AB Sciex QTRAP 4500 LC/MS/MS system System User's Manual
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AB Sciex QTRAP 4500 LC/MS/MS system System User's Manual

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AB SCIEX 4500 Series of Instruments
System User Guide
Document Number: RUO-IDV-05-0264-A
Release Date: April 2013

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Summary of Contents for AB Sciex QTRAP 4500 LC/MS/MS system

  • Page 1 AB SCIEX 4500 Series of Instruments System User Guide Document Number: RUO-IDV-05-0264-A Release Date: April 2013...
  • Page 2 This document is provided to customers who have purchased AB SCIEX equipment to use in the operation of such AB SCIEX equipment. This document is copyright protected and any reproduction of this document or any part of this document is strictly prohibited, except as AB SCIEX may authorize in writing.
  • Page 3 Revision Log Revision Description Date D5030863 A First release of document. March 2012 RUO-IDV-05-0264-A Assigned new document number. Updated template. April 2013 Applied new content model. System User Guide 4500 Series of Instruments RUO-IDV-05-0264-A 3 of 138...
  • Page 4 Revision Log 4500 Series of Instruments System User Guide 4 of 138 RUO-IDV-05-0264-A...

  • Page 5: Table Of Contents

    Contents Chapter 1 Operational Precautions and Limitations ..... . 9 General Safety Information ......... .9 Regulatory Compliance .
  • Page 6 Contents Create a Hardware Profile ........39 Add Devices to a Hardware Profile .
  • Page 7 Contents Navigate Between Samples in a Data File ......77 Show Experimental Conditions ........78 Show Data in Tables .
  • Page 8 Contents Prepare for Cleaning ......... . .123 Clean the Curtain Plate .

  • Page 9: Chapter 1 Operational Precautions And Limitations

    Operational Precautions and Limitations 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. In addition to this section, refer to Hazards Symbols on page 17 for information on the symbols and conventions used in the laboratory environment, on the system, and in this documentation.

  • Page 10: Regulatory Compliance

    Operational Precautions and Limitations Regulatory Compliance This system complies with the standards and regulations listed in this section. Applicable labels have been affixed to the system. Australia and New Zealand • Electromagnetic Interference—AS/NZ CISPR 11 (Class A) • Safety—AS/NZ 61010-1 Canada •...

  • Page 11: International

    Operational Precautions and Limitations International • Electromagnetic Compatibility—IEC 61326-1, IEC CISPR 11 Class A • Safety—IEC 61010-1, IEC 61010-2-061 For more information, refer to the Declaration of Conformity included with the system. Electrical Precautions AC Mains Supply WARNING! Electrical Shock Hazard: Use only qualified personnel for the installation of all electrical supplies and fixtures, and make sure that all installations adhere to local regulations.

  • Page 12: System Safe Fluids

    The following fluids can safely be used with the system. Caution: Potential System Damage: Do not use any other fluid until confirmation is received from AB SCIEX that it will not present a hazard. This is not an exhaustive list. •...

  • Page 13: Ventilation Precautions

    Operational Precautions and Limitations Ventilation Precautions The venting of fumes and disposal of waste must be in accordance with all federal, state, provincial, and local health and safety regulations. Use the system indoors in a laboratory that complies with the environmental conditions recommended in the Site Planning Guide for the system.

  • Page 14: Decommissioning And Disposal

    Familiarization Checklist to familiarize the customer with system operation, cleaning, and basic maintenance. Only qualified AB SCIEX personnel shall install and service the equipment. Only personnel qualified by AB SCIEX shall operate and maintain the equipment. Contact an FSE for more information.
  • Page 15 Erroneous data may be generated if the system is operating outside the recommended environmental conditions or with unauthorized modifications. Contact an AB SCIEX representative for more information on servicing the system. System User Guide...
  • Page 16 Operational Precautions and Limitations 4500 Series of Instruments System User Guide 16 of 138 RUO-IDV-05-0264-A...

  • Page 17: Chapter 2 Hazards Symbols

    Hazards Symbols This section lists the hazard symbols and conventions used in the laboratory environment, on the system, and in the documentation. Occupational Health and Safety Symbols This section describes some occupational health and safety symbols found in the documentation and laboratory environment.

  • Page 18: Symbols, Indicators, And Labels

    Hazards Symbols Table 2-3 Mechanical Hazard Symbols (Continued) Safety Symbol Description Radiation Hazard Table 2-4 Pressurized Gas Hazard Warning Symbols Safety Symbol Description Pressurized Gas Hazard Symbols, Indicators, and Labels Packaging Table 2-5 Labels on the Mass Spectrometer Shipping Materials External Labels Definition Action...

  • Page 19: Mass Spectrometer

    Hazards Symbols Table 2-5 Labels on the Mass Spectrometer Shipping Materials (Continued) External Labels Definition Action Impact Indicator The indicator is activated if the Write on the Bill of Lading and container has suffered a shock check for damage. Any claims greater than the level marked for shock damage require a on the indicator.

  • Page 20: Documentation

    Hazards Symbols Table 2-6 Labels on the Mass Spectrometer (Continued) External Labels Definition This system is for research use only. It is not intended for use in diagnostic procedures. FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES. Caution, refer to accompanying documents. Minimum of six persons required to safely lift this equipment.
  • Page 21 Hazards Symbols WARNING! Warning signifies an operation that could cause personal injury if precautions are not followed. Caution: Caution signifies an operation that could cause damage to the system or loss of data if precautions are not followed. Tip! A 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.
  • Page 22 Hazards Symbols 4500 Series of Instruments System User Guide 22 of 138 RUO-IDV-05-0264-A...

  • Page 23: Chapter 3 Principles Of Operation

    ® Nanospray ion source NanoSpray Ion Source Operator Guide, available monitors (optional) from the ion source documentation CD, or from the AB SCIEX web site, at www.absciex.com Syringe pump Adjust the Integrated Syringe Pump Position on page Ion source Turbo V™ Ion Source Operator Guide, available from...

  • Page 24: Panel Symbols

    The diverter valve is installed below the DuoSpray valve. For information about the DuoSpray ion source, refer to the DuoSpray™ Ion Source Operator Guide, available from the ion source documentation CD, or from the AB SCIEX web site, at www.absciex.com Panel Symbols Table 3-1 shows the mass spectrometer status LEDs.
  • Page 25 Principles of Operation Figure 3-2 Change and Side Views Item Description For more information... Roughing pump vacuum connection Contact an FSE. Nitrogen gas supply (Curtain Gas™ Contact an FSE. supply, CAD gas) Source exhaust supply Contact an FSE. Source communication connection Contact an FSE.

  • Page 26: Theory Of Operation

    Principles of Operation Theory of Operation Mass spectrometry measures the mass-to-charge ratio of ions to identify unknown compounds, to quantify known compounds, and to provide information about the structural and chemical properties of molecules. The 4500 series of instruments has a series of quadrupole filters that transmit ions according to ®...

  • Page 27: Chapter 4 Operating Instructions - Hardware

    Operating Instructions — Hardware Start Up the System WARNING! Lifting Hazard: Risk of personal injury or system damage. If the system must be moved, contact an FSE. Note: Before operating the system, read the safety information in the Operational Precautions and Limitations on page Before the system is turned on, make sure the site requirements specified in the Site Planning Guide are met.

  • Page 28: Shut Down The System

    Operating Instructions — Hardware Shut Down the System Tip! If the mass spectrometer will not be used for a length of time, we recommend that it be left in standby with the ion source in place. If the mass spectrometer must be shut down, follow these instructions.
  • Page 29 Operating Instructions — Hardware Figure 4-1 Lowering the Base Item Description Syringe plunger. Release button. Press to raise or lower the base. 2. Adjust the post so that it triggers the automatic syringe stop before the syringe plunger hits the bottom of the glass syringe. Figure 4-2 Safety Stop Item Description...
  • Page 30 Operating Instructions — Hardware Item Description Post. Adjust the height to prevent the syringe plunger from hitting the syringe during sample infusion. Post lock screw. Tighten the screw after the height of the post is adjusted. 3. Turn the side screws to secure the syringe. Figure 4-3 Turning the Side Screws 4.
  • Page 31 Operating Instructions — Hardware Figure 4-4 Syringe Pump Button and LED Item Description Syringe pump status LED Syringe pump on/off button System User Guide 4500 Series of Instruments RUO-IDV-05-0264-A 31 of 138...

  • Page 32: Plumb The Diverter Valve

    Operating Instructions — Hardware Plumb the Diverter Valve Plumb the diverter valve for both injector and diverter modes. Plumb the Diverter Valve in Injector Mode The diverter valve is a two position, 6 port valve. If you put the valve in Position A (Figure 4-5), the sample flows through the external loop.
  • Page 33 Operating Instructions — Hardware Figure 4-6 Diverter Valve—Injector Mode Position B Item Description Sample in Waste out Sample loop Mobile phase in To column System User Guide 4500 Series of Instruments RUO-IDV-05-0264-A 33 of 138...

  • Page 34: Plumb The Diverter Valve In Diverter Mode

    Operating Instructions — Hardware Plumb the Diverter Valve in Diverter Mode Figure 4-7 Diverter Valve—Diverter Mode Position A Item Description To mass spectrometer From column Waste out 4500 Series of Instruments System User Guide 34 of 138 RUO-IDV-05-0264-A...
  • Page 35 Operating Instructions — Hardware Figure 4-8 Diverter Valve—Diverter Mode Position B Item Description To mass spectrometer From column Waste out System User Guide 4500 Series of Instruments RUO-IDV-05-0264-A 35 of 138...
  • Page 36 Operating Instructions — Hardware 4500 Series of Instruments System User Guide 36 of 138 RUO-IDV-05-0264-A...

  • Page 37: Chapter 5 Operating Instructions - Sample Workflows

    Operating Instructions — Sample Workflows Table 5-1 Instrument Setup Step To do this... Find the What does it do? information in... Create a hardware profile. Create a Hardware Each hardware profile must Profile on page 39 include a mass spectrometer. Only devices included in the active hardware profile can be used when creating acquisition...
  • Page 38 Operating Instructions — Sample Workflows Table 5-2 Sample Acquisition Workflow (Continued) Step To do this... Find the information What does it do? in... Acquire data. Acquire Data on page 66 Running samples involves managing the acquisition queue and monitoring instrument and device status.

  • Page 39: Chapter 6 Operating Instructions - Hardware Profiles And Projects

    Operating Instructions — Hardware Profiles and Projects Hardware Profiles A hardware profile tells the software which mass spectrometer and devices to use, and how the instrument and the devices are configured and connected to the computer. Each hardware profile must include a mass spectrometer. Before creating an acquisition method, make sure that all devices used in the method are included in the hardware profile.
  • Page 40 Operating Instructions — Hardware Profiles and Projects Figure 6-2 Create New Hardware Profile Dialog 3. In the Profile Name field, type a name. 4. Click Add Device. In the Available Devices dialog, in the Device Type field, Mass Spectrometer is the preset value.
  • Page 41 Operating Instructions — Hardware Profiles and Projects Figure 6-3 Available Devices Dialog 6. Click OK. 7. In the Devices in current profile list, select the mass spectrometer. 8. Click Setup Device. 9. (Optional) To configure the mass spectrometer for the integrated syringe pump, on the Configuration tab, select Use integrated syringe pump.
  • Page 42 Operating Instructions — Hardware Profiles and Projects Figure 6-4 Configuration Tab with Syringe Pump Configured 10. (Optional) To configure the mass spectrometer for the diverter valve, on the Configuration tab, select Use integrated injector/diverter valve. Figure 6-5 Configuration Tab with Diverter Valve Configured 11.

  • Page 43: Add Devices To A Hardware Profile

    Operating Instructions — Hardware Profiles and Projects 14. In the Create New Hardware Profile dialog, click OK. 15. In the Hardware Configuration Editor, click the hardware profile. 16. Click Activate Profile. The check mark turns green. If a red x is shown, then there is an issue with the hardware profile activation.

  • Page 44: Troubleshoot Hardware Profile Activation

    Operating Instructions — Hardware Profiles and Projects Note: For devices using serial communication, make sure that the serial port selected matches the serial port to which the device is physically connected. If a serial expansion cable is used, then the number selected in the profile is the number on the cable plus two.

  • Page 45: Projects And Subprojects

    Operating Instructions — Hardware Profiles and Projects Tip! On computers with two built-in serial ports, the first port on the serial port expansion card is usually COM3, even though the cable indicates P1. 4. Verify that the communication settings with the device (for example, dip switch settings) are set correctly and match the settings on the Communication tab.

  • Page 46: Create Subprojects

    Operating Instructions — Hardware Profiles and Projects Figure 6-7 Create New Project/Subproject Dialog 4. (If subprojects are used) In the Subproject name field, type a name for the first subproject or use the existing date. 5. (Optional) To use this project and subproject folder organization for all new projects, select the Set configuration as default for new projects check box.

  • Page 47: Switch Between Projects And Subprojects

    Operating Instructions — Hardware Profiles and Projects 1. Click Tools > Project > Copy Subproject. 2. In the Copy Subproject dialog, click Browse to navigate to the subproject source. 3. Click OK. 4. In the Source Subproject list, select the subproject. 5.

  • Page 48: Installed Project Folders

    Operating Instructions — Hardware Profiles and Projects Table 6-1 Icons on the Toolbar (Continued) Icon Name Function Copy Subproject Copies a Subproject folder. Subprojects can be copied only from another project that has existing subprojects. If the same folders exist at both the project and subproject levels, the software uses the project level folders.

  • Page 49: Chapter 7 Operating Instructions - Tune And Calibrate

    Required Materials • Tuning solutions that are supplied in the Standards Chemical Kit shipped with the system. If needed, a new kit can be ordered from AB SCIEX. • 5 mL, 1 mL, and 250 µL serial gas-tight syringes. • red PEEK sample tubing.

  • Page 50: Verify Or Adjust Performance

    Operating Instructions — Tune and Calibrate 8. Select a Tuning Solution. Depending on the solution selected, different modes are available. Click a polarity. ii. If available, click Q1 and Q3 in the Quad section. If available, click the required scan speeds. iii.

  • Page 51: System User Guide 4500 Series Of Instruments

    Operating Instructions — Tune and Calibrate Figure 7-1 Results Summary System User Guide 4500 Series of Instruments RUO-IDV-05-0264-A 51 of 138...
  • Page 52 Operating Instructions — Tune and Calibrate 4500 Series of Instruments System User Guide 52 of 138 RUO-IDV-05-0264-A...

  • Page 53: Chapter 8 Operating Instructions - Acquisition Methods

    Operating Instructions — Acquisition Methods An acquisition method consists of experiments and periods. Use the Acquisition Method editor to create a sequence of periods and experiments for the instrument and devices. Create Acquisition Methods Only devices configured in the active hardware profile appear in the Acquisition method pane. Any devices added to the hardware profile must also be added to existing acquisition methods.

  • Page 54: Add A Period

    Operating Instructions — Acquisition Methods Add a Period • In the Acquisition method pane, right-click the Mass Spec icon, and then click Add period. A period is added below the last period created. Copy an Experiment into a Period Prerequisite Procedures •...

  • Page 55: Lit-Mode Scan Types

    Operating Instructions — Acquisition Methods Q1 Multiple Ions (Q1 MI): A zero width scan type using the Q1 quadrupole. The ion intensity is returned for the specified masses only. Q3 MS (Q3): A full scan using the third quadrupole (Q3). The ion intensity is returned for every mass in the scan range.

  • Page 56: About Spectral Data Acquisition

    Operating Instructions — Acquisition Methods MS/MS/MS (MS3): In this scan mode, a precursor ion is selected by the Q1 quadrupole and fragmented with collisionally activated dissociation in the Q2 collision cell. The resulting product ions are all transmitted to the linear ion trap, where a single product ion is then isolated. The isolated ion is further fragmented in the linear ion trap, and the resulting product ions are scanned out of the ion trap at one of three scan speeds.
  • Page 57 Operating Instructions — Acquisition Methods Figure 8-1 shows the location of the parameters on the ion optics path. Figure 8-1 Ion Optics Path and Parameters Item Parameter Parameter Scan Type Type IS (IonSpray Source and The IS parameter controls the Voltage) voltage applied to the electrode that ionizes the sample in the ion source.
  • Page 58 Operating Instructions — Acquisition Methods Item Parameter Parameter Scan Type Type DP (Declustering Compound The DP parameter controls the Potential) voltage on the orifice, which controls the ability to decluster ions between the orifice and the skimmer (or for ® systems with an IonDrive QJet guide, between the orifice and IonDrive QJet ion guide).
  • Page 59 Operating Instructions — Acquisition Methods Item Parameter Parameter Scan Type Type EP (Entrance Compound The EP parameter controls the Potential) potential difference between the voltage on Q0 and ground. The entrance potential guides and focuses the ions through the high- pressure Q0 region.
  • Page 60 Operating Instructions — Acquisition Methods Item Parameter Parameter Scan Type Type CE (Collision Compound The CE parameter controls the MRM, MS2, Energy) potential difference between Q0 and Prec, NL, Q2 (collision cell). It is used only in and LIT MS/MS-type scans. This parameter is the amount of energy that the precursor ions receive as they are accelerated into the collision cell,...
  • Page 61 Operating Instructions — Acquisition Methods Item Parameter Parameter Scan Type Type MCS (Multi- Compound The MCS Barrier parameter controls Charge the voltage used to eliminate the Separation) singly-charged ions from the LIT. Barrier Use the preset value. Q3 Cool Time Compound The Q3 Cool Time parameter controls the amount of time that the...

  • Page 62: Acquisition Method Editor Icons

    Operating Instructions — Acquisition Methods Acquisition Method Editor Icons Table 8-2 Acquisition Method Editor Icons Icon Name Function Mass Spec Shows the MS tab in the Acquisition Method editor. Period Right-click to add an experiment, add an IDA Criteria Level, or delete the period. Autosampler Opens the Autosampler Properties tab.

  • Page 63: Chapter 9 Operating Instructions - Batches

    Operating Instructions — Batches A batch is a collection of information about the samples to be analyzed. Batches tell the software the order in which to analyze the samples. For information about importing batches, refer to the Advanced User Guide. Set Queue Options The queue goes one by one through the list, acquiring each sample with the selected acquisition method.

  • Page 64: Add Sets And Samples To A Batch

    Operating Instructions — Batches If an LC method is used, then before the run is started, make sure that there is enough solvent in the reservoirs for the primary flow rate for all of the sample runs and the maximum idle time. 5.
  • Page 65 Operating Instructions — Batches add incremental numbering to the end of the sample name, select the Sample number check box. 7. If the Sample number check box is selected, in the Number of digits field, type the number of digits to include in the sample name. For example, if 3 is typed, the sample names would be samplename001, samplename002, samplename003.

  • Page 66: Submit A Sample Or Set Of Samples

    Operating Instructions — Batches • Select Vial Positions using the Locations Tab (Optional) on page 67 Submit a Sample or Set of Samples 1. In the Batch Editor, click the Submit tab. 2. If the Submit Status section contains a message about the status of the batch, do one of the following: •...

  • Page 67: Set Sample Locations In The Batch Editor

    Operating Instructions — Batches Item Description Queue status should be Stand By. Queue Server should be in Normal mode. Refer to Queue States on page 3. Click Acquire > Start Sample. Note: It is recommended that the user runs the sample again in the event of an abnormal termination during sample acquisition.
  • Page 68 Operating Instructions — Batches Figure 9-4 Batch Editor, Locations Tab 2. In the Set list, select the set. 3. In the Autosampler list, select the autosampler. The appropriate number of rack spaces for the autosampler is shown in the graphic rack display.

  • Page 69: Stop Sample Acquisition

    Operating Instructions — Batches Stop Sample Acquisition When a sample acquisition is stopped, the current scan finishes before the acquisition is stopped. 1. In the Queue Manager, click the sample in the queue after the point where acquisition should stop. 2.

  • Page 70: Batch Editor Right-Click Menu

    Operating Instructions — Batches Batch Editor Right-Click Menu Right-click in the Batch Editor table to access the following options. Figure 9-5 Batch right-click menu Menu Function Open Opens a batch file. Import From Imports a file. Save As Batch Saves the batch with a different name. Save As a Template Saves the batch as a template.

  • Page 71: Queue States

    Operating Instructions — Batches Queue States The current state of the queue is indicated in the Queue Server. Figure 9-6 Queue Server Indicator Showing Normal Mode Figure 9-7 Queue Server Indicator Showing Tune Mode The first icon in Figure 9-6 shows the queue state.

  • Page 72: View Instrument And Device Status Icons

    Operating Instructions — Batches Table 9-2 Queue States (Continued) Icons State Definition PreRun In the PreRun state, the method is being downloaded to each device and device equilibration is occurring. This state occurs before the acquisition of each sample in a batch. Acquiring In the Acquiring state, the method is run and data acquisition occurs.

  • Page 73: Queue Right-Click Menu

    Operating Instructions — Batches Table 9-3 Instrument and Device Status (showing the instrument icon) (Continued) Status Icon Background Color Description Aborting Green The device is aborting a run. Downloading Green A method is being transferred to the device. Ready Green The device is not running, but is ready to run.

  • Page 74: Icon Quick Reference: Acquire Mode

    Operating Instructions — Batches Menu Function Sort Sorts by the preselect column. Column Settings Changes the column settings. Icon Quick Reference: Acquire Mode Table 9-4 Acquire Mode Icons Icon Name Function View Queue Shows the sample queue. Instrument Queue Shows a remote instrument station. Status for Remote Instrument Shows the status of a remote instrument.
  • Page 75 Operating Instructions — Batches Table 9-4 Acquire Mode Icons (Continued) Icon Name Function Standby Puts the instrument in standby mode. Ready Puts the instrument in ready mode. Reserve Instrument for Reserves the instrument for tuning and calibrating. Tuning IDA Method Wizard Starts the IDA Method Wizard.
  • Page 76 Operating Instructions — Batches 4500 Series of Instruments System User Guide 76 of 138 RUO-IDV-05-0264-A...

  • Page 77: Chapter 10 Operating Instructions - Analyze And Process Data

    Operating Instructions — Analyze and Process Data Use the sample files installed in the Example folder to learn how to view and analyze data using the most common analysis and processing tools. For more information about the following topics, refer to the Advanced User Guide. •...

  • Page 78: Show Experimental Conditions

    Operating Instructions — Analyze and Process Data • To skip to the next sample in the data file, click the icon with the arrow pointing to the right. • To skip to a non-sequential sample, click the icon with the arrow curving to the right. •...

  • Page 79: Show Data In Tables

    Operating Instructions — Analyze and Process Data Show Data in Tables Prerequisite Procedure • Open Data Files on page 77 • Click Explore > Show > Show List Data. The data is shown in a pane below the graph. Figure 10-1 Peak List Tab Table 10-2 RIght-Click Menu for the Spectral Peak List Tab Menu Function...

  • Page 80: Show Adc Data

    Operating Instructions — Analyze and Process Data Table 10-3 Right-Click Menu for the Chromatographic Peak List Tab Menu Function Analyst Classic Opens the Analyst Classic dialog. Parameters IntelliQuan Parameters Opens the Intelliquan dialog. Save As Text Saves the data as text file. Delete Pane Deletes the pane.

  • Page 81: Show Basic Quantitative Data

    Operating Instructions — Analyze and Process Data Show Basic Quantitative Data Prerequisite Procedure • Open Data Files on page 77 1. In the Peak List tab, right-click and select Show Peaks in Graph. Peaks are shown in two colors. 2. To change the peak finding algorithm settings, right-click and then select either Analyst Classic Parameters or Intelliquan Parameters, which ever is active.

  • Page 82: Show Tics From A Spectrum

    Operating Instructions — Analyze and Process Data Show TICs from a Spectrum Prerequisite Procedure • Open Data Files on page 77. Open a data file containing spectra. Tip! To see an example data file, make sure that the Example project is selected. Open the LIT folder, and then open the Reserpine.wiff file.
  • Page 83 Operating Instructions — Analyze and Process Data Table 10-5 Summary of XIC Generation Methods (Continued) Method Use with Use with Extraction Chromatogram Spectrum Base peak Can be used only with BPCs (Base masses Peak Chromatograms.) Use the Use Base Peak Masses command to extract ions results in an XIC with a different colored trace for each mass.

  • Page 84: Generate Bpcs

    Operating Instructions — Analyze and Process Data 2. Click Explore > Extract Ions > Use Base Peak Masses. An XIC of the specified selection opens below the spectrum pane. The experiment information at the top of the pane shows the mass range and the maximum intensity in counts per second.
  • Page 85 Operating Instructions — Analyze and Process Data The selection is highlighted in blue. 2. Click Explore > Show > Show Base Peak Chromatogram. The selections are shown in the Start Time and End Time fields. Figure 10-4 Base Peak Chromatogram Options Dialog 3.

  • Page 86: Generate Xwcs

    Operating Instructions — Analyze and Process Data Generate XWCs Up to three ranges can be extracted from a DAD spectrum to generate the XWC. For more information about using the available icons, refer to Table 10-8. Prerequisite Procedure • Open Data Files on page 77.

  • Page 87: Generate Twcs

    Operating Instructions — Analyze and Process Data Generate TWCs A TWC shows total absorbance (mAU) on the y-axis plotted against time on the x-axis. For more information about using the available icons, refer to Table 10-8. Prerequisite Procedure • Open Data Files on page 77.
  • Page 88 Operating Instructions — Analyze and Process Data Table 10-6 Right-Click Menu for Chromatogram Panes (Continued) Menu Function Show Contour Plot Shows a color-coded plot of a data set, where the color represents the intensity of the data at that point. Only certain MS modes are supported.

  • Page 89: Data Processing

    Operating Instructions — Analyze and Process Data Table 10-7 Right-Click Menu for Spectra Panes (Continued) Menu Function Show Last Scan Shows the scan prior to the selection. Select Peaks For Label In this dialog, select the parameters to reduce peak labeling. Delete Pane Deletes the selected pane.
  • Page 90 Operating Instructions — Analyze and Process Data Table 10-8 Graph Options (Continued) To do this... use this menu option..or click this icon Rescale graph to its • Select the graph. Click Explore > Home Graph. original size Move a pane •...

  • Page 91: Zoom In On The Y-Axis

    Operating Instructions — Analyze and Process Data Table 10-8 Graph Options (Continued) To do this... use this menu option..or click this icon Tile panes • Select the graph. Click Window > Tile all Panes. Zoom In on the Y-axis 1.
  • Page 92 Operating Instructions — Analyze and Process Data Table 10-9 Explore Quick Reference: Chromatograms and Spectrum (Continued) Icon Name Function Show TIC Generates a TIC from a spectrum. Extract Using Dialog Extracts ions by selecting masses. Show Base Peak Generates a BPC. Chromatogram Show Spectrum Generates a spectrum from a TIC.
  • Page 93 Operating Instructions — Analyze and Process Data Table 10-9 Explore Quick Reference: Chromatograms and Spectrum (Continued) Icon Name Function Set Selection Defines start and stop points for a selection. This feature provides more accurate selection than is possible by highlighting the region using the cursor. Normalize to Max Scales a graph to maximum, so that the most intense peak is scaled to full scale, whether or not it...
  • Page 94 Operating Instructions — Analyze and Process Data 4500 Series of Instruments System User Guide 94 of 138 RUO-IDV-05-0264-A...

  • Page 95: Chapter 11 Operating Instructions - Analyze And Process Quantitative Data

    Operating Instructions — Analyze and Process Quantitative Data Use the sample files found in the Example folder to learn how to select samples for quantitation, how to select preset queries and create table-specific queries, and how to analyze the acquired data.

  • Page 96: About Results Tables

    Operating Instructions — Analyze and Process Quantitative Data cannot be be selected nor can peaks be reviewed. With this process, only the method components are defined. About Results Tables Results Tables summarize the calculated concentration of an analyte in each unknown sample based on the calibration curve.

  • Page 97: Create A Results Table Using The Quantitation Wizard

    Operating Instructions — Analyze and Process Quantitative Data ii. In the Internal Standard column, from the list, select the internal standard to be associated with each analyte. iii. In the Q1/Q3 column, select 609.400/195.039. iv. If required, add one or more of the other compounds for a more complex analysis.

  • Page 98: Create A Standard Query

    Operating Instructions — Analyze and Process Quantitative Data 8. Click Next. Note: To create a query at the same time, refer to Create a Standard Query on page The Create Quantitation Set - Select Method page opens. 9. Click Choose Existing Method. 10.
  • Page 99 Operating Instructions — Analyze and Process Quantitative Data Figure 11-1 Create Quantitation Set - Select Settings & Query Page 6. Click Next. Figure 11-2 Create Default Query Page 7. In the Maximum Allowed Accuracy Variation for QCs (%) table in the Max. Variation column, type the maximum allowable percent of variation for each QC (for example, 5 is ±...
  • Page 100 Operating Instructions — Analyze and Process Quantitative Data standard (for example, 10 is ±10%) in the same row as the corresponding concentration. If the concentrations were not specified during acquisition, they are not shown here. In that case, type them in the Concentration column. 9.

  • Page 101: Results Table Right-Click Menu

    Operating Instructions — Analyze and Process Quantitative Data Results Table Right-Click Menu Right-click in the Results Table table to access the following options. Figure 11-4 Results Table Right-Click Menu Menu Function Full Shows all the columns. Summary Shows specific columns. Analyte Shows a specific analyte.

  • Page 102: Peak Review And Manual Integration Of Peaks

    Operating Instructions — Analyze and Process Quantitative Data Peak Review and Manual Integration of Peaks Use peak review to survey the peaks that the software has identified, and then redefine the peak or the start and end points where necessary. After identifying the analytes and internal standards that the software must find, the software searches for the peaks in the samples.
  • Page 103 Operating Instructions — Analyze and Process Quantitative Data Figure 11-5 Peak Review Options Dialog Item Definition Number of rows Number of columns Zoom Y-axis to 100% of largest peak to show the entire peak 7. Click OK. 8. To move through the peaks, click the right-pointing arrow. Refer to Figure 11-6.
  • Page 104 Operating Instructions — Analyze and Process Quantitative Data Figure 11-6 Peak Review Pane Item Description Arrows: Click to move through the peaks. Show or Hide Parameters: Click to show the integration parameters. Integration parameters: Click to change the parameters. 10. Click Show or Hide Parameters twice. 11.

  • Page 105: Manually Integrate Peaks

    Operating Instructions — Analyze and Process Quantitative Data Figure 11-7 Update Method Manually Integrate Peaks Manually integrating peaks should be done last, to limit person-to-person variability. Manually integrate peaks only if all the peaks have not been found after the algorithm parameters have been adjusted and updated.
  • Page 106 Operating Instructions — Analyze and Process Quantitative Data Item Description Manual Integration mode 2. Zoom in on the lower 10% of the peak. Figure 11-9 Peak Review Pane: Zooming in on a Peak Item Description Lower 10% of the peak 3.

  • Page 107: Peak Review Right-Click Menu

    Operating Instructions — Analyze and Process Quantitative Data Peak Review Right-Click Menu Right-click in the Peak Review window or pane to access the following options. Figure 11-10 Peak Review Right-Click Menu Menu Function Options Opens the Peak Review Options dialog. Sample Annotation Opens the Sample Annotation dialog.

  • Page 108: View Calibration Curves

    Operating Instructions — Analyze and Process Quantitative Data versus the ratio of the standard peak height or area to the internal standard peak height or area is plotted. The area or height ratio of a sample is then applied to this curve to find the concentration of the sample, as shown in the Results Table.

  • Page 109: Overlay Calibration Curves

    Operating Instructions — Analyze and Process Quantitative Data Overlay Calibration Curves Note: To examine the curve for one table more closely, right-click the curve and click Active Plot. Select the curve to be plotted on top. 1. With two or more open Results Tables, view a calibration curve for one of the tables. 2.

  • Page 110: Sample Statistics

    Operating Instructions — Analyze and Process Quantitative Data Menu Function Exclude (Include) Right-click the point and then click Exclude to exclude the point from the curve. Right-click the point and then click Include to include the dropped point. Exclude All Analytes Right-click a point and then click Exclude All Analytes to exclude (Include All Analytes) all the analytes from the curve.

  • Page 111: Compare Results Between Batches

    Operating Instructions — Analyze and Process Quantitative Data 6. If required, select the Display Low/High values check box and then examine the Low, High, and Mean for each row in the grid. Each row represents standards that have the same concentration levels. 7.
  • Page 112 Operating Instructions — Analyze and Process Quantitative Data Table 11-1 Integration Tab and Quantitation Wizard Icons (Continued) Icon Name Function Use Default View for Graph Returns to the preset (view all data) view (if, for example, the user has zoomed in on a chromatogram).
  • Page 113 Operating Instructions — Analyze and Process Quantitative Data Table 11-3 Icon Quick Reference: Quantitate Mode (Continued) Icon Name Function Show First Peak Shows the first peak in the pane or window. Show Last Peak Shows the last peak in the pane or window. Show Audit Trail Shows the audit trail for the Results Table.
  • Page 114 Operating Instructions — Analyze and Process Quantitative Data 4500 Series of Instruments System User Guide 114 of 138 RUO-IDV-05-0264-A...

  • Page 115: Chapter 12 Reporter Software

    Reporter Software ® The Reporter software extends the reporting functionality available in the Analyst software. It is recommended that the user validate the results if a Reporter template that contains a query is used. Overview The Reporter software can be used to create custom reports with Microsoft Word and Excel (2007, 2010, or 2013).

  • Page 116: Reporter User Interface

    The language tags are replaced with text from a matching tag in the dictionary file for the selected language. These dictionary files are contained in the folder: C:\Program Files\AB SCIEX\AnalystReporter\Resources \Languages. Settings > Select Browse to an spectral library. This library will be used for...

  • Page 117: Generate Reports

    Reporter Software Item Option Description Current Output Displays the currently selected language dictionary used for Language replacing language tags within a report template. The language dictionary can be selected using Settings > Select Output Language. Current Spectral Displays the currently selected spectral library. The spectral Library library can be selected using Settings >...
  • Page 118 Reporter Software 1. Open a Results Table. 2. Under Companion Software, double-click Reporter 3.2. 3. In the Analyst Reporter dialog, in the Available Templates field, select a template. 4. Click an output format. The Word option is pre-selected and the report is automatically saved in the current project Results folder.

  • Page 119: Chapter 13 Service And Maintenance Information

    Table 13-1 provides a recommended schedule for cleaning and maintaining the system. Contact a Qualified Maintenance Person (QMP) to order consumable parts. Contact an AB SCIEX representative for maintenance service and support. Table 13-1 Maintenance Tasks...

  • Page 120: Clean The Surfaces

    Contact a Qualified Maintenance Person or AB SCIEX Field Service Employee (FSE). • Clean the mass spectrometer surfaces after a spill, or when they become dirty.

  • Page 121: Clean The Front-End

    • 100% isopropanol • 50:50 acetonitrile:water solution (freshly prepared) • 50:50 acetonitrile:water with 0.1% acetic acid solution (freshly prepared) Table 13-2 Tools and Supplies Available from AB SCIEX Description Small polyester swab (thermally bonded). Available in the Cleaning kit. 1017396 Small lint-free wipe (11 cm x 21 cm).

  • Page 122: Best Practices

    Service and Maintenance Information Best Practices WARNING! Toxic Chemical Hazard: Follow all safety guidelines and applicable local regulations when handling, storing, and disposing of chemicals. For health and safety guidelines, refer to Chemical Precautions on page WARNING! Potential Radiation Hazard, Biohazard, or Toxic Chemical Hazard: Determine whether decontamination is required prior to cleaning.

  • Page 123: Prepare For Cleaning

    Service and Maintenance Information • Only dampen the wipe or swab slightly when applying water or cleaning solution. Water, more so than organic solvents, may cause the wipe to deteriorate, leaving residue on the mass spectrometer. Prepare for Cleaning In routine cleaning, clean the curtain plate and the front of the orifice plate. Routine cleaning can be performed while the mass spectrometer remains under vacuum.

  • Page 124: Clean The Curtain Plate

    Service and Maintenance Information Clean the Curtain Plate Caution: Potential System Damage: Do not rest the curtain plate on the aperture tip. Make sure that the conical side faces up. 1. Remove the curtain plate and put it, conical side up, on a clean, stable surface. Figure 13-3 Interface with Curtain Plate Removed 2.

  • Page 125: Put The System Back Into Service

    Service and Maintenance Information 2. Dampen the lint-free wipe with water and then wipe the front of the orifice plate. Caution: Potential System Damage: Do not insert a wire or metal brush into the aperture, to avoid damaging the aperture. 3.
  • Page 126 Service and Maintenance Information Figure 13-4 Source Exhaust Drain Bottle Item Description Connection to mass spectrometer Source exhaust drain bottle (In this drawing, the capped drain bottle is shown at the back of the mass spectrometer to make connection points visible.

  • Page 127: Storage And Handling

    If the mass spectrometer needs to be stored for a long time or prepared for shipping, contact an AB SCIEX FSE for decommissioning information. To disconnect power from the mass spectrometer, remove the mains supply connector from the AC mains supply.
  • Page 128 Service and Maintenance Information 4500 Series of Instruments System User Guide 128 of 138 RUO-IDV-05-0264-A...

  • Page 129: Chapter 14 Troubleshooting

    Contact an FSE or the local Qualified Maintenance Person. For sales, technical assistance or service, contact an FSE or visit the AB SCIEX web site at www.absciex.com for contact information. System User Guide 4500 Series of Instruments...
  • Page 130 Troubleshooting 4500 Series of Instruments System User Guide 130 of 138 RUO-IDV-05-0264-A...

  • Page 131: Appendix A Parameters For 4500 Series Instruments

    (3) APCI probe (4) DuoSpray™ ion ® ® source (1=TIS, and 2=HN) (5) PhotoSpray ion source (6) NanoSpray ion source ® (a) AB SCIEX QTRAP 4500 system (b) AB SCIEX Triple Quad™ 4500 system System User Guide 4500 Series of Instruments RUO-IDV-05-0264-A 131 of 138...
  • Page 132 (3) APCI probe (4) DuoSpray™ ion ® ® source (1=TIS, and 2=HN) (5) PhotoSpray ion source (6) NanoSpray ion source ® (a) AB SCIEX QTRAP 4500 system (b) AB SCIEX Triple Quad™ 4500 system 4500 Series of Instruments System User Guide 132 of 138 RUO-IDV-05-0264-A...
  • Page 133 (3) APCI probe (4) DuoSpray™ ion ® ® source (1=TIS, and 2=HN) (5) PhotoSpray ion source (6) NanoSpray ion source ® (a) AB SCIEX QTRAP 4500 system (b) AB SCIEX Triple Quad™ 4500 system System User Guide 4500 Series of Instruments RUO-IDV-05-0264-A 133 of 138...
  • Page 134 Table A-2 QTRAP 4500 System Parameters for LIT Scan Types Only Access ID Positive Ion Mode Negative Ion Mode 10 to 55 10 to 55 (1)(2)(3)(4)(5) 10 to 55 10 to 55 High High Low; Medium; High Low; Medium; High (1)(2) 5500 -4500...
  • Page 135 Table A-2 QTRAP 4500 System Parameters for LIT Scan Types Only (Continued) Access ID Positive Ion Mode Negative Ion Mode (Q0 - ROS) 5 to 180 -180 to -10 0 to 250 0 to 250 1 or 2 1 or 2 ®...
  • Page 136 4500 Series of Instruments System User Guide 136 of 138 RUO-IDV-05-0264-A...

  • Page 137: Appendix B Calibration Ions And Solutions

    585.4 933.6 1223.8 1572.1 1863.3 1979.3 4500 system QTRAP 4500 LC/MS/MS 45.0 411.2 585.4 933.6 1223.8 1572.1 1863.3 1979.3 system Table B-6 Masses and Polarity for the QTRAP 4500 LC/MS/MS System (Agilent) Instrument/ Masses Polarity LIT Positive 118.087 322.049 622.030 922.010 1521.972 –...
  • Page 138 Calibration Ions and Solutions 4500 Series of Instruments System User Guide 138 of 138 RUO-IDV-05-0264-A...

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