Thermo Scientific TSQ Quantum GC User Manual
Thermo Scientific TSQ Quantum GC User Manual

Thermo Scientific TSQ Quantum GC User Manual

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TSQ Series
TSQ Quantum XLS
and TSQ Quantum GC
User Guide
70111-97220 Revision A
March 2010

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Summary of Contents for Thermo Scientific TSQ Quantum GC

  • Page 1 TSQ Series TSQ Quantum XLS and TSQ Quantum GC User Guide 70111-97220 Revision A March 2010...
  • Page 2 © 2009 Thermo Fisher Scientific Inc. All rights reserved. Swagelok™ is a trademark of the Crawford Fitting Company. Dranetz™ is a trademark of Dranetz Technologies, Inc. Styrofoam™ is a trademark of Dow Chemical Company. Teflon™ is a trademark of E. I. du Pont de Nemours &...
  • Page 3 Regulatory Compliance Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent electromagnetic compatibility (EMC) and safety standards as described in the next section or sections by product name. Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
  • Page 4: Fcc Class A, Cfr 47 Part

    TSQ Quantum GC EMC Directive 89/336/EEC as amended by 92/31/EEC and 93/68/EEC TUV Rheinland of North America Inc EMC compliance has been evaluated by EN 55011 1998, 1999, 2002 EN 61000-4-3 2002 EN 61000-3-2 1995, A1; 1998, A2; 1998, A14; 2000 EN 61000-4-4 1995, A1;...
  • Page 5 Notice on Lifting and Handling of Thermo Fisher Scientific San Jose Instruments For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific San Jose instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one person alone to handle safely.
  • 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 CAUTION Symbol CAUTION VORSICHT ATTENTION PRECAUCION AVVERTENZA Electric Shock: This instrument uses Elektroschock: In diesem Gerät werden Choc électrique: L’instrument utilise des Descarga eléctrica: Este instrumento Shock da folgorazione. L’apparecchio è high voltages that can cause personal Hochspannungen verwendet, die tensions capables d’infliger des blessures utiliza altas tensiones, capaces de alimentato da corrente ad alta tensione...
  • Page 10 CAUTION Symbol CAUTION Electric Shock: This instrument uses high voltages that can cause personal injury. Before servicing, shut down the instrument and disconnect the instrument from line power. Keep the top cover on while operating the instrument. Do not remove protective covers from PCBs. Chemical: This instrument might contain hazardous chemicals.
  • Page 11: Table Of Contents

    Gas Chromatograph ..........19 Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 12 Starting Up the System after a Complete Shutdown ..... 55 Restoring Power to the TSQ Quantum XLS or TSQ Quantum GC system .
  • Page 13 Cleaning Lenses of the TSQ Quantum XLS Ion Source ....88 Cleaning the Lenses of the TSQ Quantum GC Ion Source ....95 Reinstalling the Ion Source .
  • Page 14 Index ............. . .163 TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 15: Preface

    The Thermo Scientific TSQ Quantum XLS™ and TSQ Quantum GC™ systems are members of the TSQ™ Quantum family of mass spectrometers. This TSQ Quantum XLS and TSQ Quantum GC User Guide contains a description of the modes of operation and principle hardware components of your TSQ Quantum XLS or TSQ Quantum GC system.
  • Page 16 Preface Tip Highlights helpful information that can make a task easier. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 17: Safety Precautions

    CAUTION Do Not Perform Any Servicing Other Than That Contained in the TSQ Quantum XLS and TSQ Quantum GC User Guide. To avoid personal injury or damage to the instrument, do not perform any servicing other than that contained in the TSQ Quantum XLS and TSQ Quantum GC User Guide or related manuals unless you are authorized to do so.
  • Page 18: Solvent And Gas Purity Requirements

    Deionized water contains chemicals and is not recommended. For a wide variety of solvents and consumables, visit www.FisherLCMS.com. The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers use argon as a collision gas. The argon must be high purity (99.995%). The required gas pressure is 135 ± 70 kPa (20 ±...
  • Page 19: Contacting Us

    To suggest changes to documentation or to Help • Fill out a reader survey online at www.thermo.com/lcms-techpubs. • Send an e-mail message to the Technical Publications Editor at techpubs.finnigan-lcms@thermofisher.com. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 21: Introduction

    Introduction The TSQ Quantum XLS™ and TSQ Quantum GC™ are members of the TSQ™ Quantum family of Thermo Scientific mass spectrometers. The TSQ Quantum XLS and the TSQ Quantum GC are advanced analytical instrument that includes a mass spectrometer, liquid chromatograph, and the Xcalibur™...
  • Page 22 TSQ Quantum GC mass spectrometer, TriPlus autosampler, and TRACE GC Ultra gas chromatograph The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers include an electron ionization/chemical ionization (EI/CI) ion source, ion optics, a triple-stage mass analyzer, and an ion detection system, all of which are enclosed in a vacuum manifold. Ionization of the sample takes place in the ion source.
  • Page 23: Ionization Modes

    Ionization Modes The specific process used to ionize the analyte is referred to as the ionization mode. You can operate the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers in either of two ionization modes: • Electron ionization mode •...
  • Page 24: Electron Ionization Mode

    • An ion association reaction in which 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 and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 25: Ion Polarity Modes

    Scan Modes You can operate the TSQ Quantum XLS and TSQ Quantum GC 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 MS/MS scan modes. The scan modes in each category are as follows: •...
  • Page 26 This separation allows the rod assembly to serve as a mass analyzer. On the TSQ Quantum XLS and TSQ Quantum GC 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 27: 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. The Product scan mode is illustrated in Figure Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 28: Parent Scan Mode

    Q1 (the parent ions), whereas data for the ion intensity axis are obtained from Q3 (from monitoring the product ion). The Parent scan mode is illustrated in Figure TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 29: Neutral Loss Scan Modes

    CID to produce product ions. The product mass analyzer then separates these product ions by mass-to-charge ratio. Neutral Loss scan mode is illustrated in Figure 4. Examples of compounds with a common neutral loss fragment appear Figure Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 30 CO from aldehydes, HX from halides, and H O from alcohols). Figure 4. Illustration of the Neutral Loss scan mode R F O nly + A r Q3 = Q1 - Δ Q1 Scanning Q1 m/z TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 31: Data-Dependent Scan Mode

    Examples of compounds with a common neutral-loss fragment Data-Dependent Scan Mode The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers use the information in a data-dependent scan mode experiment to make automatic decisions about the next step of the experiment without input from a user. 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 32: Scan Types

    Introduction Scan Types Scan Types You can operate the TSQ Quantum XLS and TSQ Quantum GC systems with a variety of scan types. The most common scan types are as follows: • Full Scan • Selected Ion Monitoring (SIM) •...
  • Page 33: Selected Reaction Monitoring (Srm)

    Intelligent Selected Reaction Monitoring (iSRM) In intelligent selected reaction monitoring (iSRM) experiments, the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers perform multiple “primary” selected reaction monitoring (SRM) scans for each analyte (parent ion) of interest. The mass spectrometer uses for quantification the sum of the intensities of an analyte’s primary SRM scans.
  • Page 34: 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 and TSQ Quantum GC mass spectrometers in one of two data types: • Profile data type • Centroid data type Profile Data Type In the profile data type, you can see the shape of the peaks in the mass spectrum.
  • Page 35: Centroid Data Type

    In general, use the centroid scan data type for data acquisition for faster scan speed. Data processing is also much faster for centroid data. Mass/Charge Range The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers can operate in a mass/charge range of 10 to 3000 Da. Thermo Scientific...
  • Page 37: Functional Description

    • Mass Spectrometer • Data System A functional block diagram of the TSQ Quantum XLS or TSQ Quantum GC system is shown in Figure 6. 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 38: Autosampler

    Functional Description Autosampler Figure 6. Functional block diagram of the TSQ Quantum XLS or TSQ Quantum GC system Sample flow Electrical connection Mass spectrometer Data system Autosampler (Optional) Printer (optional) Instrument Personal Ion detection Mass control electronic computer analyzer system...
  • Page 39: Gas Chromatograph

    Configuration. Refer to Xcalibur Help for a description of TRACE GC Ultra configuration options. The TSQ Quantum XLS and TSQ Quantum GC data system computers can directly control the TRACE GC Ultra. Choose Start > Programs > Xcalibur > Xcalibur and click Instrument Setup to open the Instrument Setup window.
  • Page 40: 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. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 41: Mass Spectrometer

    The mass spectrometer uses a triple-quadrupole mass analyzer with an ion source external to the mass analyzer. Several important features of the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers are as follows: •...
  • Page 42: Controls And Indicators

    The Communication LED illuminates green when the Ethernet communication link between the mass spectrometer and the data system has been made. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 43 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 and TSQ Quantum GC User Guide...
  • Page 44 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 and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 45: Ei Ci Ion Source

    The ion source forms gas phase sample ions from sample molecules that elute from the GC or are introduced by the direct sample probe. You can operate the ion source in either the electron ionization (EI) or chemical ionization (CI) mode. See “Ionization Modes” page Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 46 Figure 13. Ion source of the TSQ Quantum XLS Magnets and magnet yoke EI/CI Source Filament Ion source block Heater ring Q00 quadrupole lens assembly L1, L2, L3, lens assembly TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 47 Functional Description Mass Spectrometer Figure 14. Ion source of the TSQ Quantum GC Magnets and magnet yoke EI/CI Source Filament Ion source block Heater ring L1, L2, L3, and L4 lens assembly The ion volume, located in the center of the ion source, is the site where electrons interact with sample or reagent gas molecules to form ions.
  • Page 48 In positive ion mode, the lenses are adjusted to a negative potential, and in negative ion mode, the lenses are adjusted to a positive potential. The arrangement of the lenses and their spacers enables quick and efficient pump-out of the ion source. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 49: Inlet Valve

    When the ball valve is closed, it prevents the vacuum manifold from venting to atmosphere. Figure 16. Inlet valve, I/R tool, guide bar, and ball valve lever Inlet valve I/R tool Ball valve lever Guide bar Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 50: Ion Optics

    The Q0 offset voltage increases the translational kinetic energy of ions emerging from the ion source. Figure 17. Q0 quadrupole Figure 18 gives a cross-sectional view of the transfer line, ion source, and Q0 quadrupole. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 51 Figure 18. Cross-sectional view of the transfer line, ion source, and Q0 quadrupole of the TSQ Quantum XLS Lens L1 Ion source Lens L2 Q00 quadrupole ion volume Q0 quadrupole Lens L3 Transfer line Capillary column Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 52: Mass Analyzer

    Functional Description Mass Spectrometer Figure 19. Cross-sectional view of the transfer line, ion source, and Q0 quadrupole of the TSQ Quantum GC Lens L2 Lens L1 Q0 quadrupole Lens L3 Ion source Lens L4 ion volume Transfer line Capillary column The L11 and L12 lenses are metal disks with a circular hole in the center through which the ion beam can pass.
  • Page 53 Technically, the collision cell is the chamber that encloses Q2 where collision-induced dissociation can take place if the argon collision gas is present. See Figure Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 54 0 to ±840 V. Voltages of the same amplitude and sign are applied to each rod pair. However, the voltages applied to the other rod pair are equal in amplitude but opposite in sign. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 55 Figure 23. Magnitude of the rf and dc voltages applied to the rods of the Q1 and Q3 mass analyzers 10,000 V P/P 840 V DC VOLTAGE Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 56 (TKE) of the ion into internal energy. This collision places the ion in an excited state. If the internal energy is sufficient, the ion fragments. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 57 The quadrupole offset voltage accelerates or decelerates ions and, therefore, sets theTKE of the ions as they enter the quadrupole rod assembly. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 58 During tuning, the mass spectrometer determines the optimum quadrupole offset voltage for Q1 and for Q3. Mass Analyzer Lenses The TSQ Quantum XLS and TSQ Quantum GC mass analyzers have three lens sets. See Figure 21 page 34. Those between Q1 and Q2 are designated L21, L22, L23; those between Q2 and Q3 are designated L31, L32, L33;...
  • Page 59: Ion Detection System

    Its purpose is to shield Q3 from the high voltage applied to the ion detection system and to shield the ion detection system from the high rf voltages applied to Q3. Ion Detection System The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers are equipped with a high-sensitivity, off-axis ion detection system. See Figure 24.
  • Page 60 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. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 61: 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 Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 62 1 mTorr by the interstage port of the turbomolecular vacuum pump. A second vacuum manifold houses the ion source, which is open to the Q0 quadrupole chamber. The interstage port of the turbomolecular pump evacuates the ion source region. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 63 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 and TSQ Quantum GC User Guide...
  • Page 64 CAUTION Always plug the forepump power cord into the outlets labeled Forepump on the right side power panel of the mass spectrometer. Never plug it directly into a wall outlet. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 65 See “Collision Cell and CID Efficiency” page Argon enters the mass spectrometer through a 1/8 in. port on the left side of the mass spectrometer. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 66: Electronic Assemblies

    • Line filter • Electronics service switch • Vacuum service switch The “brains” of the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers are the System Control PCB. The System Control PCB and embedded computer include the following: • PowerPC processor •...
  • Page 67 The Analyzer Control PCB controls and monitors the rf voltages for Q0, Q1, Q2, and Q3 quadrupoles. It also has lens voltage drivers that convert ±330 V dc power from the DC Rod Driver PCB to dc voltages that are applied to the lenses Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 68: Data System

    Functional Description Data System Data System The data system controls and monitors the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers. The data system also processes data that the mass spectrometer acquires. The data system is composed of the following: •...
  • Page 69: Data System / Local Area Network Interface

    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 and TSQ Quantum GC User Guide...
  • Page 71: Chapter 3 System Shutdown, Startup, And Reset

    System Shutdown, Startup, and Reset Many maintenance procedures for the TSQ Quantum XLS and TSQ Quantum GC systems require that the mass spectrometer be shut down completely. In addition, you can place the mass spectrometer in Standby mode if the system is not to be used for 12 hours or more.
  • Page 72: Placing The System In Standby Mode

    Placing the System in Standby Mode If you are not going to use the TSQ Quantum XLS or TSQ Quantum GC system for a short period of time, such as overnight or over weekends, it does not need to be shut down completely.
  • Page 73: Shutting Down The System Completely

    Shutting Down the System Completely Shut down the TSQ Quantum XLS or TSQ Quantum GC system completely only if it is to be unused for an extended period or if it must be shut down for a maintenance or service procedure.
  • Page 74 • After about two minutes, the pressure of the vacuum manifold reaches atmospheric pressure. 6. Unplug the power cord for the mass spectrometer. CAUTION Allow heated components to cool before servicing them. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 75: Starting Up The System After A Complete Shutdown

    CAUTION 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 or TSQ Quantum GC system after it has been shut down completely requires the following: •...
  • Page 76: Starting Up The Gc

    To start the mass spectrometer CAUTION If you turn on the mass spectrometer without column flow, air can damage the GC column. This large air leak into the TSQ Quantum GC also causes the ion source to require cleaning. 1. Turn on the flow of argon at the tank if it is off.
  • Page 77 Table 3.Maximum allowed pressure to turn on high voltage Carrier gas Ar collision gas Maximum pressure (Torr) 6 × 10 5 × 10 5 × 10 1 × 10 Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 78: Starting Up The Autosampler

    Setting Up Conditions for Operation To set up your TSQ Quantum XLS or TSQ Quantum GC mass spectrometer for operation 1. Before you begin data acquisition with your TSQ Quantum XLS 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 79: Resetting The Data System

    2. Select Restart and click OK to start the Windows shutdown and restart procedure. 3. Observe the Windows shutdown and restart procedure on the monitor. Press CTRL+ALT+DELETE when you are prompted to do so. To complete the shutdown and Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 80: 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 and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 81 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 Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 82 Table 4. On/Off status of mass spectrometer components and voltages (Sheet 2 of 2) Standby Electronics Vacuum service MS Main power service switch in switch in circuit breaker Mass spectrometer component Service Mode Service Mode switch in Off position position position Ion gauge...
  • Page 83: 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 or TSQ Quantum GC mass spectrometer automatically with TSQ EZ Tune uses perfluorotributylamine (FC-43) as the tuning and calibration compound.
  • Page 84: Displaying The Fc-43 Mass Spectrum

    3. Click the Define Scan button to display the Define Scan dialog box. 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 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 85 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 32, see “Diagnostics and Troubleshooting” page 129. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 86: 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. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 87 Troubleshoot and correct the problem that caused the tuning and calibration procedure to fail. See “Tuning Issues” page 143. d. Go to step 5 and restart the tuning and calibration procedure. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 88 8. Save the calibration file as follows: a. Click Save Calib. As to open the Save Calibration File dialog box. b. In the File Name box, enter a name for your calibration file. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 89: 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. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 90 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 and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 91 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 and TSQ Quantum GC User Guide...
  • Page 93: Chapter 5 Changing Ionization Modes

    Changing Ionization Modes You can operate the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers in either EI or CI ionization mode. Changing ionization modes requires changing ion volumes. It is not necessary to shut down the mass spectrometer to change ion volumes.
  • Page 94 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 and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 95 3. Choose Start > All Programs > Thermo Instruments > TSQ > TSQ Tune to open the EZ Tune window. 4. Click the Probe button in the EZ Tune toolbar. The Insert Probe message appears (Figure 39). Figure 39. Insert Probe message Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 96 Tighten the inlet valve knob clockwise to ensure a leak-tight seal. Figure 40. I/R tool at the first stop on guide bar and the inlet valve knob tightened Inlet valve knob First stop of I/R tool guide bar TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 97 7. Once evacuation is complete, pull the inlet valve lever up to open the inlet valve. Figure 42. I/R tool at first stop and inlet valve lever up Inlet valve lever First stop of I/R tool guide bar Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 98 Withdraw the I/R tool (with the ion volume attached) until the guide ball reaches the first stop (see Figure 42). d. Pull the lever down to close the inlet valve. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 99 113. 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 and TSQ Quantum GC User Guide...
  • Page 100: Installing The Ion Volume

    8. Click OK. The forepump evacuates the inlet valve. Wait for the safe to insert probe message to appear (Figure 41); then click OK. 9. Once evacuation is complete, pull the inlet valve lever up to open the inlet valve. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 101 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. 13. Remove the guide bar by rotating it 90° counter-clockwise and sliding it out of the entry housing. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 102 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 and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 103: Maintenance

    Maintenance This chapter describes routine maintenance procedures that you must perform to ensure optimum performance of the TSQ Quantum XLS or TSQ Quantum GC mass spectrometer. Optimum performance of the mass spectrometer depends on the maintenance of all parts of the instrument.
  • Page 104 Cleaning of the Q0, Q1, Q2, and Q3 quadrupoles is rarely (if ever) required. **A Thermo Fisher Scientific Field Service Engineer must perform this maintenance procedure. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 105: Cleaning Ion Source Components

    Removing and Installing a GC Capillary Column Cleaning Ion Source Components An important part of maintaining your TSQ Quantum XLS or TSQ Quantum GC 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 106 Figure 46. Ion source assembly of the TSQ Quantum XLS, exploded and assembled views TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 107 Figure 47. Ion source assembly of the TSQ Quantum GC, exploded and assembled views TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 108: Cleaning Ion Volumes

    115, respectively. 5. Reassemble L1, L2, L3 lens assembly and install it and the Q00 quadrupole onto the ion source. See “Reassembling the L1, L2, L3 Lens Assembly” page TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 109 Pull back the column. (You can first mark the column’s position with white out or something similar.) 3. Prepare a clean work area by covering the area with lint-free cloth. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 110 7. Pull the ion source assembly away from the Q0 quadrupole mount and 2 mm to the right to clear the transfer line bellows. 8. Slide the ion source off the magnet yoke. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 111 Figure 2. Remove the Q00 quadrupole lens assembly and the L1, L2, L3 lens assembly from the heater cartridges of the ion source. Place them on a clean surface. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 112 1. Remove the lens retainer clip by pinching the ends with your fingers or a pair of tweezers. Figure 2. Remove the lenses and spacers from the lens holder. 3. Place the components on a clean surface. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 113 “Cleaning Non-Stainless Steel or Hybrid Part” page 115. Reassembling the L1, L2, L3 Lens Assembly Ensure that the lenses are clean and dry before you reassemble the lens assembly. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 114 5. Align the 3-pin connector such that the side with the beveled edge is closest to the L3 lead pin and the side with the rounded corners is closest to the L1 lead pin. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 115: Cleaning The Lenses Of The Tsq Quantum Gc Ion Source

    8. Close and secure the cover to the ion source vacuum manifold. Cleaning the Lenses of the TSQ Quantum GC Ion Source If cleaning the ion volume does not restore system performance, clean the ion source lenses. Note Lens L4 requires cleaning less often than lens L1, L2, and L3.
  • Page 116 To remove the ion source CAUTION Do not remove the ion source without first pulling back the capillary column, or else the capillary column might break. 1. Shut down and vent the TSQ Quantum GC mass spectrometer. See “Shutting Down the System Completely”...
  • Page 117 7. Pull the ion source assembly away from the Q0 quadrupole and 2 mm to the right to clear the transfer line bellows. 8. Slide the ion source off the magnet yoke. 9. Place the ion source and magnet yoke on a clean, lint-free cloth. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 118 Ion source Retainer clip Threaded standoff Disassembling the Ion Source Lens Assembly To disassemble the lens assembly 1. Pull the L1, L2, L3 lens assembly from the L4 lens assembly. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 119 Remove the lens clip by pinching the ends with your fingers or a pair of tweezers. b. Remove the lenses and spacers from the lens holder. c. Place the components on a clean surface. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 120 Remove the lens clip by pinching the ends with your fingers or a pair of tweezers. b. Remove the lens L4 from the lens holder. c. Place the components on a clean surface. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 121 Reinstall the lens clip by pinching the ends with your fingers or a pair of tweezers and seating it in the lens holder. c. Insert the lens alignment tool (in the TSQ Quantum GC Accessory Kit) into the lens assembly and align the lenses 3.
  • Page 122: Reinstalling The Ion Source

    TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 123 3. Remove the ion source. See “Removing the TSQ Quantum XLS Ion Source” page 4. Wearing clean, lint- and powder- free gloves, remove the ion source from the magnet yoke. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 124 , in the P/N 120320-0030 TSQ Quantum XLS Accessory Kit a. Verify that the filament wire is centered in the electron lens hole. b. Insert the filament into the centering ring. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 125: Replacing The Filament Of The Tsq Quantum Gc Ion Source

    Maintenance Replacing the Filament of the TSQ Quantum GC Ion Source c. Align the filament leads with the EI/CI Source PCB connectors and gently press the leads into the connectors. Normally, there is a small gap (about 0.016 in.) between the filament and the connectors.
  • Page 126 Maintenance Replacing the Filament of the TSQ Quantum GC Ion Source 2. Shut down and vent the TSQ Quantum GC. See “Shutting Down the System Completely” page CAUTION Shock Hazard. Unplug the TSQ Quantum GC before proceeding. 3. Remove the ion source. See “Removing the TSQ Quantum GC Ion Source”...
  • Page 127: Disassembling And Reassembling The Tsq Quantum Xls Ion Source Completely

    • Gloves, cleanroom grade (P/N 23827-0008 and 23827-0009) • Lint-free cloth Frequency As needed To disassemble the ion source completely 1. Prepare a clean work area by covering the area with lint-free cloth. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 128 5. Pull the Q00 quadrupole lens assembly and the L1, L2, L3 lens assembly off the ion source. 6. Pull the heater ring off the ion source. 7. Unscrew and remove the three base studs. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 129 4. Reinstall the ion source into the vacuum manifold. See “Reinstalling the TSQ Quantum XLS Ion Source” page 5. Restart the system. See “Starting Up the System after a Complete Shutdown” page Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 130: Disassembling And Reassembling The Tsq Quantum Gc Ion Source Completely

    Maintenance Disassembling and Reassembling the TSQ Quantum GC Ion Source Completely Disassembling and Reassembling the TSQ Quantum GC Ion Source Completely Disassemble the ion source completely to clean the ion source block or replace the EI/CI Source PCB. Figure 58 for the location of the ion source components.
  • Page 131 Maintenance Disassembling and Reassembling the TSQ Quantum GC Ion Source Completely Figure 59. Disassembling the ion source Filament retainer clip Filament Heater ring Centering ring Ion source block Lens assembly Heater ring and lens assembly retainer clip Threaded standoff EI/CI Source PCB Base studs 5.
  • Page 132 Maintenance Disassembling and Reassembling the TSQ Quantum GC Ion Source Completely 11. Clean the ion source block and lenses. See “Cleaning Stainless Steel Parts” page 113. Clean non-stainless steel parts as described in “Cleaning Non-Stainless Steel or Hybrid Part” page 115.
  • Page 133: Cleaning Stainless Steel Parts

    Maintenance Disassembling and Reassembling the TSQ Quantum GC Ion Source Completely Cleaning Stainless Steel Parts Tools Needed • Acetone, reagent grade (or other suitable polar solvent) • Aluminum oxide abrasive, number 600 (P/N 32000-60340) • Applicators, cotton-tipped (P/N 00301-01-00015) • Beaker, 450 mL •...
  • Page 134 Maintenance Disassembling and Reassembling the TSQ Quantum GC Ion Source Completely 2. Rinse the parts with clean water. Use a clean applicator or toothbrush to remove the aluminum oxide slurry. Do not let the slurry dry on the metal; dried aluminum oxide is difficult to remove.
  • Page 135: Cleaning Non-Stainless Steel Or Hybrid Part

    Maintenance Disassembling and Reassembling the TSQ Quantum GC Ion Source Completely Cleaning Non-Stainless Steel or Hybrid Part Tools Needed • Acetone, reagent grade (or other suitable polar solvent) • Aluminum oxide abrasive, number 600 (P/N 32000-60340) • Applicators, cotton-tipped (P/N 00301-01-00015) •...
  • Page 136: 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. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 137: Adding Calibration Compound

    The calibration compound is a liquid whose mass spectrum of ions is used to tune and calibrate the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers. The mass spectrometer uses FC-43 as its calibration compound. Although you cannot visually determine when a calibration compound needs to be added, Xcalibur Automatic Tune produces an error message indicating that “the intensity of calibration gas ions is too low.”...
  • Page 138 (calibrant covers the top of the frit), then you have too much in the vial. Immediately pour out the excess calibrant according to local environmental regulations. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 139 10. Reinstall the cover to the calibration compound vial compartment. 11. Position the GC next to the mass spectrometer. 12. Restart your system. See “Starting Up the System after a Complete Shutdown” page Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 140: Replacing The Ball Valve Seal

    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 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 141 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. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 142: Removing And Installing A Gc Capillary Column

    As needed for maintenance or column replacement Removing a GC Capillary Column To remove a GC capillary column 1. Shut down the TSQ Quantum XLS or TSQ Quantum GC and the gas chromatograph. a. Shut down and vent the mass spectrometer. See “Shutting Down the System Completely”...
  • Page 143 Figure 64. GC injector and transfer line unions 3. Remove the column from the injector. Refer to the Column chapter of the TRACE GC Ultra Operating Manual for instructions. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 144: Installing A Gc Capillary Column

    Set the oven and injector temperatures to 30 °C. c. Set the injector flow to 1.0 mL/min. d. Turn off vacuum compensation (under the Right or Left Carrier menu). TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 145 Shut down and vent the mass spectrometer. See“Shutting Down the System Completely” page b. Lower the GC oven temperature to 30 °C and allow it to cool before continuing. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 146 CAUTION The oven might be hot. Allow it to cool to room temperature before opening it. Do not touch the injector, which will still be hot. d. Re-tighten the transfer line nut and the transfer line union. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 147 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). Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 149: Chapter 7 Diagnostics And Troubleshooting

    Replacing PCBs and Power Supplies TSQ Quantum XLS and TSQ Quantum GC System Diagnostics The TSQ Quantum XLS and TSQ Quantum GC system diagnostics are used to test the major electronic circuits within the instrument and indicate whether the circuits pass or fail the tests.
  • Page 150 Diagnostics and Troubleshooting TSQ Quantum XLS and TSQ Quantum GC System Diagnostics • Did problems occur after you performed maintenance on the instrument, data system, or peripherals? • Did you change the configuration of the system, cables, or peripherals just before the...
  • Page 151: Troubleshooting

    • Error messages How does the MS communication work? The flow of digital information in the TSQ Quantum XLS and TSQ Quantum GC systems is bi-directional; 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 and TSQ Quantum GC systems report their readiness state, current tasks, various voltages, heated zones, and pressure readings.
  • Page 152 Issue: Acquisition does Possible causes/solutions not begin as expected. • The TSQ Quantum XLS or TSQ Quantum GC start mode is not properly configured. Verify that the instrument is configured properly. Refer to Xcalibur Help for more information. • The TSQ Quantum XLS or TSQ Quantum GC Instrument Setup file has incorrect settings.
  • Page 153: Contamination Issues

    Issue: Acquisition Possible causes/solutions terminates • The end run time in the TSQ Quantum XLS or TSQ Quantum GC instrument method unexpectedly. is incorrect. 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 154 • Carrier gas tubing is contaminated. contamination (Typical ions are m/z 43, 57, 71, • Isolate source of hydrocarbon contamination and remedy. 85, 99). • Replace carrier gas tubing. • Change carrier gas filters. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 155: Filament And Lens Control Issues

    Diagnostics test the lenses of the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers. A flat line, which represents voltage readback versus the predicted voltage ramp, indicates a lens or other control fault.
  • Page 156: Heated Zone Issues

    • The ion source, transfer line, or both are not hot enough. Increase the transfer line tailing. temperature. It should be at least as hot as the highest GC oven temperature. Then, try increasing the ion source temperature. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 157 GC and set transfer line temperature in the GC Method Editor. • Transfer line heater elements are defective. Replace the transfer line. • The transfer line temperature sensor (RTD) is defective. Replace the transfer line. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 158: High Vacuum Issues

    • The vacuum service switch is in the Off position. Place the vacuum service switch in the operating position. • The forepump power cable from the TSQ Quantum XLS or TSQ Quantum GC is not connected. Connect the power cable.
  • Page 159: Linearity Issues

    • The electron multiplier setting is incorrect. Run Auto Tune - Calibration as described in “Tuning and Calibrating” page • The injection port liner or capillary column is dirty. Change the injection port liner and trim the capillary column. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 160: Power Supply Issues

    Improper GC maintenance is another cause of diminished sensitivity. It is important to establish a routine maintenance program for the GC. See the TRACE GC Maintenance Manual for more information on establishing a maintenance program. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 161 • The injector or septum is leaking. Replace septum and perform leak check on the GC. • The capillary column is at the end of its life span. Replace the capillary column. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 162 Stability Issues Stability helps provide consistent instrument precision and the reproducibility of accurate results. Good operating conditions for the mass spectrometer, gas chromatograph, and autosampler contribute to instrument stability. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 163: Stability Issues

    • The electron multiplier has not been given sufficient time to outgas since venting. Allow calibration fails. more time to pump out. • The GC column flow is too high. Lower it to1 mL/min. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 164 • The injection rf is not calibrated. Run Auto Tune - Calibration as described in “Tuning and Calibrating” page • There is a problem with the filament or lens control. See “Filament and Lens Control Issues” page 135 for more information. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 165: Replacing A Fuse

    CAUTION Fuses protect the various circuits by opening the circuits whenever overcurrent occurs. On the TSQ Quantum XLS and TSQ Quantum GC 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 166: Replacing Pcbs And Power Supplies

    Diagnostics and Troubleshooting Replacing PCBs and Power Supplies TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 167: Appendix 8 Using The Direct Sample Probe

    3. Choose TSQ > Regular Method to open the regular method Scan Editor page. 4. On the Scan Editor page, create a one segment, one scan event instrument method. In this example, the segment is 8 minutes long (see Figure 65). Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 168 5. Specify the mass spectrometer settings, for this example, full-scan scan type, Q1MS scan mode, and positive polarity. Figure 65. Scan Editor page of Instrument Setup 6. Click the EI/CI tab to display the EI/CI page (see Figure 66). TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 169 This example is an EI experiment with a 200 μA emission current. 8. Save the instrument method. a. Choose File > Save As to open the Save As dialog box. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 170: Creating A Sequence

    3. 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 67. Sequence Setup view, showing one sample in the sequence TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 171: Preparing The Probe And Inlet Valve

    IMPORTANT The TSQ EZ Tune window must be open for the mass spectrometer to initiate the probe insertion sequence. 2. Ensure that the TSQ Quantum XLS or TSQ Quantum GC mass spectrometer is the only instrument in use and that there are no start instruments.
  • Page 172 In Sequence Setup, choose Actions > Run Sequence. The Run Sequence dialog box opens (see Figure 68). Figure 68. Run Sequence dialog box, showing instruments in use c. Click Change Instruments to open the Change Instruments In Use dialog box. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 173: Running The Sequence

    Xcalibur can display instrument methods. To run the sequence 1. In the Run Sequence dialog box (see Figure 68 page 152), click OK to start the acquisition. Xcalibur displays the Insert Probe message. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 174 Figure 71. Probe at the first stop on guide bar 3. Click OK. The forepump evacuates the inlet valve. 4. When the Safe to Open Valve message to appears, click OK. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 175 Figure Figure 73. Probe inserted into the inlet valve 7. When you receive the Acquisition Ready message, click OK. The TSQ Quantum XLS is now waiting for contact closure. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 176 9. Start the probe method from the probe controller to initiate data acquisition. See Figure 75 Figure Figure 75. Perfluorotetracosane mass spectrum at 0.56 minute retention time TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 177: Examining The Raw Data In Qual Browser

    1. On the Xcalibur Home Page, 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. See Figure Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 178: Removing The Probe

    3. Loosen the inlet valve knob by turning it counter-clockwise. 4. Continue withdrawing the probe completely from the inlet valve by sliding it through the guide ball track in the guide bar. TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 179 You can also remove the inlet valve lever by pulling it free. Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide...
  • Page 181: Replaceable Parts And Consumables

    To ensure proper results in servicing the TSQ Quantum XLS or TSQ Quantum GC mass spectrometer, order only the parts listed or their equivalent. Contact Thermo Fisher Scientific San Jose and have your TSQ Quantum XLS or TSQ Quantum GC serial number ready.
  • Page 182: Chemicals Kit

    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 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific...
  • Page 183: Index

    Chemicals Kit circuit breaker 23–24 cleaning cables aluminum parts ceramic parts calibrating frequency and H-SRM (note) ion volumes discussed lenses L1, L2, L3, L4 frequency (note) Thermo Scientific TSQ Quantum XLS User Guide...
  • Page 184 1 creating an instrument method observed peaks 2 creating a sequence on, off 3 preparing the probe and inlet valve part number 4 preparing the mass spectrometer spectrum, positive EI mode TSQ Quantum XLS User Guide Thermo Scientific...
  • Page 185 Q0 quadrupole lock position transfer line unlock position TSQ Quantum GC withdrawal (Caution) fuses, mass spectrometer, replacing Instrument Configuration window, opening 18–19 instrument method, creating intelligent selected reaction monitoring (iSRM) ion detection system...
  • Page 186 (CI) ion source lenses, cleaning discussed ion volumes, cleaning electron ionization (EI) procedures (table) iSRM scan type mass analysis collision-induced dissociation discussion leak check, GC mass analyzer TSQ Quantum XLS User Guide Thermo Scientific...
  • Page 187 On/Off status installing the ion volume MS/MS scan modes maintaining forepump Neutral Loss operating the inlet valve Parent placing system in standby Product reassembly ion source lenses Thermo Scientific TSQ Quantum XLS User Guide...
  • Page 188 Neutral Loss Q0, description Neutral Loss, example (figure) Q1 and Q3 Neutral Loss, illustrated (figure) RF and dc fields Parent RF and dc fields (figure) 34–35 Parent, illustrated (figure) Qual Browser Product TSQ Quantum XLS User Guide Thermo Scientific...
  • Page 189 (GC) sensitivity operating conditions, setting stability switch tuning System Control PCB, description TSQ Quantum GC System LED autosampler figure calibrating mass spectrometer reset data system mass spectrometer startup data types system power off button...
  • Page 190 (figure) On/Off status of mass spectrometer components vacuum system collision gas valve Convectron gauge description forepump functional block diagram (figure) ion gauge leak checking maximim allowed pressures TSQ Quantum XLS User Guide Thermo Scientific...

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