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Thermo Scientific TSQ Quantum XLS User Manual

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TSQ Series
TSQ Quantum XLS
Series
User Guide
Revision A
December 2011
70111-97225

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Summary of Contents for Thermo Scientific TSQ Quantum XLS

  • Page 1 TSQ Series TSQ Quantum XLS Series User Guide Revision A December 2011 70111-97225...
  • Page 2 © 2011 Thermo Fisher Scientific Inc. All rights reserved. TriPlus is a trademark and TSQ Quantum and TRACE GC Ultra are registered trademarks of Thermo Fisher Scientific Inc. in the United States. The following are registered trademarks in the United States and possibly other countries: Teflon and Vespel are registered trademarks of E.
  • Page 5 Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards, replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives. TSQ Quantum XLS and TSQ Quantum XLS Ultra EMC Directive 2004/108/EC TUV Rheinland of North America Inc...
  • Page 6 FCC Compliance Statement THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED, INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION. WARNING Read and understand the various precautionary notes, signs, and symbols contained inside this manual pertaining to the safe use and operation of this product before using the device.
  • Page 7 WEEE Compliance This product is required to comply with the European Union’s Waste Electrical & Electronic Equipment (WEEE) Directive 2002/96/EC. It is marked with the following symbol: Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union (EU) Member State, and these companies should dispose of or recycle this product.
  • Page 8 Conformité DEEE Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et Electroniques (DEEE). Il est marqué par le symbole suivant: Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état membre de l’union européenne et ce produit devrait être collecté...

  • Page 9: Table Of Contents

    Transfer Line........... 20 Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 10 Starting Up the System after a Complete Shutdown ..... 53 Restoring Power to the TSQ Quantum XLS Series System ....54 Starting Up the GC .
  • Page 11 Index ............. . .151 Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 13: Preface

    Preface The Thermo Scientific TSQ Quantum XLS and TSQ Quantum XLS Ultra systems make up the TSQ Quantum XLS Series and are member of the TSQ Quantum™ family of mass spectrometers. This TSQ Quantum XLS Series User Guide contains a description of the modes of operation and principle hardware components of your TSQ Quantum XLS Series system.

  • Page 14: Safety And Special Notices

    Note Highlights information of general interest. Tip Highlights helpful information that can make a task easier. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 15: Contacting Us

    Customer Manuals in the left margin of the window. To suggest changes to documentation or to Help • Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62. • Send an e-mail message to the Technical Publications Editor at techpubs-lcms@thermofisher.com. Thermo Scientific TSQ Quantum XLS Series User Guide xiii...

  • Page 17: Chapter 1 Introduction

    Introduction The TSQ Quantum XLS Series systems are advanced analytical instruments that include a mass spectrometer, gas chromatograph, and the Xcalibur™ data system. See Figure 1 Figure Contents • Ionization Modes • Ion Polarity Modes • Scan Modes • Scan Types •...
  • Page 18 Introduction Figure 1. TSQ Quantum XLS Ultra mass spectrometer, TriPlus autosampler, and TRACE GC Ultra gas chromatograph Figure 2. TSQ Quantum XLS mass spectrometer, TriPlus autosampler, and TRACE GC Ultra gas chromatograph TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 19: Ionization Modes

    As a result, the TSQ Quantum XLS Series systems make investigating all pathways for the formation and fragmentation of each ion in the mass spectrum possible.

  • Page 20: Electron Ionization Mode

    • An ion association reaction where an adduct ion is formed between a reagent gas ion and a sample molecule In methane positive ion mode CI, the relevant peaks observed are MH , [M+CH , and [M+C ; but mainly MH TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 21: Ion Polarity Modes

    Scan Modes You can operate the TSQ Quantum XLS Series mass spectrometers in a variety of scan modes. The most commonly used scan modes can be divided into two categories: single mass spectrometry (MS) scan modes and tandem mass spectrometry (MS/MS) scan modes. The scan modes in each category are as follows: •...
  • Page 22 This separation allows the rod assembly to serve as a mass analyzer. On the TSQ Quantum XLS Series mass spectrometers, the quadrupole rod assemblies can operate with rf and dc voltages or with only rf voltage. That is, Q1 and Q3 can act either as mass analyzers or ion transmission devices.

  • Page 23: Q1Ms And Q3Ms Scan Modes

    A mass spectrum obtained in the Product scan mode (product mass spectrum) is the mass spectrum of a selected parent ion. Figure 3 illustrates the Product scan mode. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 24: Parent Scan Mode

    Q1 (the parent ions), whereas data for the ion intensity axis is obtained from Q3 (from monitoring the product ion). Figure 4 illustrates the Parent scan mode. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 25: Neutral Loss Scan Modes

    CID to produce product ions. The product mass analyzer then separates these product ions by mass-to-charge ratio. Figure 5 illustrates the Neutral Loss scan mode. Examples of compounds with a common neutral loss fragment appear in Figure 6 page Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 26 CO from aldehydes, HX from halides, and H O from alcohols). Figure 5. Illustration of the Neutral Loss scan mode R F O nly + A r Q3 = Q1 - Δ Q1 Scanning Q1 m/z TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 27: Data-Dependent Scan Mode

    Examples of compounds with a common neutral-loss fragment Data-Dependent Scan Mode The TSQ Quantum XLS Series mass spectrometers use the information in a data-dependent scan mode experiment to make automatic decisions about the next step of the experiment without user input. In data-dependent scan mode you specify criteria to select one or more ions of interest on which to perform subsequent scans, such as MS/MS.

  • Page 28: Scan Types

    Introduction Scan Types Scan Types You can operate the TSQ Quantum XLS Series systems with a variety of scan types. The most common scan types are as follows: • Full Scan • Selected Ion Monitoring (SIM) • Selected Reaction Monitoring (SRM) •...

  • Page 29: Selected Reaction Monitoring (Srm)

    Highly-Selective Reaction Monitoring (HSRM) Highly-selective reaction monitoring (HSRM) is SRM performed at higher Q1 resolution (0.4 u fwhm [less for TSQ Quantum XLS Ultra mass spectrometers] versus 0.7 u fwhm for SRM). Intelligent Selected Reaction Monitoring (iSRM) In intelligent selected reaction monitoring (iSRM) experiments, the mass spectrometer performs multiple “primary”...

  • Page 30: Quantitation-Enhanced, Data-Dependent Ms (Qed Ms)

    Data Types You can acquire and display mass spectral data (intensity versus mass-to-charge ratio) with the TSQ Quantum XLS Series mass spectrometers in one of two data types: • Profile Data Type •...

  • Page 31: Centroid Data Type

    Data processing is also much faster for centroid data. Mass/Charge Range The TSQ Quantum XLS and TSQ Quantum XLS Ultra mass spectrometers can operate in a mass/charge range of 10 to 3000 Da, and 10 to 1500 Da, respectively.

  • Page 33: Chapter 2 Functional Description

    • Mass Spectrometer • Data System A functional block diagram of the TSQ Quantum XLS Series system is shown in Figure 7. A sample transfer line connects the gas chromatograph (GC) to the mass spectrometer. The autosampler and GC are installed on the left side of the mass spectrometer.

  • Page 34: Autosampler

    Vacuum monitor system Autosampler You can use the optional Thermo Scientific TriPlus™ autosampler to inject samples automatically into the GC inlet. With an autosampler, you can automate your GC/MS/MS analyses. The TriPlus autosampler is shown in Figure 1 Figure 2 page Autosampler Start/Stop signals with the mass spectrometer are provided by contact closure.

  • Page 35: Gas Chromatograph

    Foundation 2.0 > Instrument Configuration. For a description of TRACE GC Ultra configuration options, refer to the Xcalibur Help. The TSQ Quantum XLS Series data system computers can directly control the TRACE GC Ultra. Choose Start > All Programs > Thermo Xcalibur > Xcalibur and click Instrument Setup to open the Instrument Setup window.

  • Page 36: Transfer Line

    GC into the ion source in the mass spectrometer. This prevents the sample from condensing. The transfer line includes an inlet for calibration gas and chemical ionization gas. See Figure TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 37: Mass Spectrometer

    Several important features of the TSQ Quantum XLS Series mass spectrometers are as follows: • High sensitivity and resolution • m/z 10 to 3000 mass range for the TSQ Quantum XLS, and m/z 10 to 1500 mass range for the TSQ Quantum XLS Ultra • EI and CI ionization modes •...

  • Page 38: Controls And Indicators

    Table Figure 10. Front panel LEDs of the TSQ Quantum XLS Ultra mass spectrometer System Scan...
  • Page 39 In the On (|) position, power is supplied to the mass spectrometer, gas chromatograph, and autosampler. In the standard operational mode, the circuit breaker is kept in the On (|) position. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 40 The Vent Valve Closed LED is green whenever the vent valve current sensor detects current through the vent valve and the vent valve is closed. The LED is off when the vent valve is open. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 41 The LED is off when there is no communication between the System Control PCB and the data system computer. Figure 14. Right-side power panel of the mass spectrometer Pump On Vacuum Electronics Qualified Service Personnel Only Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 42: Ei/Ci Ion Source

    15. You can operate the ion source in either the electron ionization (EI) or chemical ionization (CI) mode. See “Ionization Modes” page Figure 15. Ion source of the TSQ Quantum XLS Series mass spectrometer Magnets and magnet yoke EI/CI source Ion source...
  • Page 43 This ensures optimum ionization of the sample. The ion source of the TSQ Quantum XLS Series mass spectrometer has two ion source len assemblies, called the L1, L2, and L3 lens assembly and the heated Q0 quadrupole assembly.

  • Page 44: Inlet Valve

    When the ball valve is closed, it prevents the vacuum manifold from venting to atmosphere. Figure 17. Inlet valve, I/R tool, guide bar, and ball valve lever Inlet valve I/R tool Ball valve lever Guide bar TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 45: Ion Optics

    Q0 quadrupole make electrical contact with the rods of the larger Q0 quadrupole. Figure 18. Heated Q0 quadrupole (left) and Q0 quadrupole (right) Figure 19 gives a cross-sectional view of the transfer line, ion source, heated Q0 quadrupole, and Q0 quadrupole. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 46 The value ranges between 0 and ±300 V. Lenses L11 and L12 also act as a vacuum baffle between the Q0 quadrupole chamber and the mass analyzer chamber. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 47: Mass Analyzer

    The mass analyzer separates ions according to their mass-to-charge ratio and then passes them to the ion detection system. The mass analyzers on the TSQ Quantum XLS Series mass spectrometers consist of three quadrupole rod assemblies (Q1, Q2, and Q3) and three lens sets.
  • Page 48 Voltages of the same amplitude and sign are applied to the rods of each pair. However, the voltages applied to the different rod pairs are equal in amplitude but opposite in sign. See Figure TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 49 The square quadrupole rod assembly (Q2) operates in the ion transmission mode only. Surrounding Q2 is a collision cell where CID can take place if the argon collision gas is present in the cell. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 50 During this same time, all other ions undergo unbounded oscillations. These ions strike one of the rod surfaces, become neutralized, and are pumped away, or they are ejected from the rod assembly. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 51 50 percent for comparatively less massive ions (which are more prone to scatter) up to 75 percent for comparatively more massive ions (which are less prone to scatter). Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 52 (Q2 and Q3 rf voltage only), and tunes Q3 in the Q3MS scan mode (Q1 and Q2 rf voltage only). During tuning, the mass spectrometer determines the optimum quadrupole offset voltage for Q1 and for Q3. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 53 Functional Description Mass Spectrometer Mass Analyzer Lenses The TSQ Quantum XLS Series mass analyzers have three lens sets. See Figure 22 page Those between Q1 and Q2 are designated L21, L22, L23; those between Q2 and Q3 are designated L31, L32, L33; and the lens between Q3 and the ion detection system is designated the exit lens.

  • Page 54: Ion Detection System

    Functional Description Mass Spectrometer Ion Detection System The TSQ Quantum XLS Series mass spectrometers are equipped with a high-sensitivity, off-axis ion detection system. See Figure 25. This system produces a high signal-to-noise ratio and provides for voltage polarity switching between positive ion and negative ion modes of operation.
  • Page 55 Because of the off-axis orientation of the ion detection system relative to the mass analyzer, neutral molecules from the mass analyzer tend not to strike the conversion dynode or electron multiplier. As a result, noise from neutral molecules is reduced. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 56: Vacuum System And Inlet Gasses Hardware

    (4 x 10 - 5 Torr) (3 x 10 - 6 Torr) Inlet gauge valve Dual-inlet Convectron turbomolecular pump gauge Convectron gauge Collision gas Exhaust divert valve Forepump Argon Collision gas port gas valve TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 57 Two removable side cover plates on the left side of the vacuum manifold allow access to the Q0 ion optics, mass analyzer, and ion detection system. Two electrically conductive O-rings provide a vacuum-tight seal between the side cover plates and the vacuum manifold. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 58 • A high-vacuum inlet at the top of the rotor stack, which evacuates the analyzer chamber • An interstage inlet about halfway down the rotor stack, which evacuates the ion source and Q0 quadrupole chambers TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 59 Positive ions formed in the ion gauge are attracted to a collector. The collector current is related to the pressure in the vacuum manifold. The ion gauge is also involved in vacuum protection. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 60 The CI gas flow control valve controls the flow of chemical ionization reagent gas into the ion source, via the transfer line. The maximum CI gas flow rate is about 4 mL/min, depending on the gas. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 61: Electronic Assemblies

    • Serial Peripheral Interconnect (SPI) bus • I/O coprocessor • Super Harvard Architecture Computer (Sharc) bus • Scan generator DSP • Acquisition processor DSP • Interbus bridge • 100 base-T Ethernet port Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 62: Data System

    The data system controls and monitors the mass spectrometer. The data system also processes data that the mass spectrometer acquires. The data system is composed of the following: • Computer Hardware • Data System/Mass Spectrometer/GC Interface • Data System/Local Area Network Interface TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 63: Computer Hardware

    The data system computer contains a secondary Ethernet adapter. This secondary Ethernet adapter is not involved in data system/mass spectrometer or GC communications. You can use this secondary Ethernet adapter to access your local area network. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 65: Chapter 3 System Shutdown, Startup, And Reset

    System Shutdown, Startup, and Reset Many maintenance procedures for the TSQ Quantum XLS Series systems require that the mass spectrometer be shut down completely. In addition, you can place the mass spectrometer in Standby mode if you plan to not use the system for 12 hours or more.
  • Page 66 Figure 29. Power panel on the back of the electronics module Quantum Power Out Power In GC Power Out A/S Power Out V~230 V~230 V~230 V~230 50/60 Hz, 2A MAX 50/60 Hz, 10A MAX Hz, 30A MAX 50/60 Hz, 16A MAX TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 67: Placing The System In Standby Mode

    Placing the System in Standby Mode If you are not going to use the TSQ Quantum XLS Series system for a short period of time, such as overnight or over weekends, you do not need to shut it down completely. When you are not going to operate the system for 12 hours or more, you can leave the system in Standby mode.
  • Page 68 • After about two minutes, the pressure of the vacuum manifold reaches atmospheric pressure. 6. Unplug the power cord for the mass spectrometer. WARNING Burn Hazard. Allow heated components to cool before servicing them. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 69: Starting Up The System After A Complete Shutdown

    WARNING Burn Hazard. The ion source, GC oven, injector, and transfer line are hot. Allow them to cool to room temperature before touching them. Starting Up the System after a Complete Shutdown Starting the TSQ Quantum XLS Series system after it has been shut down requires completion of these tasks: •...

  • Page 70: Restoring Power To The Tsq Quantum Xls Series System

    Starting Up the System after a Complete Shutdown Restoring Power to the TSQ Quantum XLS Series System To restore power to the TSQ Quantum XLS Series system, place the main power circuit breaker, located on the back of the electronics module...
  • Page 71 Carrier gas Ar collision gas Maximum pressure (Torr) – 8 × 10 – 5 × 10 Figure 31. Front panel LEDs of the TSQ Quantum XLS Ultra mass spectrometer System Scan Power Communication Vacuum Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 72: Starting Up The Autosampler

    To set up your TSQ Quantum XLS Series mass spectrometer for operation 1. Before you begin data acquisition with your TSQ Quantum XLS Series system, allow the system to pump down for at least one hour. Operation of the system with excessive air and water in the vacuum manifold can cause reduced sensitivity, tuning problems, and reduced lifetime of the electron multiplier.

  • Page 73: Resetting The Mass Spectrometer

    3. Observe the Windows shutdown and restart procedure on the monitor. At the prompt, press CTRL+ALT+DELETE. 4. Click OK or enter your password (if you have one) in the Logon Information dialog box. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 74: Turning Off Selected Mass Spectrometer Components

    • Press the System Power Off button. Pressing the System Power Off button removes all power to the mass spectrometer, gas chromatograph, and autosampler. Table 4 summarizes the on/off status of mass spectrometer components, voltages, and gas flows. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 75 PS2 power supply, +5, ±15, ±24 V dc PS3 power supply, +36, –28 V dc Fan, turbomolecular pump Fan, above manifold Fan, center wall Convectron gauge, foreline Convectron gauge, collision cell Ion gauge Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 77: Chapter 4 Tuning And Calibrating

    Tune parameters are instrument parameters that affect the intensity of the ion signal. Calibration parameters are instrument parameters that affect the mass accuracy and resolution of the mass spectrum. Tuning and calibrating the TSQ Quantum XLS Series mass spectrometer automatically with TSQ EZ Tune uses perfluorotributylamine (FC-43) as the tuning and calibration compound.

  • Page 78: Displaying The Fc-43 Mass Spectrum

    4. In the Define Scan dialog box, select or enter the following settings: • Scan type: Full Scan • Scan mode: Q1MS • Scan range entry mode: FM/LM • First mass: 50 • Last mass: 650 • Scan time: 0.500 TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 79 8. Choose Control > On to start the mass spectrometer scanning. 9. Observe the mass spectrum. If your mass spectrum looks very different from the one in Figure 34, see “Diagnostics and Troubleshooting” page 113. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 80: Running Auto Tune And Calibration

    1. Display the FC-43 positive ion mass spectrum as described in the previous section. 2. Click the System Tune and Calibration button (or choose Setup > System Tune and Calibration) to display the System Tune and Calibration dialog box (see Figure 35). TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 81 Troubleshoot and correct the problem that caused the tuning and calibration procedure to fail. See “Tuning Issues” page 128. d. Go to step 4 and restart the tuning and calibration procedure. Figure 36 shows a typical parameter optimization plot. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 82 Note If you intend to perform high-sensitivity, negative-ion mass spectrum analysis, Thermo Fisher Scientific recommends that you also perform a full tune and calibration of the instrument in the negative ion mode. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 83: Saving The Tune And Calibration Report

    You can save the information that appears in the Status box and in the parameter optimization plots as a PDF file. Examples of status information and parameter optimization plots from the tune and calibration report follow in Figure 37, and Figure 38 page Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 84 Previous Setting = -50.14, New Setting = -51.11 10:57:30: Maximum Intensity = 4.35e+05 10:57:30: 6 % Improvement 10:57:30: Optimizing Lens 2-1 for ion 501.97 m/z Signature: __________________________________________ May 09, 2007 11:17:28 Page 1 of 10 TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 85 To save the tune and calibration report 1. In the System Tune and Calibration dialog box, click Save Report. The Save As dialog box appears. 2. Enter the name and the path of the report, and click Save. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 86: Running Maintenance Tune

    L11 DAC Scan #A: 19 Peak: -2.69; 1.45e+004 -36.71 -2.69 -10.16 -11.35 -17.07 -4.76 -7.61 -11.07 -8.34 -6.17 -3.65 -30.00 -24.59 -3.76 -13.42 -9.37 -1.89 -21.53 -33.83 -27.03 -41.71 -38.92 Parameter Setting (Arb) Parameter Setting (Arb) TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 87: Creating A Quality Control (Qc) Tune Report

    • Q1/MS full scan centroid spectrum from m/z 50 to 650 • FC-43 peak positions and intensity ratios • Results of a leak check (pass or fail) Figure 40 shows a QC tune report. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 88 1. Choose View > QC Report to open the TSQ QC Report dialog box. 2. Click Start to start the QC report procedure. 3. After the procedure terminates, click View Report to view the QC report as a PDF file. 4. Save the PDF file. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 89: Chapter 5 Changing Ionization Modes

    Changing Ionization Modes You can operate the TSQ Quantum XLS Series mass spectrometers in either EI or CI ionization mode. Changing ionization modes requires changing ion volumes. You do not need to shut down the mass spectrometer to change ion volumes.
  • Page 90 Turn the I/R tool to the unlock position , which indicates the I/R tool is in position to accept the ion volume. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 91 Slide the I/R tool forward into the inlet valve until the guide ball is at the guide bar’s first stop (see Figure 44). c. Tighten the inlet valve knob clockwise to ensure a leak-tight seal. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 92 6. Click OK. The forepump evacuates the inlet valve. Wait until you can safely insert the probe (Figure 45), and then click OK. Figure 45. Safe to insert the probe message 7. Once evacuation is complete, pull the inlet valve lever up (Figure 46). TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 93 See Figure 47. The head of the arrow on the I/R tool, when viewed through the window of the ion source manifold, should not be visible. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 94 Loosen the inlet valve knob by turning it counterclockwise to release the seal. Continue withdrawing the I/R tool completely from the inlet valve by sliding the I/R tool through the guide ball track in the guide bar. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 95 98. If you are cleaning a CI ion volume, be sure to clean out the small electron entrance hole. Aluminum oxide can get trapped in this hole, which can adversely affect sensitivity. Use a dental pick or old syringe needle to clean the hole. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 96: Installing The Ion Volume

    8. Click OK. The forepump evacuates the inlet valve. Wait until you can safely insert the page 76); then click OK. probe (Figure 45 9. Once evacuation is complete, pull the inlet valve lever up to open the inlet valve. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 97 Loosen the inlet valve knob by turning it counterclockwise. d. Continue withdrawing the I/R tool completely from the inlet valve by sliding the I/R tool through the guide ball track in the guide bar. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 98 15. Tighten the inlet valve knob clockwise to create a leak-tight seal. 16. (Optional) To prevent the inlet valve from being opened accidentally, pull free and remove the inlet valve lever. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 99: Maintenance

    Maintenance This chapter describes routine maintenance procedures that you must perform to ensure optimum performance of the TSQ Quantum XLS Series mass spectrometer. Optimum performance of the mass spectrometer depends on the maintenance of all parts of the instrument. You are responsible for properly maintaining your instrument through regular performance of these maintenance procedures.
  • Page 100 Cleaning of the Q0, Q1, Q2, and Q3 quadrupoles is rarely (if ever) needed. A Thermo Fisher Scientific Field Service Engineer must perform this maintenance procedure. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 101: Cleaning Ion Source Components

    Cleaning Ion Source Components Cleaning Ion Source Components An important part of maintaining your TSQ Quantum XLS Series mass spectrometer is making sure that the ion source components are clean. Follow the cleaning procedures in this section to clean stainless steel and non-stainless steel parts.
  • Page 102 Figure 50. Ion source assembly, assembled and exploded views TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 103: Cleaning Ion Volumes

    1. Shut down and vent the system. See “Shutting Down the System Completely” page WARNING Shock Hazard. Unplug the TSQ Quantum XLS Series system before proceeding. WARNING Burn Hazard. The ion source might be hot. Allow the ion source to cool to room temperature before touching it.
  • Page 104 3. Prepare a clean work area by covering the area with lint-free cloth. 4. Undo the two latches that secure the lid of the ion source vacuum manifold, and open the lid. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 105 5. Disconnect the connectors from the lead pins at the EI/CI Source PCB, and L1, L2, L3 lens assembly. See Figure Figure 51. TSQ Quantum XLS Series ion source, installed Q0 quadrupole mount Lens L1, L2, L3 connector EI/CI Source PCB...
  • Page 106 Figure 52. L1, L2, L3 lens assembly and heated Q0 quadrupole assembly removed from the ion source Heated Q0 quadrupole assembly L1, L2, L3 lens assembly Ion source Retainer clip Threaded standoff TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 107 Note To clean the ion source lenses, follow the procedure in “Cleaning Stainless Steel Parts” page 98. To clean the remaining parts, follow the procedure in “Cleaning Non-Stainless Steel or Hybrid Parts” page 100. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 108 2. Reinstall the lens clip by pinching the ends with your fingers or a pair of tweezers and seating it in the lens holder. 3. Insert the lens alignment tool (in the TSQ Quantum XLS Accessory Kit) into the lens assembly and align the lenses.

  • Page 109: Replacing The Filament Of The Ion Source

    To replace the filament of the ion source 1. Prepare a clean work area by covering the area with lint-free cloth. 2. Shut down and vent the mass spectrometer. See “Shutting Down the System Completely” page 51 Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 110 Place them on a clean surface. 7. Remove the retainer clip that secures the filament and centering ring to the ion source block. 8. Remove the filament and centering ring from the ion source block. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 111: Completely Disassembling And Reassembling The Ion Source

    Disassemble the ion source completely to clean the ion source block or to replace the EI/CI Source PCB. Tools Needed • Gloves, cleanroom grade (P/N 23827-0008 and 23827-0009) • Lint-free cloth Frequency As needed Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 112: Complete Disassembly And Reassembly Of The Ion Source

    To disassemble the ion source completely 1. Prepare a clean work area by covering the area with lint-free cloth. 2. Shut down and vent the TSQ Quantum XLS Series system. See“Shutting Down the System Completely”...
  • Page 113 3. Press the heater ring and lens assemblies onto the ion source block. 4. Use the retainer clip and threaded standoff to secure the heater ring lens assembly to the ion source. See Figure 55 page Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 114: Cleaning Stainless Steel Parts

    As needed to clean these stainless steel parts: • Ion volumes • Ion source block • Ion source lenses WARNING Material and Eye Hazard. Wear impermeable laboratory gloves and eye protection when performing cleaning procedures. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 115 7. Using forceps, place the parts in a beaker, cover the beaker with aluminum foil, and put the beaker in the oven. 8. Dry the parts in an oven set at 100 C for 30 minutes. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 116: Cleaning Non-Stainless Steel Or Hybrid Parts

    To clean the inside corners, use the wooden end of an applicator cut at an angle. d. Use a Dremel tool with the polishing swab at its lowest speed. This will increase cleaning efficiency as well as decrease the time required to clean the items. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 117: Maintaining The Forepump

    CAUTION If you use ammonia as a chemical ionization reagent gas, change the oil every month. Ammonia is highly basic and quickly damages seals in the forepump. Purging the oil with the Gas Ballast Control helps remove dissolved ammonia from the oil. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 118: Adding Calibration Compound

    The calibration compound is a liquid whose mass spectrum of ions is used to tune and calibrate the TSQ Quantum XLS Series mass spectrometers. The mass spectrometers use FC-43 as their calibration compound. Although you cannot visually determine when to add a calibration compound, Xcalibur Automatic Tune produces the error message: “the intensity of...
  • Page 119 3. Twist the calibration compound vial counterclockwise and remove it from the calibration gas flow module. See Figure 58. Set the vial on the work table. Figure 58. Calibration compound vial Calibration compound vial Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 120 5. Remove the syringe from the calibration compound vial. 6. Reinstall the calibration compound vial to the calibration gas flow module. Turn the vial clockwise to tighten it. 7. Reinstall the cover to the calibration compound vial compartment. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 121: Replacing The Ball Valve Seal

    Inlet valve insert Inlet valve knob You use the ball valve seal extraction tool (part of the Ball Valve Seal Kit, P/N 119265-0003) to remove the ball valve seal. See Figure Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 122 3. Insert the ball valve seal into the ball valve manifold with your finger. 4. Install the inlet valve knob and insert. 5. Install the inlet valve plug and tighten the inlet valve knob clockwise. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 123: Removing And Installing A Gc Capillary Column

    Once the oven, injector, and transfer line are cool, turn off the gas chromatograph. 2. Remove the column from the transfer line. See Figure a. Unscrew the transfer line nut. b. Remove the column from the transfer line. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 124 Ferrule Column retaining Transfer line (end) Ferrule Transfer line nut 3. Remove the column from the injector. For instructions, refer to the Columns chapter of the TRACE GC Ultra Operating Manual. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 125: Installing A Gc Capillary Column

    Set the injector flow to 1.0 mL/min. d. Turn off vacuum compensation (under the Right or Left Carrier menu). e. Dip the column outlet in a small vial of methanol. Bubbles indicate there is flow through the column. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 126 Lower the GC oven temperature to 30 °C and allow it to cool before continuing. WARNING Burn Hazard. The GC oven and transfer line might be hot. Allow them to cool to room temperature before touching them. Do not touch the injector when it is hot. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 127 Retighten the transfer line nut and the transfer line union. 9. Set up the gas chromatograph: a. Make sure the column does not have any sharp bends and that it does not touch any metal objects or walls inside the oven. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 128 Removing and Installing a GC Capillary Column b. Raise the oven temperature to the initial temperature that you will use (normally 40 °C). c. Turn on the vacuum compensation (under the Right or Left Carrier menu). TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 129: Diagnostics And Troubleshooting

    Diagnostics and Troubleshooting The TSQ Quantum XLS Series system diagnostics can test many components of the TSQ Quantum XLS Series mass spectrometers. If there is a problem in the instrument electronics, the diagnostics can often locate it. Replacing a faulty PCB or assembly will usually correct the problem.

  • Page 130: Troubleshooting

    • Error messages How does the MS communication work? The flow of digital information in the TSQ Quantum XLS Series systems is bidirectional; the data system downloads analytical methods to the instrument and activates functions to start, stop, shut down, start up, and initialize. The TSQ Quantum XLS Series systems report their readiness state, current tasks, various voltages, heated zones, and pressure readings.
  • Page 131 • An incorrect Ethernet cable is used for the mass spectrometer. Use the supplied 10 Base-T Category 5 crossover cable (P/N 76396-0052, in the TSQ Quantum XLS Accessory Kit). Note You can extend the length of the Ethernet cable by plugging a standard Category 5 cable in series with the supplied crossover cable.
  • Page 132 Issue: Acquisition Possible causes/solutions terminates • The end run time in the TSQ Quantum XLS Series instrument method is incorrect. unexpectedly. Check the instrument method for the GC and the MS. • The data system is out of disk space. Check disk space; back up and remove files.

  • Page 133: Contamination Issues

    • The capillary column is damaged as a result of exposure to oxygen. Find the source of the oxygen in the carrier gas or air leak. Recondition or replace the capillary column. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 134 Acetone (m/z 43, 58, 59) Hexane (m/z 41, 43, 56, 57, 58, 85, 86) Methanol (m/z 31) Methylene chloride (m/z 84, 83) Toluene (m/z 91, 92) Trichloroethane (m/z 151, 153) Xylene (m/z 105, 106) TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 135: Filament And Lens Control Issues

    Diagnostics test the lenses of the TSQ Quantum XLS Series mass spectrometers. A flat line, which represents voltage readback versus the predicted voltage ramp, indicates a lens or other control fault.

  • Page 136: Heated Zone Issues

    GC effluent will contact the inside wall of the tip. Follow the procedure described in “Installing a GC Capillary Column” page 109. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 137: High Vacuum Issues

    Xcalibur data system (see Table 3 page 55), then the TSQ Quantum XLS Series system turns off. • If the vacuum is consistent enough that it does not exceed the maximum allowed pressure and avoids automatic shutdown of the Xcalibur system, non-reproducible false chromatographic peaks can be generated in the chromatogram.
  • Page 138 • The GC column broke at the transfer line. Replace the GC column. See “Removing and Installing a GC Capillary Column” page 107. • The foreline was cut. Replace the foreline hose. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 139: Linearity Issues

    A well-maintained instrument provides good linear response over a wide range of concentrations for most compounds. Like all instruments, however, the TSQ Quantum XLS Series mass spectrometers have a saturation point.

  • Page 140: Power Supply Issues

    Improper GC maintenance is another cause of diminished sensitivity. It is important to establish a routine maintenance program for the GC. For more information on establishing a maintenance program, refer to the TRACE GC Maintenance Manual. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 141 Contact Thermo Fisher Scientific Technical Support. • Reagent gas is leaking into the analyzer and suppressing EI signal. Check for presence of CI reagent ions in the spectrum. Replace CI Gas Flow Module if necessary. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 142 • The electron multiplier is faulty. Contact Thermo Fisher Scientific Technical Support. • The injection port liner or capillary column is contaminated. Replace the injection port liner and trim the capillary column. TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 143: Stability Issues

    • There is a contamination problem. See “Contamination Issues” page 117 for more information. • Dust has collected in the electron multiplier or on the conversion dynode. Contact Thermo Fisher Scientific Technical Support. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 144: Tuning Issues

    See “High Vacuum Issues” page 121 for more information. • The difference between the electron energy and the setpoint is greater than 5 V. Contact Thermo Fisher Scientific Technical Support for assistance. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 145 • Reagent gas is leaking into the analyzer and suppressing the EI signal. Check for the presence of CI reagent ions in the spectrum. Replace the CI Reagent Gas Flow Module if necessary. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 146: Replacing Fuses

    CAUTION Fuses protect the various circuits by opening the circuits whenever overcurrent occurs. On the TSQ Quantum XLS Series mass spectrometers, a failed fuse indicates a failed board or electronic module that must be replaced by a Thermo Fisher Scientific field service engineer.

  • Page 147: Appendix A Using The Direct Sample Probe

    • Removing the Probe Creating an Instrument Method An instrument method contains the settings that the TSQ Quantum XLS Series mass spectrometer uses during an experiment. Use the Instrument Setup view to create the instrument method. To create an instrument method 1.
  • Page 148 5. Specify the mass spectrometer settings: for this example, Full-Scan (Scan Type list), Q1MS (Scan Modes|MS Mode option), and Positive (Polarity area). Figure 62. Scan Editor page of Instrument Setup 6. Click the EI/CI tab to display the EI/CI page (see Figure 63). TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 149 Choose File > Save As to open the Save As dialog box. b. Save the instrument method as a .meth file. In this example we name the instrument method Dip test.meth. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 150: Creating A Sequence

    4. Enter a file name and path for the raw file that contains the acquired data. In this example, it is C:\Xcalibur\Data\data01. Figure 64. Sequence Setup view, showing one sample in the sequence TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 151: Preparing The Probe And Inlet Valve

    IMPORTANT You must have the TSQ EZ Tune window open for the mass spectrometer to initiate the probe insertion sequence. 2. Ensure that the TSQ Quantum XLS Series mass spectrometer is the only instrument in use and that there are no start instruments.
  • Page 152 Click Change Instruments to open the Change Instruments In Use dialog box (see Figure 66). Figure 66. Change Instruments In Use dialog box, showing the TSQ Quantum mass spectrometer in use and no start instruments TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 153: Running The Sequence

    Slide the probe forward into the inlet valve until the guide ball is at the guide bar’s first stop. See Figure c. Tighten the inlet valve knob clockwise to ensure a leak-tight seal. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 154 5. Pull the inlet valve lever up to open the inlet valve. 6. Slide the probe into the vacuum manifold until the tip of the probe is fully inserted into the ion volume holder. See Figure TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 155 8. In Sequence Setup, choose View > Real Time Plot View to display the mass spectrum and chromatogram. 9. Start the probe method from the probe controller to initiate data acquisition. See Figure 72, and Figure 73 page 141. Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 156 Using the Direct Sample Probe Running the Sequence Figure 72. Perfluorotetracosane mass spectrum at 0.56 minute retention time TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 157: Examining The Raw Data In Qual Browser

    1. On the Thermo Xcalibur Roadmap, click the Qual Browser icon to open the Qual Browser window. 2. Click on the chromatogram to display the mass spectrum at that retention time. Figure Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 158: Removing The Probe

    1. Withdraw the probe until the guide ball on the probe reaches the first stop on the guide bar (see Figure 68 page 138). 2. Close the inlet valve by pushing the lever down. 3. Loosen the inlet valve knob by turning it counterclockwise. TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 159 7. Replace the inlet valve plug and tighten the inlet valve knob clockwise to form a seal. The inlet valve plug prevents air from entering the vacuum manifold in case the inlet valve is accidentally opened. You can also remove the inlet valve lever by pulling it free. Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 161: Appendix B Replaceable Parts And Consumables

    Contact Thermo Fisher Scientific Austin and have your TSQ Quantum XLS Series mass spectrometer serial number ready. These kits with replaceable parts and consumables are available for the TSQ Quantum XLS Series systems: Contents •...
  • Page 162 Ion volume holder (70001-20532-T) L1, L2, L3 lens assembly (70111-60842) Heater ring and lens assemblies retainer clip (70111-22070) Threaded standoff Ion volume retaining (70111-22060) Base studs EI/CI Source PCB thumbscrew (70111-22056) (70111-60848) (70111-22059) TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 163: Miscellaneous Replaceable Parts And Consumables

    Calibration compound vial Holds frit and FC-43 tuning and 120428-0002 calibration compound. Calibration compound frit Holds FC-43 tuning and calibration 120432-0001 compound. Ion volume, closed EI, P type Ni-Cr, for pesticides 70001-22202 Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 164: Accessory Kit

    For aligning ion source lenses 1, 2, 120271-0001 and 3 Filament assembly For replacing a failed filament in the 120320-0030 ion source Nitrile gloves medium For handling clean parts that are 23827-0008 under vacuum TSQ Quantum XLS Series User Guide Thermo Scientific...

  • Page 165: Chemicals Kit

    Table 9. Chemicals Kit P/N 70111-62078) Description Function Part number Perfluorotributylamine (FC-43) Tuning and calibration compound 50010-02500 Aluminum oxide Cleaning stainless steel parts 32000-60340 Benzohexane Performance testing 120150-TEST Octafluoronaphthalene Performance testing 120150-TEST Thermo Scientific TSQ Quantum XLS Series User Guide...

  • Page 167: Index

    H-SRM (note) list of procedures (table) discussed stainless steel parts frequency (note) running procedure tune and calibration report Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 168 1 creating an instrument method Ethernet 2 creating a sequence Ethernet Link OK LED 3 preparing the probe and inlet valve 4 preparing the mass spectrometer 5 running the sequence TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 169 (I/R) tool, inserting Q0 quadrupole ion volumes, installing transfer line lever, removing fuses, mass spectrometer, replacing plug orientation Safe to Insert Probe message using, procedure Insert Probe message (figure) Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 170 I/R tool reinstalling cleaning L1, L2, L3 figure TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 171 Parent scan mode ion optics discussed ion source illustration (figure) LEDs and system startup part numbers maintenance procedures (table) Accessory Kit mass analyzer Chemicals Kit Off condition miscellaneous parts On/Off status of components Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 172 (figure) Product scan mode reference scans (iSRM) discussed reference SRM reactions illustration (figure) regulatory compliance profile data type replaceable parts pumps accessory kit forepump calibration compound vial oil, part number TSQ Quantum XLS Series User Guide Thermo Scientific...
  • Page 173 (SRM) complete shutdown selected ion monitoring (SIM) scan type emergency procedure selected reaction monitoring (SRM) scan type System Tune and Calibration workspace (figure) sensitivity problems, troubleshooting septum bleed contamination Thermo Scientific TSQ Quantum XLS Series User Guide...
  • Page 174 Thermo Xcalibur Roadmap, opening functional block diagram (figure) toluene solvent peaks gas chromatograph TRACE GC Ultra gas chromatograph TSQ Quantum XLS system (photo) configuration TSQ Quantum XLS Ultra system (photo) photo tune and calibration report transfer line figure capillary column saving...
  • Page 175 Vent Valve Closed LED voltages conversion dynode Q0 offset quadrupole rf and dc Warnings burn hazard GC oven, injector, transferline removing ion source shock hazard, removing ion source WEEE compliance xylene solvent peaks Thermo Scientific TSQ Quantum XLS Series User Guide...

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