through a 0.2 μm filter and with resistance above 18 M ) 3.

  • Page 25: Release And Label The N-Glycans

    Prepare the Samples 4. Add 100 µg of the glycoprotein sample (prepared in step 2) to each well of the 96-well plate, put the 96-well plate on the orbital shaker and then shake at 1500 rpm for 15 sec to 30 sec. Do not touch the beads with the pipette tip.

  • Page 26: Label The Released N-Glycans

    Prepare the Samples 6. Put the 96-well plate on a magnetic stand. After the beads are pulled to the side of the wells, use a pipette to slowly and carefully remove the supernatant from the bottom of the wells without touching the beads with the pipette tip.
  • Page 27 Prepare the Samples 2. Perform the second sample clean-up step. a. Using a multi-channel pipette, add 20 µL of DDI water to each well of the 96-well plate. b. Put the 96-well plate on the orbital shaker and then shake at 1000 rpm for 15 sec to 30 sec. c.

  • Page 28: Waste Disposal

    Prepare the Samples d. After the beads are pulled to the side of the wells, remove the supernatant from the bottom of each well by slowly and carefully pipetting from the bottom of the well and then transfer the supernatant to the 96-well plate provided with the C100 Glycan Labeling and Analysis kit.

  • Page 29: Normalize The Cartridge

    Normalize the Cartridge This option is available to all users except those with the Administrator User role. The cartridge should be normalized before use. If it is used on a different C100 Biologics Analyzer system, then it must be normalized on that system. Note: A new cartridge has five normalization runs.
  • Page 30 Normalize the Cartridge b. Put the tube strip in the CAL position in the buffer plate. Figure 4-1 Buffer Plate Item Description Location of buffer tray Notch for the buffer tray Location for the alignment marker Location for the calibration solution 4.
  • Page 31 13. Inspect the results in the table on the right. If any of the rows in the table say "Failed", then repeat the normalization. If the normalization fails a second time, then refer to Troubleshooting or contact sciex.com/request-support. Operator Guide C100 Biologics Analyzer System...
  • Page 32 14. Click Finish Normalization and then click Yes in the message. The results are saved in a file located in C:\ProgramData\SCIEX\C100HT\Data\CartridgeCalibrationData\Carbohydrate in the Carbohydrate folder. The file is named "cartridge-id_instrument-id.xcc", where "cartridge_id" is the ID of the current cartridge and "instrument_id"...

  • Page 33: The Normalization Tab Toolbar

    2. In Data View mode, click (Open) in the Experiments pane. 3. Navigate to the folder C:\ProgramData\SCIEX\C100HT\Data\CartridgeCalibrationData\Carbohydrate. 4. Click the file cartridge-id_instrument-id.xcc and then click Load. A message stating that a copy of the file will be created is shown.
  • Page 34 Normalize the Cartridge 6. As needed, review the data in the Gel Image and Electropherogram tabs. 7. (Optional) To save the normalization data to an experiment file, click (Save), type a file name, and then click Save. C100 Biologics Analyzer System Operator Guide 34 / 122 RUO-IDV-05-3828-A...

  • Page 35: Separate The Glycans

    Separate the Glycans Prepare the Buffer Plate Required Materials • C100 buffer tray • Reconstituted BST • Mineral oil • 12-well tube strips 1. Remove the buffer tray from the refrigerator and then allow it to stand at room temperature for at least 20 minutes before use.
  • Page 36 Separate the Glycans Figure 5-1 Buffer Plate Item Description Location of buffer tray Notch for the buffer tray Location for the alignment marker 4. Pull the foil cover off of the buffer tray and then put it in the buffer plate with the buffer tray tab aligned with the notch in the buffer plate.

  • Page 37: Load The Buffer Plate

    Separate the Glycans Figure 5-2 Buffer Tray 6. Turn the buffer tray so the tab is aligned with the notch on the front of the buffer plate and then put it in the buffer plate (item 2 in Figure 5-1). Figure 5-3 Buffer Tray End View with Tab Circled Load the Buffer Plate WARNING! Personal Injury Hazard.

  • Page 38: Install The Cartridge In The System

    Separate the Glycans Make sure to keep the tray level so the buffers do not spill. 6. (Optional) Put the samples in the sample tray. 7. Close the sample door and then click (Park) to move the buffer plate carrier to the back. After a few moments, the buffer plate carrier moves to the wash park position.
  • Page 39 Separate the Glycans Figure 5-4 Cartridge Status Panel 7. If the cartridge is new or has not been normalized in this system, then normalize it. Refer to Normalize the Cartridge. Note: If Perform normalization automatically is selected in the C100 software Settings, then the C100 software opens to the Normalization tab after the cartridge door is closed.

  • Page 40: Condition The Cartridge

    Separate the Glycans Condition the Cartridge Required Materials • Cartridge • C100 buffer tray Condition the cartridge once before running the first separation. 1. Install the cartridge. Refer to Install the Cartridge in the System. 2. Load the buffer plate. Refer to Load the Buffer Plate.

  • Page 41: Perform A Run

    Process profiles include the following information: • The rows in the sample plate that are to be run and the capillary electrophoresis method to be used. The capillary electrophoresis methods are provided by SCIEX and cannot be edited. • Alignment marker...

  • Page 42: Start A Run As A Basic Or Advanced User

    Separate the Glycans • Instructions for processing the results, saved as an export profile. Each user in the C100 software is assigned a user role which has different permissions. Depending on the user role of the logged-in user, the steps to perform a run are different. •...
  • Page 43 Separate the Glycans 5. Load the buffer plate, cartridge, and samples in the C100 Biologics Analyzer system. Load the Buffer Plate. Install the Cartridge in the System. c. If this is the first time the cartridge has been used, condition the cartridge. Refer to Condition the Cartridge.
  • Page 44 Separate the Glycans b. In the Sample Row Selection area, click to select the rows in the plate that contain the samples. Figure 5-10 Sample Row Selection Area The new rows are added at the bottom of the Method Details table. c.
  • Page 45 Separate the Glycans Figure 5-12 Method Details Tab 11. (Optional) Click Marker to view the marker associated with the process profile. CAUTION: Potential Wrong Result. The analysis requires the Carbohydrate alignment marker. Do not select a different alignment marker or the data analysis might fail. 12.
  • Page 46 Separate the Glycans Figure 5-13 Sample Selection Pane 14. Click Sample Information and add sample information by typing, by copying and pasting, or by importing a file. Figure 5-14 Sample Information Pane 15. (Advanced Users only) Save any changes to the profile. Click Save process profile as and then: •...
  • Page 47 Separate the Glycans a. Complete the tasks in the Please Confirm area and then select the corresponding check boxes. Figure 5-15 Please Confirm Area b. Resolve any issues listed in the Errors and Warnings area. Figure 5-16 Errors and Warnings Area c.
  • Page 48 Separate the Glycans Figure 5-17 Gel Image Tab After data for all of the samples has been acquired, the DataReviewer software automatically opens and then the data is processed. At the top of the DataReviewer software window is a banner showing the time remaining for the data processing.

  • Page 49: Analyze The Data And Review The Results

    Separate the Glycans Figure 5-18 DataReviewer Software Window Analyze the Data and Review the Results This is an outline of the steps to analyze and review the data. Refer to Review the Results with the DataReviewer Software for detailed instructions on any of the following steps. 1.
  • Page 50 Separate the Glycans Figure 5-19 Plate Image with All Wells Selected 2. Inspect the wells in the plate image. Image Meaning All of the glycans in the well meet the criteria in the qualification profile. One or more glycans in the well did not meet the criteria in the qualification profile.
  • Page 51 Separate the Glycans Image Meaning The well is selected. The well is assigned to the currently selected qualification profile. The well is empty. 3. Move the cursor over any well in the Plate pane to view the results for that well. The qualification profile and the data analysis results are shown in the lower part of the tooltip.

  • Page 52: Store The Cartridge

    8. Click (Save As), type a name, and then click Save to save the changes to the plate. By default, the plate is saved to a file in C:\ProgramData\SCIEX\DataReviewer\Plates. Store the Cartridge CAUTION: Potential System Damage. Do not store the cartridge below 2 °C. The cartridge might be damaged if it is stored at temperatures below 2 °C.

  • Page 53: Long-Term Storage

    Separate the Glycans • To store in the packaging, click (Disengage) to disengage the cartridge and then remove it from the C100 Biologics Analyzer system. Close the purge port with the seal, and then put the cartridge in the original packaging and store in the upright position. Long-Term Storage 1.

  • Page 54: Review The Results With The Datareviewer Software

    Review the Results with the DataReviewer Software Use the procedures in this section to review the results of the analysis. About the DataReviewer Software Matching Each well in the plate is marked as passed or failed based on the results of matching to the qualification profile. The DataReviewer software performs the following steps to assign pass or fail to each well: 1.

  • Page 55: Create A Qualification Profile

    (Save As), type a name, and then click Save to save the changes to the qualification profile. The qualification profile is saved to a file in C:\ProgramData\SCIEX\DataReviewer\Profiles. CAUTION: Potential Wrong Result. Do not save the qualification profile to a different folder or it will not be available for use in the DataReviewer software.

  • Page 56: View The Qualification Profile Assigned To A Well

    Review the Results with the DataReviewer Software To select... Click... The entire plate (Select Plate) A row The letter to the left of the row A column The number at the top of the column Individual wells Each well Tip! To select more than one row or column, click the letter or number for each additional row or column. 2.

  • Page 57: View The Data Trace For A Well

    Review the Results with the DataReviewer Software Figure 6-3 Qualification Profile All wells associated with the profile update in the Plate pane. Figure 6-4 Wells Associated with Profile View the Data Trace for a Well The Data Trace tab shows the electropherogram and allows the data to be inspected. 1.
  • Page 58 Review the Results with the DataReviewer Software To select... Click... A column The number at the top of the column Individual wells Each well Tip! To select more than one row or column, click the letter or number for each additional row or column. 2.

  • Page 59: Zoom And Scroll The Electropherogram

    Review the Results with the DataReviewer Software Figure 6-6 Electropherogram Zoom and Scroll the Electropherogram Additional functions are available from the right-click menu. Refer to Additional Functions in the Data Trace Tab. 1. (Optional) Drag a selection in the electropherogram to zoom in on the data. 2.

  • Page 60: Manually Integrate The Data

    Review the Results with the DataReviewer Software Manually Integrate the Data In the Data Trace tab, the data can be manually integrated, one well at a time. After the integration is acceptable, the well must be analyzed and the reports generated before the qualification profile can be applied. 1.
  • Page 61 Review the Results with the DataReviewer Software Note: If data analysis in the C100 software begins while the DataReviewer software is in Reanalysis mode, then the DataReviewer software puts the Qualification tab to the front. If this occurs, wait until the data processing is finished, and then click the Data Trace tab to continue with the analysis.
  • Page 62 Review the Results with the DataReviewer Software 9. (Optional) To view a table with the original integration events, press F3. Figure 6-9 Integration Events Table 10. (Optional) To view a table with the added integration events, press Alt-D and then type i. Figure 6-10 Manual Integration Fixes Table 11.
  • Page 63 14. Click (Save As), type a name, and then click Save to save the changes to the plate. By default, the plate is saved to a file in C:\ProgramData\SCIEX\DataReviewer\Plates. 15. If necessary, select another well for reanalysis. Operator Guide...

  • Page 64: View Reports

    Review the Results with the DataReviewer Software View Reports View the Data Report The Data Report shows the electropherogram labeled with the identified glycans. The report also contains information about the sample, the cartridge, and the method used to acquire the data on the C100 Biologics Analyzer system.
  • Page 65 Review the Results with the DataReviewer Software Figure 6-13 Data Report Electropherogram Figure 6-14 Data Report GU Value and Property Table 3. Click (Save As), type a name, and then click Save to save the report to a PDF file. By default, the report is saved to a file in C:\Users\<User Name>\Documents, where <User Name>...
  • Page 66 Review the Results with the DataReviewer Software About the Glycan IDs The electropherograms in the Glycan Analysis Report and in the Data Trace tab are labeled with the glycan name for the peaks identified as glycans. Use the glycan names to find the structure by referring to Table 6-1.

  • Page 67: View The Plate Report

    Review the Results with the DataReviewer Software The glycan structures are based on Harvey D.J., Merry A.H., Royle L., Campbell M.P., Dwek R.A., Rudd P.M., Proposal for a standard system for drawing structural diagrams of N- and O-linked carbohydrates and related compounds., Proteomics.
  • Page 68 Review the Results with the DataReviewer Software Figure 6-15 Plate Report Report Heading Figure 6-16 Plate Report Plate Image C100 Biologics Analyzer System Operator Guide 68 / 122 RUO-IDV-05-3828-A...
  • Page 69 Review the Results with the DataReviewer Software Figure 6-17 Plate Report GU Values Figure 6-18 Plate Report Corrected Area % Operator Guide C100 Biologics Analyzer System RUO-IDV-05-3828-A 69 / 122...

  • Page 70: Analyze The Data Manually

    Review the Results with the DataReviewer Software Figure 6-19 Plate Report Relative Migration Time 3. Click (Save As), type a name, and then click Save to save the report to a PDF file. By default, the report is saved to a file in C:\Users\<User Name>\Documents, where <User Name> is the current user.

  • Page 71: Open A Plate

    Plate. Open a Plate The results from the data analysis are saved to a plate file in C:\ProgramData\SCIEX\DataReviewer\Plates. The plate file can be opened and analyzed again. Note: To maintain data integrity, a plate can only be saved once. If the plate is analyzed with a different qualification profile, then the plate must be saved with a different name.
  • Page 72 Assign a Qualification Profile to a Plate. 6. Click (Save As), type a name, and then click Save to save the changes to the plate. By default, the plate is saved to a file in C:\ProgramData\SCIEX\DataReviewer\Plates. C100 Biologics Analyzer System Operator Guide...

  • Page 73: Routine Maintenance

    Routine Maintenance This chapter describes procedures to maintain the C100 Biologics Analyzer system. WARNING! Ionizing Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Determine whether decontamination is required prior to cleaning or maintenance. The customer must decontaminate the system prior to cleaning or maintenance if radioactive materials, biological agents, or toxic chemicals have been used with the system.

  • Page 74: Test The Detector

    7. On the Windows desktop, double-click the C100 software icon and then log on to the software If the system does not operate normally or if the fuse blows again, contact sciex.com/request-support. Test the Detector This option is only available to users with the Basic User or Advanced User role.

  • Page 75: Fill The Capillaries And Cartridge

    5. Follow the prompts in the software to complete the test. At the end of the test, the status is shown and the results are saved to the SystemTest folder (by default C:\ProgramData\SCIEX\C100HT\Data\SystemTest). If the test fails, replace the purge filter (refer to Replace the Purge Filter).

  • Page 76: Test System Movement

    4. Remove the cartridge, put it in the cartridge stand, and then click Done. At the end of the test, the status is shown and the results are saved to the SystemTest folder (by default C:\ProgramData\SCIEX\C100HT\Data\SystemTest). Replace the Purge Filter Required Materials •...

  • Page 77: Manage Users

    Manage Users This option is only available to users with the Administrator User role. During installation, the SCIEX Field Service Employee (FSE) will create some system users in the C100 software. After installation, a user with the Administrator User role can add users and the properties of existing users can be modified as needed.

  • Page 78: Default Users

    Routine Maintenance Figure 7-2 User Manager Tab Default Users The users in the following table are present by default. Refer to Table 7-1. Additional users can be added to the system by a user with the Administrator User role. Refer to Add a New User.

  • Page 79: Add A New User

    Routine Maintenance Add a New User This option is only available to users with the Administrator User role. 1. In the C100 software, click to go to Configure mode. 2. In Configure mode, click the User Manager tab. 3. Click Add. 4.

  • Page 80: Modify An Existing User

    Routine Maintenance • May skip confirmation of run checks: Allows the user to start a run even if there are unresolved errors or warnings in the Run Check pane. • May revise sample information after run: Allows the user to edit sample information in Data View mode after the run is completed.

  • Page 81: Prepare The System To Be Moved

    Prepare the System to Be Moved WARNING! Lifting Hazard. Make sure that at least three people or a lifting device are available to lift the CE system. Follow established safe lifting procedures. Refer to the Site Planning Guide for the weights of system components. CAUTION: Potential System Damage.
  • Page 82 Prepare the System to Be Moved Figure 8-1 Transport Lock Installed in System 10. Close the sample door. 11. Close the C100 software. 12. Turn off the power to the monitor and the controller. 13. Remove the RS-232 cable from the controller and the C100 Biologics Analyzer system.

  • Page 83: Troubleshooting

    Troubleshooting Troubleshooting Tables Table 9-1 Initialization Symptom Possible Cause Corrective Action The system does not The power cable is not Connect the power cable. turn on. connected. The fuse is blown. Replace the fuse. Refer to Replace the Fuse. The C100 software The COM port is not detected.
  • Page 84 (Engage). If the problem persists, turn the system off and on. The cartridge data key was Insert the data key. If the problem persists, contact not detected. sciex.com/request-support. The cartridge door is open. Close the door. If the problem persists, contact sciex.com/request-support. Cannot start a run.
  • Page 85 One or more LEDs is not lit: Test the detector to make sure that all of the LEDs are lit. Refer to Test the Detector. If the test fails, then contact sciex.com/ request-support. Blocked purge filter: Perform a filter check. Refer Test the Filter.
  • Page 86 Troubleshooting Table 9-2 Operation (continued) Symptom Possible Cause Corrective Action There are no peaks. There are issues with the Air bubble at the bottom of the sample well: hardware. Centrifuge the sample plate or 12-well tube strip to make sure that there are no bubbles at the bottom. Capillary window or tip is broken: Inspect the capillary tip.
  • Page 87 Troubleshooting Table 9-2 Operation (continued) Symptom Possible Cause Corrective Action The peaks are low The deglycosylation was not Make sure that the amount of protein is 100 µg. If it is intensity. complete. acceptable, then prepare the sample again and increase the incubation time for the deglycosylation step, increase the quantity of enzyme, or use a new enzyme lot.

  • Page 88: Run A Test Sample

    Troubleshooting Run a Test Sample This test can be used to determine if there is an issue with the system hardware. Required Materials • 12-well tube strip • 20 µL pipette • Calibration solution • C100 Glycan Labeling and Analysis buffer tray 1.

  • Page 89: Export Log Files For Troubleshooting

    Troubleshooting If the system is working correctly, each gel lane should contain a single band. Refer to Figure 9-1 Figure 9-2. Figure 9-1 Test Sample Gel Image Figure 9-2 Test Sample Electropherogram Export Log Files for Troubleshooting This option is only available to users with the Basic User or Advanced User role. 1.
  • Page 90 Troubleshooting 2. In Service mode, click System Check or Maintenance. 3. At the bottom of the pane, click Troubleshooting folder. 4. In the Troubleshooting Setup dialog, specify the settings for the export. a. Select the date range for the information to be exported. By default, the range is the previous 24 hours. b.

  • Page 91: A System Specifications

    System Specifications System Cover open: 68 cm × 58 cm × 59 cm (27 inches × 22 inches × 23 inches) Dimensions (H × W × D) Cover closed: 41 cm × 58 cm × 59 cm (16 inches × 22 inches × 23 inches) Weight 52 kg (115 pounds)
  • Page 92 System Specifications Item Description Intel Core I5-4670 Memory 4 GB, DDR3 Hard Drive 500 GB Monitor LED 68.5 cm (27 inches) Operating System Microsoft Windows (64-bit) C100 Biologics Analyzer System Operator Guide 92 / 122 RUO-IDV-05-3828-A...

  • Page 93: B Reagents And Accessories

    Reagents and Accessories Order Parts • Order parts from SCIEX in any of the following ways: • Telephone: (877) 740-2129, Option 1 (toll-free, United States only), or go to sciex.com/contact-us to find a local office. • E-mail: Sales.Americas@sciex.com • Fax: (800) 343-1346...
  • Page 94 Reagents and Accessories Component Quantity D4 reagent L5 catalyst L6 (APTS) fluorophore GU (glucose ladder); process control IST (internal standard) BST (bracketing standard) Calibration solution Mineral oil Glycan buffer tray 12-well tube strips (20-pack) 96-well sample plate (10-pack) C100 Biologics Analyzer System Operator Guide 94 / 122 RUO-IDV-05-3828-A...

  • Page 95: C Hazardous Substance Information

    The following information must be noted and the relevant safety measures taken. Refer to the respective safety data sheets for more information. These are available upon request or can be downloaded from our website sciex.com/tech-regulatory. Hazard classification according to HCS 2012.
  • Page 96 Hazardous Substance Information HR-NCHO Separation Gel WARNING! May be harmful if swallowed. L5 Catalyst DANGER! Causes severe skin burns and eye damage. Other Reagents These components are not classified as hazardous: • D4 reagent • GU glucose ladder • IST internal standard •...

  • Page 97: D Start A Run As A Routine User

    Start a Run as a Routine User Users with the Routine User role acquire data using a pre-defined process profile and a wizard interface in the C100 software. Refer to Add a New User for information about user roles. Refer to the C100 Software Help for detailed instructions on using the software.
  • Page 98 Start a Run as a Routine User d. Put the samples in the system and then close the sample door. Note: If the samples are in tube strips, make sure to put them in the positions specified in the process profile.
  • Page 99 Start a Run as a Routine User Figure D-3 Sample Information Pane 9. Click and then prepare for the run. a. Complete the tasks in the Please Confirm area and then select the corresponding check boxes. Figure D-4 Please Confirm Area Operator Guide C100 Biologics Analyzer System...
  • Page 100 Start a Run as a Routine User b. Resolve any issues listed in the Errors and Warnings area. Figure D-5 Errors and Warnings Area c. Click The Data pane opens with the results shown in the Gel Image tab. As the run progresses, the Instrument Status panel updates.
  • Page 101 Start a Run as a Routine User Figure D-6 Gel Image Tab After data for all of the samples has been acquired, the DataReviewer software automatically opens and then the data is processed. At the top of the DataReviewer software window is a banner showing the time remaining for the data processing.
  • Page 102 Start a Run as a Routine User Figure D-7 DataReviewer Software Window 10. In the DataReviewer software, assign a qualification profile to the wells in the plate and then analyze and review the data. Refer to Analyze the Data and Review the Results.

  • Page 103: E Additional Functions In The Data Trace Tab

    Additional Functions in the Data Trace Tab Right-click in the electropherogram in the Data Trace tab to access the context menu. Table E-1 Context Menu in the Electropherogram Menu Item Description Add Trace Opens the Add Trace dialog. Refer to New Trace Properties Dialog.

  • Page 104: Open Data File Dialog

    Additional Functions in the Data Trace Tab Table E-2 New Trace Tab in the New Trace Properties Dialog Label Description Data source Click (Open) and select: • Current Data: to select a trace in the current data file. • Open Data: to select a different data file from which a trace can be selected. •...

  • Page 105: Axis Properties Dialog

    Additional Functions in the Data Trace Tab Table E-3 Open Data File Dialog Label Description Look in Select the location of the data files. Click to show or hide a pane with text information about the file selected in the table (View Description) at the top of the dialog.

  • Page 106: Trace Annotation Properties Dialog

    Additional Functions in the Data Trace Tab Table E-4 Axis Properties Dialog Label Description Graph title Type a title for the graph. The title appears at the top of the graph. Axis Select the axis: Left Y-Axis, Right Y-Axis, or X-Axis. (Y-axis only) Use limits of Select one of the traces to set as the range for the Y-axis or select (None) to hide trace...

  • Page 107: Appearance Properties Dialog

    Additional Functions in the Data Trace Tab Table E-5 Trace Annotation Properties Dialog Label Description Trace Select the trace to be annotated. Peaks/Groups List Click to select what will be annotated in the trace: Peaks or Groups. Available Annotations Lists all available annotations. Click an item in the list and then click (Add) to add it to the Show the following annotations list.

  • Page 108: The Operations Submenu

    Additional Functions in the Data Trace Tab Table E-6 Appearance Properties Dialog (continued) Label Description Line Style, Size, Color Set options for the sub-item, when the sub-item is a line. Font, Size, Color, Angle, Set options for the sub-item, when the sub-item is text. Text Properties Click to apply the changes and close the dialog.

  • Page 109: The Utilities Submenu

    Description Print Prints the electropherogram to a file named Data Graph.pdf located in C:\ProgramData\SCIEX\DataReviewer\MethodReports. A print dialog does not open. If a file by that name already exists, it is overwritten and no message is shown. Copy to Clipboard Copies the electropherogram so it can be pasted into another software application.
  • Page 110 Additional Functions in the Data Trace Tab Table E-9 Graphical Programming Menu Options Menu Item Description Integration Tools Shows or hides the integration toolbar. Width Sets the width integration parameter. Threshold Sets the threshold (the first derivative) used by the integration algorithm to distinguish the start and stop of peaks from baseline noise and drift.
  • Page 111 Additional Functions in the Data Trace Tab Table E-9 Graphical Programming Menu Options (continued) Menu Item Description Reassign Peak Sets a user-selected peak as the calibrated peak in place of the peak that has been identified by the software. The expected migration time of the named peak in the peak table is adjusted to the migration time of the selected peak.

  • Page 112: Data Graph Properties Dialog

    Additional Functions in the Data Trace Tab Data Graph Properties Dialog To access this dialog, right-click Properties in the electropherogram in the Data Trace tab. Additional settings are available in the other tabs in the Data Graph Properties dialog: • For the Axis Setup tab, refer to Axis Properties Dialog.
  • Page 113 Additional Functions in the Data Trace Tab Table E-10 Trace Setup Tab in the Data Graph Properties Dialog (continued) Label Description Y max If scaling is User Defined, type a number for the maximum value of the Y-axis. Units Type text for the label on the Y-axis. Annotations Click (Options) or Annotations to open the Trace Annotation Properties dialog...

  • Page 114: F Glossary Of Symbols

    Authorized representative in the European community Biohazard CE Marking of Conformity cCSAus mark. Indicates electrical safety certification for Canada and USA. Catalogue number Caution Note: In SCIEX documentation, this symbol identifies a personal injury hazard. C100 Biologics Analyzer System Operator Guide 114 / 122 RUO-IDV-05-3828-A...
  • Page 115 Glossary of Symbols Symbol Description China RoHS Caution Label. The electronic information product contains certain toxic or hazardous substances. The center number is the Environmentally Friendly Use Period (EFUP) date, and indicates the number of calendar years the product can be in operation. Upon the expiration of the EFUP, the product must be immediately recycled.
  • Page 116 Symbol Description Fragile Fuse Hertz High Voltage. Electrical Shock Hazard If the main cover must be removed, contact a SCIEX representative to prevent electric shock. Hot Surface Hazard In Vitro Diagnostic Device Ionizing Radiation Hazard Keep dry. Do not expose to rain.
  • Page 117 Glossary of Symbols Symbol Description Moving Parts Hazard Pinch Hazard Pressurized Gas Hazard Protective Earth (ground) Puncture Hazard Puncture Hazard Reactive Chemical Hazard Serial number Toxic Chemical Hazard Transport and store the system within 66 kPa to 103 kPa. Transport and store the system within 75 kPa to 101 kPa. Transport and store the system within 10% to 90% relative humidity.
  • Page 118 Glossary of Symbols Symbol Description Transport and store the system within –30 °C to +45 °C. Transport and store the system within –30 °C to +60 °C. USB 2.0 connection USB 3.0 connection Ultraviolet Radiation Hazard Volt Ampere (power) Volts (voltage) WEEE.

  • Page 119: G Glossary Of Warnings

    Glossary of Warnings Note: If any of the labels used to identify a component become detached, contact an FSE. Label Translation (if applicable) FCC Compliance. This device complies with Part 15 of FCC Compliance. This device complies with Part 15 of the FCC Rules.

  • Page 120: Index

    Data Trace tab 57 preparing 35 matching process 54 Plate Report tab 67 Qualification Profiles tab 55 C100HT Glycan Labeling and Analysis kit, contents 93 reports, saving 64, 67 calibration solution reports, viewing 64 loading 29 Decontamination Forms and system returns 11...
  • Page 121 Index undoing zooming 103 long fill 75 viewing 57 personnel requirements 12 zooming in on 59 modifying the system 12 environmental conditions, required 10 movement check 76 environmental health and safety regulations 6 moving the system 81 environmental requirements 91 experiments accepting incomplete 80 New Trace Properties dialog 103...
  • Page 122 Index Normalization tab 33 Trace Annotations Properties dialog 106 transport lock reagents, part numbers 93 installing 81 Reanalysis mode 60 troubleshooting 83, 89 regulations local 9 reports Data Report 64 User Manager tab 77 Glycan Analysis Report 64 user name Plate Report 67 for default users 78 Routine user, starting a run 97...

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