SCIEX X500 QTOF System User's Manual
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SCIEX X500 QTOF System User's Manual

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SCIEX X500 QTOF System
System User Guide
RUO-IDV-05-2334-E
August 2017

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  • Page 1 SCIEX X500 QTOF System System User Guide RUO-IDV-05-2334-E August 2017...
  • 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

    Hardware Overview.................................20 Panel Symbols................................24 Theory of Operation.................................24 Data Handling................................25 Theory of Operation—SCIEX OS............................25 Software Overview..............................25 Scan Techniques................................25 Quantitative Analysis..............................28 Integration.................................28 Results Tables................................28 Calibration Curves..............................28 Regression Equations..............................29 Weighting Factors..............................30 Regression Types...............................30 System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 3 / 234...
  • Page 4 Add a Mass Spectrum to a Compound........................64 Chapter 6 Operating Instructions Software..................66 About the Home Page..............................66 About the Ribbon and Launcher............................67 About the Status Panel..............................69 Add a Project................................71 Select a Project................................72 SCIEX X500 QTOF System System User Guide 4 / 234 RUO-IDV-05-2334-E...
  • Page 5 Show Sample Information............................114 Show the Graph Selection Information........................115 Edit Settings in Graphs.............................120 Work with Data in Graphs............................122 Use the Two-Pane Operation Tools..........................128 Move Panes or Windows............................129 Perform a Gaussian Smooth.............................131 System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 5 / 234...
  • Page 6 Chapter 7 Service and Maintenance Information.................199 Recommended Maintenance Schedule..........................199 Clean the Surfaces.................................201 Clean the Front-End...............................201 Symptoms of Contamination............................202 Required Materials ..............................202 Cleaning Best Practices............................203 Prepare the Mass Spectrometer..........................205 Clean the Curtain Plate............................206 SCIEX X500 QTOF System System User Guide 6 / 234 RUO-IDV-05-2334-E...
  • Page 7 Chapter 8 Mass Spectrometer Troubleshooting...................220 Appendix A Recommended Calibration Ions..................223 APCI Calibration Ions..............................223 ESI Calibration Ions................................225 Appendix B Exact Masses and Chemical Formulas................228 Appendix C Glossary of Symbols......................229 Appendix D Glossary of Warnings......................233 System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 7 / 234...

  • Page 8: Chapter 1 Operational Precautions And Limitations

    • Electromagnetic Compatibility (EMC): Radio Communications Act 1992 as implemented in these standards: • Electromagnetic Interference—AS/NZS CISPR 11/ EN 55011/ CISPR 11 (Class A) . Refer to Electromagnetic Interference on page SCIEX X500 QTOF System System User Guide 8 / 234 RUO-IDV-05-2334-E...

  • Page 9: Canada

    • Radio Emissions Interference Regulations: 47 CFR 15, as implemented in FCC Part 15 (Class A) • Safety: Occupational Safety and Health Regulations, 29 CFR 1910, as implemented in these standards: • UL 61010-1 • IEC 61010-2-061 System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 9 / 234...

  • Page 10: International

    WARNING! Electrical Shock Hazard. Do not remove the covers. Removing the covers might cause injury or malfunctioning of the system. 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.

  • Page 11: Protective Earth Conductor

    WARNING! Electrical Shock Hazard. Make sure that a protective earth conductor (grounding cable) is connected between the sample loop and an appropriate grounding point at the ion source. This supplementary grounding will reinforce the safety configuration specified by SCIEX. Chemical Precautions WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Determine whether decontamination is required prior to cleaning or maintenance.

  • Page 12: System Safe Fluids

    CAUTION: Potential System Damage. Do not use any other fluid until confirmation is received from SCIEX that it does not present a hazard. This is not an exhaustive list. • Organic Solvents • MS-grade acetonitrile; up to 100% •...

  • Page 13: Ventilation Precautions

    Make sure that the laboratory has appropriate air exchange for the work performed. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 13 / 234...

  • Page 14: Environmental Precautions

    WARNING! Puncture Hazard, Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Discontinue use of the ion source if the ion source window is cracked or broken and then contact a SCIEX Field Service Employee (FSE). Any toxic or injurious materials introduced into the equipment will be present in the source exhaust output.

  • Page 15: Electromagnetic Environment

    Before decommissioning, decontaminate the entire system following local regulations. When removing the system from service, separate and recycle different materials according to national and local environmental regulations. Refer to Storage and Handling on page 212. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 15 / 234...

  • Page 16: Equipment Use And Modification

    Operational Precautions and Limitations Note: SCIEX will not accept any system returns without a completed Decontamination Form. Contact an FSE to obtain a copy of the form. Do not dispose of system components or subassemblies, including computer parts, as unsorted municipal waste.

  • Page 17: Contact Us

    For the latest guidance on cybersecurity for SCIEX products, visit sciex.com/productsecurity. Technical Support SCIEX and its representatives maintain a staff of fully-trained service and technical specialists located throughout the world. They can answer questions about the system or any technical issues that might arise. For more information, visit the SCIEX website at sciex.com.
  • Page 18 Tip! Tip provides useful information that helps apply the techniques and procedures in the text for a specific need and provides shortcuts, but is not essential to the completion of a procedure. SCIEX X500 QTOF System System User Guide 18 / 234...

  • Page 19: Chapter 2 Principles Of Operation

    The SCIEX X500 QTOF system is designed for the qualitative and quantitative analysis of chemical species. This section includes information about the mass spectrometer and the SCIEX OS. Refer to the ion source Operator Guide for an overview of the ion source.

  • Page 20: Hardware Overview

    Principles of Operation Hardware Overview Figure 2-1 Front and Right Side View: X500R SCIEX X500 QTOF System System User Guide 20 / 234 RUO-IDV-05-2334-E...
  • Page 21 Alternate (left) location for diverter valve. For more information, contact an FSE. Ion source. Refer to the ion source Operator Guide. Calibrant bottles. Refer to Replace the CDS Bottle on page Panel symbols. Refer to Panel Symbols on page System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 21 / 234...
  • Page 22 Principles of Operation Figure 2-3 Back and Left Side View: X500R SCIEX X500 QTOF System System User Guide 22 / 234 RUO-IDV-05-2334-E...
  • Page 23 Zero air gas supply Exhaust waste. Refer to Empty the Source Exhaust Drain Bottle on page 207. Nitrogen gas supply Exhaust gas supply. The air supply for the ion source. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 23 / 234...

  • Page 24: Panel Symbols

    Theory of Operation Mass spectrometry measures the mass-to-charge ratio of ions to identify and quantify compounds. The SCIEX X500 QTOF system has a series of quadrupole filters that transmit ions according to their mass-to-charge ® (m/z) value. The first quadrupole in this series is the QJet ion guide, which is located between the orifice plate ®...

  • Page 25: Data Handling

    During system operation, the acquired data is sent to the SCIEX OS where it can be shown as either full mass spectra, intensity of single or multiple ions over time, or total ion current over time.
  • Page 26 XIC: An ion chromatogram created by taking intensity values at a single, discrete mass value or a mass range, from a series of mass spectral scans. It indicates the behavior of a given mass or mass range as a function of time. SCIEX X500 QTOF System System User Guide...
  • Page 27 A spectrum is the data that is obtained directly from the instrument and normally represents the number of ions detected with particular mass-to-charge (m/z) values. It is displayed as a graph with the m/z values on the x-axis and intensity (cps) represented on the y-axis. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 27 / 234...

  • Page 28: Quantitative Analysis

    A calibration curve, also know as a standard concentration curve, is a method for determining the concentration of a substance in an unknown sample by comparing the unknown sample to a set of standard samples of known SCIEX X500 QTOF System System User Guide...

  • Page 29: Regression Equations

    Table 2-2. Table 2-2 Regression Variables Internal Area Used? Standard Used? / DF / DF / DF / DF where: System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 29 / 234...

  • Page 30: Weighting Factors

    In the Analytics workspace, the following types of regression are available for the calibration curve: • Linear (y = mx + b) • Linear through Zero (y = mx) • Mean Response Factor SCIEX X500 QTOF System System User Guide 30 / 234 RUO-IDV-05-2334-E...
  • Page 31 The slope and intercept are calculated as: where: Linear Through Zero The linear through zero calibration equation is: y = mx The slope is calculated as: Mean Response Factor The mean response factor calibration is: System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 31 / 234...
  • Page 32 Quadratic The quadratic calibration equation is: y = a x + a The polynomial co-efficients are calculated as: = (b ) / (b where: SCIEX X500 QTOF System System User Guide 32 / 234 RUO-IDV-05-2334-E...

  • Page 33: Qualitative Analysis

    The protonated adduct of imazalil has a mass 297.0556. If it is suspected that imazalil is in a sample, then compare the mass of the compound found to the mass of the protonated imazalil and determine System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 33 / 234...
  • Page 34 Retention Time Most accurate mass spectrometry systems use some type of chromatography. The SCIEX X500 QTOF System uses liquid chromatography (LC). A set retention time using a known standard for the compound on the LC system is used to identify a known target compound in a sample.
  • Page 35 A list of possible formula is determined using precursor mass accuracy, isotopic pattern, and MS/MS fragmentation. Proposed formulas are scored based on precursor mass accuracy and average MS/MS mass accuracy of matching fragments. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 35 / 234...

  • Page 36: Chapter 3 Operating Instructions Hardware

    WARNING! Personal Injury Hazard. Follow the instructions in the documentation when using the system. The protection provided by the equipment might be impaired if the equipment is used in a manner not specified by SCIEX. Start Up the System WARNING! Electrical Shock Hazard. Make sure that the system can be disconnected from the mains supply outlet in an emergency.

  • Page 37: Shut Down And Vent The System

    Figure 2-4. 3. Turn on the computer. 4. Open the SCIEX OS software. Shut Down and Vent the System Some procedures require that the system be shut down. Others require that it also be vented. Follow these steps to shut down and, if required, vent the system.

  • Page 38: Diverter Valve

    Operating Instructions Hardware 3. In the SCIEX OS software, deactivate the devices, if they are active. 4. Close the software. 5. (If required) Follow these steps to vent the system: Note: Vent the system before performing a full cleaning of the vacuum interface, before cleaning the Q0 region, and before replacing the roughing pump oil.

  • Page 39: Plumb The Diverter Valve In Injector Mode

    When the valve is in Position A, the sample flows through the external loop. When the valve switches to Position B, the sample is injected. • Plumb the valve for injector mode. Figure 3-2 Diverter Valve Injector Mode Position A Figure 3-3 Diverter Valve Injector Mode Position B System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 39 / 234...

  • Page 40: Plumb The Diverter Valve In Diverter Mode

    When the valve is in Position A, the flow goes to waste. When the valve switches to Position B, the flow goes to the mass spectrometer. • Plumb the valve for diverter mode. Figure 3-4 Diverter Valve Diverter Mode Position A SCIEX X500 QTOF System System User Guide 40 / 234 RUO-IDV-05-2334-E...

  • Page 41: Calibrant Delivery System

    The CDS supports up to two bottles of calibrant. Use bottle one for the positive calibrant solution. Use bottle two for the negative calibrant solution. Be sure to install the bottle in the correct position to avoid cross-contamination. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 41 / 234...

  • Page 42: Start The Cds

    WARNING! Toxic Chemical Hazard. Refer to the chemical product Safety Data Sheets and follow all of the recommended safety procedures when handling, storing, and disposing of chemicals. For health and safety precautions, refer to Chemical Precautions on page SCIEX X500 QTOF System System User Guide 42 / 234 RUO-IDV-05-2334-E...
  • Page 43 The container must hold at least 20 mL of additional solution that might come out of the instrument. 3. In the SCIEX OS, follow these steps to put the CDS into Wash mode: a. On the status panel, click the Direct CDS Control icon.
  • Page 44 Tip! We recommend that the tubing be flushed with the new calibrant solution before the new calibrant is allowed to recirculate back into the calibrant bottle. 13. In the SCIEX OS, clear Wash Mode. 14. Put the return tubing into the calibrant bottle, and then install the bottle.

  • Page 45: Chapter 4 Configure Devices

    All of the devices that are selected in the Devices list are activated. Edit Device Settings 1. Open the Configuration workspace. 2. Click Devices in the left panel. 3. Click Deactivate. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 45 / 234...

  • Page 46: Delete Devices

    6. Click Activate Devices. All of the devices that are selected in the Devices list are activated. Deactivate Devices 1. Open the Configuration workspace. 2. Click Devices in the left panel. SCIEX X500 QTOF System System User Guide 46 / 234 RUO-IDV-05-2334-E...
  • Page 47 Configure Devices 3. Click Deactivate. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 47 / 234...

  • Page 48: Chapter 5 Configure Access To The Software

    Method Analyst Reviewer Developer Access the Queue workspace Access the Batch workspace Yes* Access the following quantitation settings: • Project Secure Export Settings • Enable Project Modified Peak Warning SCIEX X500 QTOF System System User Guide 48 / 234 RUO-IDV-05-2334-E...
  • Page 49 Access the following basic quantitation settings and features: • Create Results Tables Review results LC methods MS methods Explore data View logs Archive logs Configure the LIS Configure devices System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 49 / 234...

  • Page 50: Access To Analytics Features

    Developer Create session file Create processing methods Modify processing methods Export and create reports of unlocked Results Table Replace existing Results Table when saved Change default processing method settings SCIEX X500 QTOF System System User Guide 50 / 234 RUO-IDV-05-2334-E...
  • Page 51 Table Modify the Sample Name Modify Sample Type Modify Sample ID Modify Actual Concentration Modify Dilution Factor Modify Comment Fields Allow manual integration Allow Set to Peak Not Found System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 51 / 234...
  • Page 52 Modify Results Table column settings Save Column Settings as Project Default Lock and save a Results Table Unlock and save a Results Table Review and save a Results Table SCIEX X500 QTOF System System User Guide 52 / 234 RUO-IDV-05-2334-E...

  • Page 53: Add Users

    7. Click Save. Deactivate a User 1. Open the Users workspace. 2. Click the user or group in the left panel. 3. Clear the Active check box. 4. Click Save. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 53 / 234...

  • Page 54: Remove A User

    2. Click the user or group in the Users list. 3. Click Remove User. Enable Full Screen Mode Select this feature to use the SCIEX OS software as the primary application. Users cannot close the software or access other software programs. 1. Open the Configuration workspace.

  • Page 55: Select Regional Settings

    4. Click Save. 5. Start the computer again. Manage the Compound Libraries Import a LibraryView Package 1. Expand the Compounds list in the Manage pane. 2. Click All Compounds. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 55 / 234...

  • Page 56: Import A Compound Database

    • Click Analyst Compound Database (*.mdb) on the Library Importer dialog. 5. Navigate to the appropriate file on the Open dialog. 6. Select the file and then click Open. SCIEX X500 QTOF System System User Guide 56 / 234 RUO-IDV-05-2334-E...

  • Page 57: Import A Cliquid Package

    Tip! To help locate compounds, use the Search field. As the search criteria is typed, the visible columns are searched and refreshed to show only the information that matches the criteria specified. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 57 / 234...

  • Page 58: Import An Excel File

    10. Select the appropriate heading for each column of information. Tip! Compound:CompoundId and Compound:Name are mandatory selections. Select ---[not used]--- for information that is not required. 11. Click Next. SCIEX X500 QTOF System System User Guide 58 / 234 RUO-IDV-05-2334-E...

  • Page 59: Import A Library Database Snapshot

    4. Click Overwrite Database with Library Snapshot (*.lbp) on the Library Importer dialog. 5. Click Yes on the Warning dialog. 6. Navigate to the appropriate file on the Open dialog. 7. Select the file and then click Open. 8. Click Finish. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 59 / 234...

  • Page 60: Import A Library Package From A Third Party

    Note: The LibraryView software must be installed. A licensed library can be installed from a DVD or from a .zip application file downloaded from the SCIEX Web site. The application file can include compound names, compound transition information, and compound library spectra.
  • Page 61 ID. On a computer with Internet access, go to the licensing page of the SCIEX Web site and then follow the instructions to obtain a license. After the required information is submitted, a license file is sent to all of the e-mail addresses provided.

  • Page 62: Compound Conflicts

    Conflict information is available to help the user make the correct choice. View Compound Conflicts 1. Click Resolve on the Library Importer dialog beside the compound to view the details of the conflict. SCIEX X500 QTOF System System User Guide 62 / 234...
  • Page 63 • Click Keep Original beside the appropriate compound on the Library Importer dialog to keep the individual compound information stored in the database and discard the compound information from the import package. 2. Click Finish after all of the conflicts are resolved. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 63 / 234...

  • Page 64: Add A Compound

    10. Click Open *.wiff file on the Add Mass Spectrum from *.wiff file to Compound dialog. 11. Browse to and then select the appropriate .wiff or .wiff2 file on the Open dialog. 12. Click Open. SCIEX X500 QTOF System System User Guide 64 / 234...
  • Page 65 • For EPS, MRM, and looped data, double-click the TIC and then click Add Spectrum in the Acquired Spectrum pane. 15. Repeat steps 7 through 11 for each spectrum to be added. 16. Click Save. 17. Click Save on the MS Spectra tab. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 65 / 234...

  • Page 66: Chapter 6 Operating Instructions Software

    Access to workspaces is determined by the role assigned to the user as well as the software license. Within each workspace, the user can manually start acquisition or view and explore data that is being acquired. Figure 6-1 Home Page SCIEX X500 QTOF System System User Guide 66 / 234...

  • Page 67: About The Ribbon And Launcher

    Shows the name of the active workspace. To return to the home page, click To go to an active workspace, click the workspace icon. Shows the currently logged in user. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 67 / 234...
  • Page 68 A light blue bar at the left indicates that the workspace is active. A light blue background indicates that the workspace is open. To close the active workspace, click To close the open workspace, click SCIEX X500 QTOF System System User Guide 68 / 234 RUO-IDV-05-2334-E...

  • Page 69: About The Status Panel

    • View device details. • Put the mass spectrometer or LC in Standby state. • Verify and calibrate the TOF MS and TOF MS/MS modes. • Equilibrate the system. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 69 / 234...
  • Page 70 Operating Instructions Software Figure 6-4 SCIEX OS Status Panel SCIEX X500 QTOF System System User Guide 70 / 234 RUO-IDV-05-2334-E...

  • Page 71: Add A Project

    The project stores acquisition methods, data, batches, processing methods, processing results, and so on. We recommend the use of separate project folders for each project. Do not create projects or copy or paste files outside of the SCIEX OS software. 1. Click the plus sign next to the Projects list on the status panel.

  • Page 72: Select A Project

    Explorer workspace. Tip! Click the top of the Data Acquisition panel up or down to resize the contents. Figure 6-5 Data Acquisition Panel SCIEX X500 QTOF System System User Guide 72 / 234...

  • Page 73: User Workflows

    Batch and Queue Workspaces on page Process and review data in Results Tables. Refer to Analytics Workspace on page 147. Explore data. Refer to Explorer Workspace on page 104. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 73 / 234...

  • Page 74: Method Developers

    Batch and Queue Workspaces The Batch workspace shows a collection of information about the samples to be analyzed. Batches tell the software the order in which to analyze the samples. SCIEX X500 QTOF System System User Guide 74 / 234...

  • Page 75: Manage The Batch

    To save the batch to the current project, click Save > Save or Save > Save As from the workspace menu. Export the batch To export the batch as a .txt or .csv file, click Save > Export from the workspace menu. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 75 / 234...

  • Page 76: Import A Batch

    14. Make sure that the column oven temperature is reached before submitting the batch. 15. Make sure that the system has been equilibrated with the same MS and LC method. SCIEX X500 QTOF System System User Guide 76 / 234...

  • Page 77: Import A Batch From The Lims

    If errors are shown at the top of the screen, then resolve them and click Submit again. Any errors in the batch must be resolved prior to submitting the batch. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 77 / 234...

  • Page 78: Create A Batch Manually

    Batch Import Set Up For the selected autosampler, the rack code, rack position, plate code, plate position, and vial position are all dependent on each other and only certain values are valid. SCIEX X500 QTOF System System User Guide 78 / 234...
  • Page 79 Sample Type The types of samples. Make sure that the sample type matches one of the predefined sample types. Anything that does not match is automatically replaced with Unknown. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 79 / 234...

  • Page 80: Use The Plate Layout Feature To Create A Batch

    Column Name Definition Field Value Requirements Dilution factor The dilution factor for individual For SCIEX-developed methods, the value samples. must be 1.00. Value greater than zero and with six decimal places. The default value is 1.000000. Do not leave the field blank.
  • Page 81 9. To remove a position, click a selected sample position in the graphical representation. The sample position in the graphical representation is no longer highlighted and the data is removed from the grid in the Batch workspace. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 81 / 234...

  • Page 82: Create An Ion Reference Table

    10. In the Reference Ions for MS/MS Calibration grid, add and then select at least two fragment masses. The Fragment Name field is optional 11. Click OK. 12. Type a name in the Save Reference Table dialog and then click OK. SCIEX X500 QTOF System System User Guide 82 / 234 RUO-IDV-05-2334-E...

  • Page 83: Calibrate The System Using The Cds

    7. Click OK to close the dialog. 8. Make sure that the check box to the left of the Auto-Calibrate button is selected. 9. Create and submit a batch. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 83 / 234...

  • Page 84: Equilibrate The System

    Table 6-4 Queue Workspace Features To do this..do this View all of the samples in the batch. Click Collapse all of the samples in the Click batch. SCIEX X500 QTOF System System User Guide 84 / 234 RUO-IDV-05-2334-E...
  • Page 85 • Double-click the sample that is in the process of being acquired. being acquired. • Click the Explorer workspace icon. View data from a sample that has Double-click the sample that has been acquired. been acquired. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 85 / 234...

  • Page 86: Submit A Single Sample To The Queue

    Acquisition begins after the samples have been submitted from the Batch workspace. Submit Multiple Samples to the Queue 1. Do one of the following: • Click Ctrl + the sample row index number of each sample. SCIEX X500 QTOF System System User Guide 86 / 234 RUO-IDV-05-2334-E...

  • Page 87: Show Or Hide Columns

    A list of components is shown. It contains all components added with the Add component concentration column command, or when a MRM method or processing method was added to the batch. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 87 / 234...

  • Page 88: Queue Icons

    MS Method Experiments on page 90 • About MS Methods on page 91 • MS Method Parameters on page 93 • Calculate the Dynamic Collision Energy for MS Methods on page 103 SCIEX X500 QTOF System System User Guide 88 / 234 RUO-IDV-05-2334-E...
  • Page 89 Tip! Use the list next to the Experiment field to change or delete the experiment. 6. Do one of the following: • Click Save > Lock Method to save and lock the MS Method. • Click Save > Save. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 89 / 234...

  • Page 90: Ms Method Experiments

    TOF MS regions. This experiment is used to determine the structure of the compounds. A data acquisition using the quadrupole mass filter. The ion intensity is returned for masses in the scan range. SCIEX X500 QTOF System System User Guide 90 / 234 RUO-IDV-05-2334-E...

  • Page 91: About Ms Methods

    Note: Only specific combinations of experiments can be used, for example, IDA + IDA, SWATH + MRM • Each experiment has specific advanced settings. • Individual scans within each experiment System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 91 / 234...
  • Page 92 • The number of experiments within a method. • The scheduling duration of each experiment within the method. • The number of TOF MSMS scans for multiple experiments. SCIEX X500 QTOF System System User Guide 92 / 234 RUO-IDV-05-2334-E...

  • Page 93: Ms Method Parameters

    Specify the gas flow between the curtain plate and TOF MS, TOF MSMS, Q1, IDA, SWATH, the orifice plate. Curtain Gas interface flow MRM HR prevents the contamination of the ion optics. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 93 / 234...
  • Page 94 The voltage applied to the needle that sprays the TOF MS, TOF MSMS, Q1, IDA, SWATH, sample. The spray voltage parameter affects the MRM HR, IDA stability of the spray and hence the signal sensitivity. SCIEX X500 QTOF System System User Guide 94 / 234 RUO-IDV-05-2334-E...
  • Page 95 (Q2). In MS/MS scans, the collision energy provides the energy for collision activated dissociation (CAD). The collision energy is compound-dependent; that is, the optimum value varies from compound-to-compound. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 95 / 234...
  • Page 96 Select to apply MRM to the precursor ion and the MRM HR stop mass specified fragment mass range. Users can enter the start and stop masses for the fragment mass range. SCIEX X500 QTOF System System User Guide 96 / 234 RUO-IDV-05-2334-E...
  • Page 97 TOF MS, TOF MSMS, IDA, MRM HR, Each channel counts ions. If all four of the channels SWATH are selected (the default setting), then all four channels are summed for the total ion count. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 97 / 234...
  • Page 98 If the candidate ion has been selected for MSMS once, and do not want to be triggered any more, in For (Sec) field, type in the method duration time as second. SCIEX X500 QTOF System System User Guide 98 / 234...
  • Page 99 M, where M is the m/z value of the ion. Users can select either ppm or mDa. Mass Tolerance can apply to the molecular weight with dynamic exclusion, or the m/z value of the ion. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 99 / 234...
  • Page 100 Tolerance helps to account for any drifts in the LC retention time. If the ion on the exclusion list is detected in the window around the specified retention time, then it is preferentially excluded for MS/MS SCIEX X500 QTOF System System User Guide 100 / 234...
  • Page 101 IDA criteria specified, with the exception of the inclusion list. Candidate ions satisfying the inclusion list will have the same priority as those satisfying the mass defect criteria. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 101 / 234...
  • Page 102 Tolerance (Abundance): This is the abundance tolerance in %. The abundance for the specified peak in the pattern must be within ± the abundance tolerance to be a match for the pattern. SCIEX X500 QTOF System System User Guide 102 / 234...

  • Page 103: Calculate The Dynamic Collision Energy For Ms Methods

    Save as Default Settings. • To apply the current values to the current method to calculate the dynamic CE, click Apply. • To close the dialog and abandon any changes, click Cancel. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 103 / 234...

  • Page 104: Lc Method Workspace

    3. In the Select Samples dialog, select the samples from the Available list and then click the arrow to move the files to the Selected list. Tip! To select one sample, expand the file, click the sample, and then click the arrow. SCIEX X500 QTOF System System User Guide 104 / 234...

  • Page 105: Extract Ions

    Used to calculate one or more overlaid extracted ion chromatograms (XICs), which is the plot of the intensity sum over a given mass range as a function of retention time. 1. Open the Explorer workspace. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 105 / 234...
  • Page 106 6. Type the Center, Width, and Compound values or import the values. Note: The default title of the XIC includes the compound names shown in the cells for a given row. SCIEX X500 QTOF System System User Guide 106 / 234...
  • Page 107 If the Only show this dialog again if the Shift key is down check box is selected, then the selected action is always used unless the user holds the Shift key to change the option. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 107 / 234...

  • Page 108: Open A Total Ion Chromatogram

    Shift key to change the option. 7. Right-click in the TIC and then use the features shown in Figure 6-14. SCIEX X500 QTOF System System User Guide 108 / 234 RUO-IDV-05-2334-E...
  • Page 109 In both cases, the special characters are not visible. This is particularly useful for chemical formulae. For example, 'H\d3O\u+' is shown as H System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 109 / 234...

  • Page 110: Open A Base Peak Chromatogram

    3. In the Select Samples dialog, select the samples from the Available list and then click the arrow to move the files to the Selected list. Tip! To select one sample, expand the file, click the sample, and then click the arrow. 4. Click OK. SCIEX X500 QTOF System System User Guide 110 / 234 RUO-IDV-05-2334-E...
  • Page 111 Otherwise, the last time range is used. The limited time range saves the user from manually typing the range. If the active graph contains overlaid series from different samples, then the Process All Overlays? dialog opens. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 111 / 234...

  • Page 112: Show The Data And Peaks Table

    This feature is used to show a pane containing two tables for the currently active data: one table for the raw (x, y) values and one for the peak list. 1. Open the Explorer workspace. SCIEX X500 QTOF System System User Guide 112 / 234...
  • Page 113 Tip! To select one sample, expand the file, click the sample, and then click the arrow. 4. Click OK. 5. Click Show > Data and Peaks Table. Figure 6-20 Show Menu Options System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 113 / 234...

  • Page 114: Show Sample Information

    This feature is useful if the user wants to compare two similar, but not identical, Sample Information panes. 1. Open the Explorer workspace. 2. Click File > Open Multiple Samples. SCIEX X500 QTOF System System User Guide 114 / 234 RUO-IDV-05-2334-E...

  • Page 115: Show The Graph Selection Information

    This window shows information about the selected region in a chromatogram or spectrum and is generated when one of those panes is active. 1. Open the Explorer workspace. 2. Click File > Open Multiple Samples. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 115 / 234...
  • Page 116 Tip! To select one sample, expand the file, click the sample, and then click the arrow. 4. Click OK. 5. Click Window > Graph Selection Window. The Graph Selection Info dialog opens. SCIEX X500 QTOF System System User Guide 116 / 234 RUO-IDV-05-2334-E...
  • Page 117 Figure 6-24 Graph Selection Info 7. Select an option from the list: Default Info, XY Info, Standard Deviations, or Signal/Noise. 8. Use the features in Table 6-12 as required. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 117 / 234...
  • Page 118 Y-values The maximum y-value in each of the selections. Peak Area The peak area of the largest peak in each of the selections. Standard Deviations SCIEX X500 QTOF System System User Guide 118 / 234 RUO-IDV-05-2334-E...
  • Page 119 The S/N calculated as the Subtracted Height of the peak divided by the entire range of the noise region (Max Y minus Min Y). 9. (Optional) Click the Options icon. The Graph Info Options dialog opens. Figure 6-25 Graph Info Options Dialog System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 119 / 234...

  • Page 120: Edit Settings In Graphs

    Edit Settings in Graphs 1. Open the Explorer workspace. 2. Click File > Open Multiple Samples. SCIEX X500 QTOF System System User Guide 120 / 234 RUO-IDV-05-2334-E...
  • Page 121 Copy Graph When a spectrum or chromatogram is active, use this option to copy the current graph to the clipboard as a picture. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 121 / 234...

  • Page 122: Work With Data In Graphs

    4. To set the threshold for labeling peaks and subsequent features such as the Data and Peaks table, drag the blue arrow that is shown on the y-axis of the graphs. SCIEX X500 QTOF System System User Guide 122 / 234...
  • Page 123 Operating Instructions Software Figure 6-28 Blue Arrow on the Y-axis 5. Use the features shown in Figure 6-29. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 123 / 234...
  • Page 124 Operating Instructions Software Figure 6-29 Graph Menu Options SCIEX X500 QTOF System System User Guide 124 / 234 RUO-IDV-05-2334-E...
  • Page 125 It removes all of the traces except the currently active one. • In a graph that has more than one overlaid trace, click Graph > Remove All Traces Except Active. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 125 / 234...
  • Page 126 Replaces the graphs with a single trace that is the sum of all of the individual traces. • In an active graph containing more than one overlaid trace, click Graph > Sum Graph Traces. SCIEX X500 QTOF System System User Guide 126 / 234 RUO-IDV-05-2334-E...
  • Page 127 Link the x-axes so that zooming one graph causes the other to zoom automatically. • In an active graph, click Graph > Duplicate Graph. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 127 / 234...

  • Page 128: Use The Two-Pane Operation Tools

    Tip! If the target graph contains more than one overlaid trace, then by default, the source data is added to the active target data only. Hold the Ctrl key to add the source to all data sets in the target pane. SCIEX X500 QTOF System System User Guide 128 / 234...

  • Page 129: Move Panes Or Windows

    Move Panes or Windows 1. Open the Explorer workspace. 2. Click File > Open Multiple Samples. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 129 / 234...
  • Page 130 Show the Graph Selection Information on page 115. Vertical Mode Pane Layout Use this option to change the layout of the information in the window from row format to column format. SCIEX X500 QTOF System System User Guide 130 / 234 RUO-IDV-05-2334-E...

  • Page 131: Perform A Gaussian Smooth

    Selected list. Tip! To select one sample, expand the file, click the sample, and then click the arrow. 4. Click OK. 5. Click Process > Gaussian Smooth. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 131 / 234...

  • Page 132: Threshold Data

    Removes any data points that have an intensity below the current threshold setting. Sets the threshold by dragging the blue arrow that is shown in the y-axis of graphs. 1. Open the Explorer workspace. 2. Click File > Open Multiple Samples. SCIEX X500 QTOF System System User Guide 132 / 234 RUO-IDV-05-2334-E...
  • Page 133 6. If the Process All Overlays? dialog opens, then do one of the following: • Select All Overlaid to generate overlaid XICs for all of the available samples. • Select Active Only to generate XICs only from the currently active sample. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 133 / 234...

  • Page 134: Subset Data (To Graph Selection)

    5. Make a selection in the graph. 6. Click Process > Subset Data (to graph selection). If the active graph contains overlaid series from different samples, then the Process All Overlays? dialog opens. SCIEX X500 QTOF System System User Guide 134 / 234...

  • Page 135: Baseline Subtract Chromatogram

    This is the baseline that is removed from the data at that point. 1. Open the Explorer workspace. 2. Click File > Open Multiple Samples. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 135 / 234...
  • Page 136 If the Only show this dialog again if the shift key is down check box is selected, then the selected action is used unless the user holds the Shift key to change the option. SCIEX X500 QTOF System System User Guide...

  • Page 137: Offset Chromatogram

    Tip! To select one sample, expand the file, click the sample, and then click the arrow. 4. Click OK. 5. Click Process > Offset Chromatogram. The Offset dialog opens. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 137 / 234...

  • Page 138: Centroid A Spectrum

    Creates a centroid of a mass spectrum, that is, replaces a profile spectrum with (mass, intensity) points for the detected peaks only. 1. Open the Explorer workspace. 2. Click File > Open Multiple Samples. SCIEX X500 QTOF System System User Guide 138 / 234 RUO-IDV-05-2334-E...
  • Page 139 Tip! To select one sample, expand the file, click the sample, and then click the arrow. 4. Click OK. 5. Click Process > Centroid Spectrum. The Centroid dialog opens. 6. Use the features shown in Figure 6-43. Figure 6-43 Centroid Dialog System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 139 / 234...

  • Page 140: Export Data As Text

    Shift key to change the option. Export Data as Text Currently active spectrum or chromatogram is saved to a tab-delimited text file. 1. Open the Explorer workspace. 2. Click File > Open Multiple Samples. SCIEX X500 QTOF System System User Guide 140 / 234 RUO-IDV-05-2334-E...
  • Page 141 If spectral data is exported, then the Add Zero Intensity Points for Export dialog opens. Figure 6-45 Add Zero Intensity Points for Export 6. Type a file name. 7. Click Save. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 141 / 234...

  • Page 142: Export The Peak List As Text

    5. Click File > Export > Peak List as Text. 6. Type a file name. 7. Click Save. Print Data 1. Open the Explorer workspace. 2. Click File > Open Multiple Samples. SCIEX X500 QTOF System System User Guide 142 / 234 RUO-IDV-05-2334-E...

  • Page 143: Reset Options

    Use the features on each tab as required. 1. Open the Explorer workspace. 2. Click Edit > Options. The Options dialog opens showing the Graph Appearance tab. 3. Use the features shown in Figure 6-48. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 143 / 234...
  • Page 144 Figure 6-48 Options Dialog Graph Appearance Tab 4. Click the Peak Labeling & Finding tab. 5. Select Mass Spectra from the list. 6. Use the features shown in Figure 6-49. SCIEX X500 QTOF System System User Guide 144 / 234 RUO-IDV-05-2334-E...
  • Page 145 Figure 6-49 Options Dialog Peak Labeling & Finding Tab Mass Spectra 7. Select Chromatograms from the list. 8. Use the features shown in Figure 6-50. Figure 6-50 Options Dialog Peak Labeling & Finding Tab Chromatograms System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 145 / 234...
  • Page 146 6-51. Auto processing options do not apply to dynamically updating spectra. Figure 6-51 Options Dialog Auto Processing Tab 11. Click the XIC tab 12. Use the features shown in Figure 6-52. SCIEX X500 QTOF System System User Guide 146 / 234 RUO-IDV-05-2334-E...

  • Page 147: Analytics Workspace

    Only a user who has been assigned to the Administrator role can perform this task. If this option is selected, then data in the text file is encrypted during export. Set a password to enable encryption. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 147 / 234...

  • Page 148: Enable Project Modified Peak Warning

    Processing methods contain quantitative and qualitative settings for data processing. The Non-targeted workflow is used for unknown components. 1. Open the Analytics workspace. 2. Click Process Method > New. SCIEX X500 QTOF System System User Guide 148 / 234 RUO-IDV-05-2334-E...
  • Page 149 Non-targeted method, which still contains the parameters at the time the method was created. Only the newly created non-targeted method use the changed parameters. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 149 / 234...

  • Page 150: About Results Tables

    Use this option to select all of the rows in the currently active Results Table. This is useful if the user subsequently wants to apply a command, such as Copy, that operates on the selected rows. SCIEX X500 QTOF System System User Guide 150 / 234...
  • Page 151 1. Open the Analytics workspace. 2. Click Results > New. 3. On the Process New Results page, use the arrows to select a sample batch. 4. Select a processing method from the list. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 151 / 234...
  • Page 152 3. Click OK. A progress bar is shown while the new samples are integrated and added to the existing table. SCIEX X500 QTOF System System User Guide 152 / 234 RUO-IDV-05-2334-E...
  • Page 153 Results Table, asymmetry factor column, total width column, and the retention time error columns (either %error column or absolute delta column). Accuracy Shows the accuracy of the standard and quality control samples tolerance. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 153 / 234...
  • Page 154 Tip! If column names are truncated, then move the cursor over the field to show the column name in a tool tip. 1. With a Results Table open, click More > Table display settings. The Results Table Display Settings dialog opens. SCIEX X500 QTOF System System User Guide 154 / 234...
  • Page 155 This option lets the user switch between different column layouts. Column Name The name of the columns, shown in alphabetical order. Visible A checkmark indicates that the column is visible. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 155 / 234...
  • Page 156 Acquisition Date & Shows the date and time at which the sample was acquired. Time Actual For standards and Quality Control samples, shows the expected Concentration known concentration. SCIEX X500 QTOF System System User Guide 156 / 234 RUO-IDV-05-2334-E...
  • Page 157 (at the start of the peak and the end of the peak) to the actual peak height. Values greater than approximately 0.1 indicate that the baseline might not have been integrated correctly and that the peak should be reviewed. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 157 / 234...
  • Page 158 N/A. Dilution Factor Shows the factor by which the sample has been diluted. This factor is used in the calculation of the calibration curve. SCIEX X500 QTOF System System User Guide 158 / 234 RUO-IDV-05-2334-E...
  • Page 159 (Optional) Shows the fragment mass, as specified in the method. The precursor of the fragment is extracted from the MS/MS in the Extraction Mass (Da) column. When provided, this value must be numeric. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 159 / 234...
  • Page 160 • N/A: Indicates that a peak was not detected. • Manual: Indicates that the peak was manually integrated. SCIEX X500 QTOF System System User Guide 160 / 234 RUO-IDV-05-2334-E...
  • Page 161 Shows whether the row is an internal standard. A selected check box indicates that the component for the row is an internal standard, not an analyte. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 161 / 234...
  • Page 162 Shows the peak comment for the internal standard associated with the current analyte. For internal standards, or for analytes without an internal standard, the value is set to N/A. SCIEX X500 QTOF System System User Guide 162 / 234 RUO-IDV-05-2334-E...
  • Page 163 Shows the difference between found mass and extraction mass, expressed in PPM (parts per million) error. Applicable to qualitative workflows only. Mass Error Shows the level of confidence in mass error. Applicable to Confidence qualitative workflows only. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 163 / 234...
  • Page 164 The processing input parameters taken from the processing method. This column is always visible in the Results Table. In the Column Settings dialog, the check box is not available. SCIEX X500 QTOF System System User Guide 164 / 234 RUO-IDV-05-2334-E...
  • Page 165 < > |= or characters 0 to 31 from the ASCII table. Sample Type Shows the type of sample. Refer to Sample Type Filter on page for a description of the different filter types. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 165 / 234...
  • Page 166 For other sample types, this field is for informational purposes only. Vial Number Shows the vial number in the autosampler used to acquire data, as originally specified in the batch. SCIEX X500 QTOF System System User Guide 166 / 234 RUO-IDV-05-2334-E...
  • Page 167 6. (Optional) Click Replace Logo to select another logo for the report. Tip! Use the options in the Replace Logo dialog to modify the logo as required. 7. Click View Pages to view the report. 8. Click Create. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 167 / 234...
  • Page 168 Use this list to change which components are visible in the results, as well as in any linked Peak Review or calibration curve windows . All of the information is shown as it was defined in the processing method. SCIEX X500 QTOF System System User Guide...

  • Page 169: Review Peaks

    6. In the Components and Group list in the left pane, click a component. 7. (Optional) Click Options > Peak review display settings to change the appearance of the Peak Review pane. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 169 / 234...
  • Page 170 Click to view the chromatogram, MS spectrum (and Formula Finder result), and MS/MS spectrum (and Library Search result). The theoretical MS spectrum and library MS/MS spectrum can also be viewed if they are available. SCIEX X500 QTOF System System User Guide 170 / 234...
  • Page 171 Paste Integration Parameters 1. In a graph with an active chromatogram open, right-click and then click Copy Integration Parameters. 2. Right-click in a different chromatogram and then click Paste Integration Parameters. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 171 / 234...
  • Page 172 After adjusting the peak-finding parameters for some chromatograms, use this feature to apply the original parameters from the copy of the processing method saved with the Results Table to all chromatograms for the SCIEX X500 QTOF System System User Guide...
  • Page 173 4. (Optional) Select a row in the table and then click the icon in the table to update the results in the Results Table to use that specific library hit in the analysis. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 173 / 234...
  • Page 174 Tip! Click Options > Get Chemspider hit count to show the ChemSpider Hit Count column in the table below the graph. 10. Click to open the ChemSpider application. Refer to ChemSpider on page 175. SCIEX X500 QTOF System System User Guide 174 / 234 RUO-IDV-05-2334-E...
  • Page 175 Spectra pane: Shows the acquired spectra (in red) and the matching fragments (in blue). More blue fragments indicate a better match. Structure pane: Shows the chemical structure of the compound selected in the results pane. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 175 / 234...

  • Page 176: About Statistics Pane

    Formula Finder Results pane in the software session. The ChemSpider session closes. About Statistics Pane To access this dialog, open a Results Table in the Analytics workspace and then click Views > Statistics pane. SCIEX X500 QTOF System System User Guide 176 / 234 RUO-IDV-05-2334-E...
  • Page 177 The individual values for the samples are shown in additional columns. If the corresponding sample could not be integrated, then N/A is shown. If the Used field has been manually cleared, then the value is shown with a strikethrough. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 177 / 234...
  • Page 178 Note: Refer to the laboratory standard operating procedures for information about accepted values for the statistics, including %CV and Accuracy. • Open a Results Table and then click Views > Statistics pane. SCIEX X500 QTOF System System User Guide 178 / 234...

  • Page 179: Calibration Curve: Options

    When this option is selected, the view between plotting Area versus Concentration and Log(Area) versus Log(Concentration) is toggled. Assign external When this option is selected, a previously exported calibration is applied to the active calibration Results Table. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 179 / 234...
  • Page 180 In the Analytics workspace, the following types of regression are available for the calibration curve: • Linear (y = mx + b) • Linear through Zero (y = mx) • Mean Response Factor SCIEX X500 QTOF System System User Guide 180 / 234 RUO-IDV-05-2334-E...

  • Page 181: Analyzing Data Using Metric Plots

    5. In the metric plot, click Link and then click Link to results table columns or Link to results table rows to link the scrolling in the Results Table to the metric plot. 6. Click Options and then use the following features as required: System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 181 / 234...
  • Page 182 If the Peak Review pane is open, then it also updates to show the corresponding chromatogram. This provides a convenient means of performing peak review for outliers. SCIEX X500 QTOF System System User Guide 182 / 234...

  • Page 183: Audit Trails

    6. Use the Next and Prev buttons to move through the matches. Filter Audited Events using a Set of Specified Criteria The user can filter the audited events in the audit trail based on a set of specified criteria. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 183 / 234...
  • Page 184 Use to filter on a partial word or phrase. Name of the Results Table (.session) file. The user can filter one file or all of the files for the active project. SCIEX X500 QTOF System System User Guide 184 / 234...
  • Page 185 Change the Column Settings in the Audit Trail Viewer 1. Open the Analytics workspace. 2. Click Views > Audit trail viewer. 3. Open a session file. 4. Click Column Settings. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 185 / 234...

  • Page 186: Integration Algorithm Parameters

    This peak is not found when the noise percentage is set to 90% but is found when the noise percentage is set to 40%. Figure 6-58 Peak of Interest Figure 6-59, the left graph shows the noise percentage set to 40%. The right graph is set to 90%. SCIEX X500 QTOF System System User Guide 186 / 234 RUO-IDV-05-2334-E...
  • Page 187 6-60, the left graph shows the Baseline Sub. Window set to 0.1 minutes and the right graph shows the Baseline Sub. Window set to 1 minute. Figure 6-60 Baseline Subtraction Window System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 187 / 234...

  • Page 188: Autopeak Integration Algorithm Parameters

    This option is only available when setting the overall algorithm default values and not during processing method creation or individual peak review, because it is not useful to use this setting for only some peaks. SCIEX X500 QTOF System System User Guide 188 / 234...

  • Page 189: Edit Report Templates

    Figure 6-62 Reporter Template Editor Item Description Report template showing the current tags. Icons: • Add new tag. • Add picture tag. • Show content area. • View document change log. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 189 / 234...
  • Page 190 Do one of the following: • If the cursor is to the left of the tag, press Delete. • If the cursor is to the right of the tag, press Backspace. SCIEX X500 QTOF System System User Guide 190 / 234...

  • Page 191: Reporter Templates

    Sample Information, and Analyte Results Table for the selected analytes. The Analyte Rows Using Visible Results table is printed as shown in the Results Table. All the qualitative confidence traffic Analyte lights are listed at the beginning of the table. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 191 / 234...

  • Page 192: Ms Tune

    If the resolution does not meet the specification, then the user can perform the TOF Tuning procedure to optimize the system. Tip! Users can assess the this procedure by clicking MS Check on the status panel. SCIEX X500 QTOF System System User Guide 192 / 234...

  • Page 193: Optimize The Detector

    3. Make sure that the spray is stable. 4. Click Next. 5. Follow the on-screen instructions. 6. Click Next. The optimization report is shown. 7. (Optional) Save the report. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 193 / 234...

  • Page 194: Tune Q1

    After channel alignment, the system is calibrated and the system performance is determined. If the performance is satisfactory, then the user can save the tuning settings to the system or discard the settings. SCIEX X500 QTOF System System User Guide 194 / 234...

  • Page 195: Tune Q1 High

    3. Double-click the CDS power icon ( ) on the status panel to turn on the CDS flow. 4. Select the correct channel, 1 or 2, click Start, and then close the window. 5. Wait at least 1 minute for the CDS to equilibrate. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 195 / 234...

  • Page 196: Perform Advanced Troubleshooting

    Restore Instrument Data feature. When each tuning procedure is performed, the report and data files are generated to track the optimized results. The .wiff2 data file and report can be found at D:\SCIEX OS Data\Optimization. 1. Open the MS Tune workspace.

  • Page 197: Event Log Workspace

    1. Open the Event Log workspace. 2. (Optional) Open an archived log. 3. Click Print. Archive Logs 1. Open the Event Log workspace. 2. Click Archive > Archive Log. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 197 / 234...
  • Page 198 The Archive Log dialog opens. Figure 6-65 Archive Log Dialog 3. In the Archive event log items older than field, click the date icon and then select a date. 4. Click Archive. SCIEX X500 QTOF System System User Guide 198 / 234 RUO-IDV-05-2334-E...

  • Page 199: Chapter 7 Service And Maintenance Information

    Tip! Perform maintenance tasks regularly to make sure that the mass spectrometer is performing optimally. For information on maintaining the ion source, refer to the ion source Operator Guide. Contact a Qualified Maintenance Person (QMP) to order consumable parts. Contact a SCIEX Field Service Employee (FSE) for maintenance service and support.
  • Page 200 Twin ESI or twin As needed Inspect and replace Refer to the ion source Operator APCI electrodes Guide. Corona discharge As needed Replace Refer to the ion source Operator needle Guide. SCIEX X500 QTOF System System User Guide 200 / 234 RUO-IDV-05-2334-E...

  • Page 201: Clean The Surfaces

    2. Wipe the external surfaces with a soft cloth moistened with water to remove any soap residue. Clean the Front-End The following warning applies to all of the procedures in this section: System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 201 / 234...

  • Page 202: Symptoms Of Contamination

    • Fresh, high-quality (pure) water (at least 18 MΩ de-ionized [DI] water or ultra-pure HPLC-grade water). Old water can contain contaminants that can further contaminate the mass spectrometer. • MS-grade methanol, isopropanol (2-propanol), or acetonitrile SCIEX X500 QTOF System System User Guide 202 / 234...

  • Page 203: Cleaning Best Practices

    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. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 203 / 234...
  • Page 204 • Do not rub the wipe across the aperture. Wipe around the aperture to prevent fibers from the wipes from entering the mass spectrometer. • Do not insert the brush in the aperture on the curtain plate or orifice plate. SCIEX X500 QTOF System System User Guide 204 / 234...

  • Page 205: Prepare The Mass Spectrometer

    2. Remove the ion source. Refer to the ion source Operator Guide. When the ion source is not in use, store it to protect it from damage and to maintain operating integrity. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 205 / 234...

  • Page 206: Clean The Curtain Plate

    4. Using a dampened wipe or small poly swab, clean the aperture. 5. Wait until the curtain plate is dry. 6. Inspect the curtain plate for solvent stains or lint, removing any residue with a clean, slightly damp, lint-free wipe. SCIEX X500 QTOF System System User Guide 206 / 234 RUO-IDV-05-2334-E...

  • Page 207: Clean The Front Of The Orifice Plate

    2. Install the ion source on the mass spectrometer. Refer to the ion source Operator Guide. Tighten the ion source by turning the source latches down into the locking position. 3. Click Activate Devices on the status panel in the SCIEX OS software. Empty the Source Exhaust Drain Bottle WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard.
  • Page 208 7. Install the cap on the bottle and then put the bottle in the holder. 8. Attach the hoses to the cap and then secure them tightly with clamps. SCIEX X500 QTOF System System User Guide 208 / 234...
  • Page 209 Connection to the mass spectrometer: 1.6 cm (0.625 inch) i.d. Roughing pump vacuum inlet hose Note: Source exhaust hose connections at the drain bottle, mass spectrometer, and the lab vent are secured with hose clamps. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 209 / 234...

  • Page 210: Replace The Check Valve And Flow Module

    1. To remove the check valve, loosen the finger-tight PEEK fittings on both sides of the check valve. Note: When installing the check valve, make sure that the arrow on the check valve points toward the ion source. SCIEX X500 QTOF System System User Guide 210 / 234...

  • Page 211: Inspect The Roughing Pump Oil Level

    • Inspect the sight glass on the roughing pump to verify that the oil is above the minimum level. If the oil is below the minimum level, then contact the qualified maintenance person (QMP) or SCIEX field service employee (FSE).

  • Page 212: Storage And Handling

    Follow local regulations when disposing of components. If the mass spectrometer must be stored for a long time or prepared for shipping, then contact a SCIEX FSE for decommissioning information. To disconnect power from the mass spectrometer, remove the mains supply connector from the AC mains supply.

  • Page 213: Move The Mass Spectrometer

    3. On the right front side of the mass spectrometer, pull out the locking pin that secures the lifting bar, pull out the bar until the hole in the bar lines up with the hole in the tube, and then secure the bar with the locking pin. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 213 / 234...
  • Page 214 5. Install a short block on each lifting bar, and then secure it with a locking pin. CAUTION: Potential System Damage. Make sure that all locking pins are fully inserted, to avoid dropping the mass spectrometer while it is being moved. SCIEX X500 QTOF System System User Guide 214 / 234...
  • Page 215 Note: The end of the bar with the longest extension past the block must be at the front of the mass spectrometer. 7. Repeat step on the left side of the mass spectrometer. 8. Install the locking pins in the long rods. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 215 / 234...
  • Page 216 Figure 7-11 Tall Block Installed 10. At the front of the mass spectrometer, insert a short rod through the tall blocks. 11. Secure the short rods with two locking pins. SCIEX X500 QTOF System System User Guide 216 / 234...
  • Page 217 Service and Maintenance Information Figure 7-12 Installing the Locking Pin on the Short Rod Figure 7-13 Lifting Kit Installed (X500R System) System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 217 / 234...
  • Page 218 13. With the assistance of one additional person, move the roughing pump to the new location. 14. Install the left and right skirts. 15. Connect the vacuum hose, gas tubing, source exhaust tubing, power cable, ethernet cable, and TDC cable to the mass spectrometer. SCIEX X500 QTOF System System User Guide 218 / 234 RUO-IDV-05-2334-E...

  • Page 219: Generate A Support Package

    2. Click About in the left panel. 3. Under Service and Support, click Generate a Support Package. The zipped report is saved to the D:\ServicePackages folder. 4. Send the zip file to support. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 219 / 234...

  • Page 220: Chapter 8 Mass Spectrometer Troubleshooting

    Troubleshooting This section contains information for troubleshooting basic system issues. Certain activities can only be carried out by a SCIEX -trained Qualified Maintenance Person (QMP) in the laboratory. For advanced troubleshooting, contact a SCIEX Field Service Employee (FSE). Table 8-1 System Issues...
  • Page 221 10. If the O-rings are on the ion source, then install them on the vacuum interface. If they are missing, then contact an FSE. 11. Troubleshoot the LC system. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 221 / 234...
  • Page 222 1. Check the CDS connections. 2. The CDS tubing is blocked. 2. Inspect the calibrant tubing for blockages. For sales, technical assistance, or service, contact an FSE or visit the SCIEX Web site at sciex.com for contact information. SCIEX X500 QTOF System...

  • Page 223: Appendix A Recommended Calibration Ions

    Recommended Calibration Ions The following table list the standards recommended by SCIEX for calibrating the SCIEX X500 QTOF system. Table A-1 Calibration Solutions Part Number Description Quantity 5042914 APCI Positive Calibration Solution for the SCIEX X500 System 100 mL 5042918 APCI Positive Calibration Solution for the SCIEX X500 System, 5 5 ×...
  • Page 224 Fragment Ion 1 277.0983 403.1122 Fragment Ion 2 249.1033 277.0983 Fragment Ion 3 217.0771 158.0611 Fragment Ion 4 200.0591 125.0067 Fragment Ion 5 158.0611 93.0344 Fragment Ion 6 130.0662 SCIEX X500 QTOF System System User Guide 224 / 234 RUO-IDV-05-2334-E...

  • Page 225: Esi Calibration Ions

    Fragment ion 2 270.104 577.254 811.529 Fragment ion 3 242.073 448.197 724.497 Fragment ion 4 235.136 397.212 706.486 Fragment ion 5 227.05 365.186 607.418 Fragment ion 6 220.112 236.128 532.334 System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 225 / 234...
  • Page 226 520.9100 928.8344 Fragment Ion 4 112.9856 154.9738 204.9706 384.9352 792.8596 Fragment Ion 5 68.99576 112.9856 154.9738 248.9604 656.8848 Fragment Ion 6 112.9856 204.9706 520.9100 Fragment Ion 7 154.9738 384.9352 SCIEX X500 QTOF System System User Guide 226 / 234 RUO-IDV-05-2334-E...
  • Page 227 Recommended Calibration Ions Table A-9 TOF MS/MS Negative Product Ions (continued) Precurcor Ion 248.9 384.9 520.9 792.8 1200.784 (m/z) Fragment Ion 8 112.9856 248.9604 204.9706 154.9738 System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 227 / 234...

  • Page 228: Appendix B Exact Masses And Chemical Formulas

    Table B-1 Reserpine Exact Masses Reserpine (C Description Mass Molecular Ion C 609.28066 Fragment C 448.19659 Fragment C 397.21218 Fragment C 365.18597 Fragment C 236.12812 Fragment C 195.06519 Fragment C 174.09134 SCIEX X500 QTOF System System User Guide 228 / 234 RUO-IDV-05-2334-E...

  • Page 229: Appendix C Glossary Of Symbols

    China RoHS logo. The device does not contain toxic and hazardous substances or elements above the maximum concentration values, and it is an environmentally-friendly product that can be recycled and reused. System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 229 / 234...
  • Page 230 Explosion Hazard Fire Hazard 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 Ionizing Radiation Hazard Keep dry. Do not expose to rain.
  • Page 231 Laser Radiation Hazard Lifting Hazard Manufacturer Personal Injury Hazard Pinch Hazard Pressurized Gas Hazard Protective Earth (ground) Puncture Hazard Serial number Toxic Chemical Hazard USB 2.0 connection Ultraviolet Radiation Hazard System User Guide SCIEX X500 QTOF System RUO-IDV-05-2334-E 231 / 234...
  • Page 232 Glossary of Symbols Symbol Description Volt Ampere (power) Volts (voltage) WEEE. Do not dispose of equipment as unsorted municipal waste. Watts yyyy-mm-dd Date of manufacture SCIEX X500 QTOF System System User Guide 232 / 234 RUO-IDV-05-2334-E...

  • Page 233: Appendix D Glossary Of Warnings

    TRIPPED IMPACT-O-GRAPH OR TIP-N-TELL INDICATORS, TRIPPED IMPACT-O-GRAPH OR TIP-N-TELL INDICATORS, ON THE WAYBILL BEFORE ACCEPTING SHIPMENT. ON THE WAYBILL BEFORE ACCEPTING SHIPMENT. NOTIFY YOUR LOCAL SCIEX CUSTOMER SUPPORT NOTIFY YOUR LOCAL SCIEX CUSTOMER SUPPORT ENGINEER IMMEDIATELY. ENGINEER IMMEDIATELY. TIP & TELL...
  • Page 234 TEN PERSONS REQUIRED TO LIFT THIS EQUIPMENT. WARNING: NO USER SERVICEABLE PARTS INSIDE. WARNING: NO USER SERVICEABLE PARTS INSIDE. REFER SERVICING TO QUALIFIED PERSONNEL. REFER SERVICING TO QUALIFIED PERSONNEL. Note: Consult instructions for use. SCIEX X500 QTOF System System User Guide 234 / 234 RUO-IDV-05-2334-E...

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