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Using the Direct Sample Probe

Examining the Raw Data in Qual Browser

Thermo Scientific

TSQ Quantum XLS and TSQ Quantum GC User Guide

157

Figure 76.

Perfluorotetracosane chromatogram

Examining the Raw Data in Qual Browser

You can use Qual Browser to display the mass spectrum at various times in the chromatogram.

To examine the raw data

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 77

Summary of Contents for TSQ Quantum GC

Page 1: ...TSQ Series TSQ Quantum XLS and TSQ Quantum GC User Guide 70111 97220 Revision A March 2010 ...

Page 2: ... contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free and assumes no responsibility and w...

Page 3: ...ls not specifically authorized and qualified by 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 not reviewed EMC Directive 89 336 EEC as amended by 92 31 EEC and 93 68 EEC EMC compliance has ...

Page 4: ...and additional components options and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives FCC Compliance Statement 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 2000 A2 2001 EN 61000 3 3 1998 2001 EN 61000 4 5 1995 A1 2001 EN 61326 1 1998 2001 2003 EN 61000 4 6 1996 A1 2003 EN 61000 4 2 2001 ...

Page 5: ...person alone to handle safely Notice on the Proper Use of Thermo Fisher Scientific San Jose Instruments In compliance with international regulations Use of this instrument in a manner not specified by Thermo Fisher Scientific San Jose could impair any protection provided by the instrument Notice on the Susceptibility to Electromagnetic Transmissions Your instrument is designed to work in a control...

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Page 7: ... Directives and the recyclers in your country WEEE Konformität Dieses Produkt muss die EU Waste Electrical Electronic Equipment WEEE Richtlinie 2002 96 EC erfüllen Das Produkt ist durch folgendes Symbol gekennzeichnet Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs Entsorgungsfirmen in allen EU Mitgliedsstaaten getroffen damit dieses Produkt durch diese Firmen wiederverwertet oder ents...

Page 8: ...ieurs compagnies de recyclage dans chaque état membre de l union européenne et ce produit devrait être collecté ou recyclé par celles ci Davantage d informations sur la conformité de Thermo Fisher Scientific à ces directives les recycleurs dans votre pays et les informations sur les produits Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont di...

Page 9: ...dati si raffreddino prima di effetturare l intervento di manutenzione Fire Use care when operating the system in the presence of flammable gases Feuer Beachten Sie die einschlägigen VorsichtsmaBnahmen wenn Sie das System in Gegenwart von entzündbaren Gasen betreiben Incendie Agir avec précaution lors de l utilisation du système en présence de gaz inflammables Fuego Tenga cuidado al operar el siste...

Page 10: ...s and proper procedures to dispose waste oil Heat Before servicing the instrument allow any heated components to cool Fire Use care when operating the system in the presence of flammable gases Eye Hazard Eye damage could occur from splattered chemicals or flying particles Wear safety glasses when handling chemicals or servicing the instrument General Hazard A hazard is present that is not included...

Page 11: ... Polarity Modes 5 Scan Modes 5 Q1MS and Q3MS Scan Modes 7 Product Scan Mode 7 Parent Scan Mode 8 Neutral Loss Scan Modes 9 Data Dependent Scan Mode 11 Scan Types 12 Full Scan 12 Selected Ion Monitoring SIM 12 Selected Reaction Monitoring SRM 13 Highly Selective Reaction Monitoring H SRM 13 Intelligent Selected Reaction Monitoring iSRM 13 Quantitation Enhanced Data Dependent MS QED MS 14 AutoSIM 14...

Page 12: ...ergency 51 Placing the System in Standby Mode 52 Shutting Down the System Completely 53 Starting Up the System after a Complete Shutdown 55 Restoring Power to the TSQ Quantum XLS or TSQ Quantum GC system 55 Starting Up the GC 56 Starting Up the Data System 56 Starting Up the Mass Spectrometer 56 Starting Up the Autosampler 58 Setting Up Conditions for Operation 58 Resetting the Mass Spectrometer 5...

Page 13: ... Forepump 116 Adding Calibration Compound 117 Replacing the Ball Valve Seal 120 Removing and Installing a GC Capillary Column 122 Removing a GC Capillary Column 122 Installing a GC Capillary Column 124 Chapter 7 Diagnostics and Troubleshooting 129 TSQ Quantum XLS System Diagnostics 129 Troubleshooting 131 Communication Issues 131 Contamination Issues 133 Filament and Lens Control Issues 135 Heated...

Page 14: ...Contents iv TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific Chapter 9 Replaceable Parts and Consumables 161 Accessory Kit 161 Chemicals Kit 162 Index 163 ...

Page 15: ...manual Thermo Fisher provides the following for the TSQ Quantum XLS and TSQ Quantum GC Preinstallation Requirements Guide Help available from within the software Safety and Special Notices Make sure you follow the precautionary statements presented in this guide The safety and other special notices appear in boxes Safety and special notices include the following CAUTION Highlights hazards to human...

Page 16: ...Preface vi TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific Tip Highlights helpful information that can make a task easier ...

Page 17: ...espect The ion source and transfer line might be very hot and might cause severe burns if they are touched Allow heated components to cool before you service them CAUTION Provide and Adequate Fume Exhaust System It is your responsibility to provide an adequate fume exhaust system Samples and solvents that are introduced into the mass spectrometer will eventually be exhausted from the forepump Ther...

Page 18: ...ards prevent system failure restore the system to an operating condition or all of the above Routine and preventive maintenance procedures are documented in this manual The user is responsible for routine and preventive maintenance during and after the warranty period Regular maintenance increases the life of the system maximizes the up time of your system and allows you to achieve optimum system ...

Page 19: ...com Y To contact Customer Service for ordering information Y 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 Phone 800 685 9535 Fax 561 688 8736 E mail TechSupport C MS thermofisher com Knowledge base www thermokb com Phone 800 532 47...

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Page 21: ... analytical instrument that includes a mass spectrometer liquid chromatograph and the Xcalibur data system See Figure 1 In a typical analysis an autosampler AS introduces a sample into the gas chromatograph GC The GC separates the sample into its various components The components elute from the GC and pass into the mass spectrometer where they are analyzed Contents Ionization Modes Ion Polarity Mo...

Page 22: ... analyzer where they are filtered according to their mass to charge ratio The polarity of the potentials applied to the lenses in the ion source and ion optics determines whether positively charged ions or negatively charged ions are transmitted to the mass analyzer You can configure the mass spectrometer to analyze positively or negatively charged ions called the positive or negative ion polarity...

Page 23: ...spectrometer can fragment and separate each ionic fragment of a molecule formed in the ion source to build up an entire structure for the molecule piece by piece Thus TSQ Quantum XLS and TSQ Quantum GC systems make investigating all pathways for the formation and fragmentation of each ion in the mass spectrum possible The two stages of mass analysis with resultant reduction of chemical noise in th...

Page 24: ...CI mode ionization of the sample molecules is a multi step process 1 Reagent gas is introduced into the CI ion volume at a flow for methane of about 2 mL min along with sample vapors typically present at partial pressures of less than one thousandth that of the reagent gas 2 The energetic typically 100 eV electrons emitted by the heated filament interact to ionize the reagent gas and form a plasma...

Page 25: ...to the ion source and ion optics The ion optics deliver the ions produced in the ion source in a collimated beam to the mass analyzer The mass spectrometer can switch between positive and negative polarity modes in under 95 ms The information obtained from a positive ion mass spectrum is different from and complementary to the information from a negative ion spectrum Thus the ability to obtain bot...

Page 26: ...nalyzers or ion transmission devices The Q2 rod assembly operates exclusively with rf voltage Thus Q2 is always an ion transmission device Surrounding Q2 is a collision cell where fragmentation can take place if the argon collision gas is present in the cell For a summary of how the rod assemblies function in several of the major scan modes see Table 1 a Scan full scan or transmission of selected ...

Page 27: ...the parent mass analyzer is referred to as the parent set mass Parent ions selected by Q1 then enter Q2 which is surrounded by the collision cell In the second stage of analysis ions in the collision cell can fragment further to produce product ions Two processes produce product ions by unimolecular decomposition of metastable ions or by interaction with argon collision gas present in the collisio...

Page 28: ...sition of metastable ions or by collision induced dissociation Ions formed in the collision cell enter the product mass analyzer which transmits a selected product ion The product set mass is the mass to charge ratio of ions transmitted by the product mass analyzer The resultant spectrum shows all the parent ions that fragment to produce the selected product ion Note that for a mass spectrum obtai...

Page 29: ...the same rate over mass ranges of the same width The respective mass ranges however are offset by a selected mass such that the product mass analyzer scans a selected number of mass units lower than the parent mass analyzer Thus in the Neutral Loss scan mode there are two stages of mass analysis In the first stage the parent mass analyzer separates ions formed in the ion source by mass to charge r...

Page 30: ...d by Q3 is offset by a selected mass above the mass range scanned by Q1 For a neutral loss or neutral gain mass spectrum as for a parent mass spectrum data for the mass to charge ratio axis are obtained from Q1 the parent ion whereas data for the ion intensity axis are obtained from Q3 the product ion being monitored Experiments that use the Neutral Loss scan mode neutral loss experiments are usef...

Page 31: ...If you have some idea of what the parent ion is or if you expect a certain kind of parent ion you can set up a list of possible parent ions Then when one of the parent ions you specified is detected you can acquire product spectra and analyze the information Conversely you can also set up a list of ions that you do not want selected for fragmentation If you have little information about your compo...

Page 32: ...ion about an analyte than does SIM but a full scan does not yield the sensitivity that the other two scan types can achieve With full scan you spend less time monitoring the signal for each ion than you do in SIM or SRM Full scan provides greater information but lower sensitivity than the other two scan types To use the SIM or SRM you need to know what ions or reactions you are looking for before ...

Page 33: ...ovides for the very rapid analysis of trace components in complex mixtures However because SRM selects two sets of ions it obtains specificity that is much greater than what SIM can obtain Any interfering compound would not only have to form an ion source product parent ion of the same mass to charge ratio as the selected parent ion from the target compound but that parent ion would also have to f...

Page 34: ...nsity of an SRM reaction that you specify for a parent ion is above its trigger threshold the mass spectrometer performs a full scan MS MS product ion scan to confirm the identity of the analyte AutoSIM In the scan type known as AutoSIM the mass spectrometer automatically selects the most intense masses m z values in a survey scan builds a SIM scan list for them and then acquires and records ion c...

Page 35: ...ensities of each set of multiple sampling intervals This sum is displayed versus the integral center of mass of the sampling intervals 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 ...

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Page 37: ... into the mass spectrometer where they are analyzed You can also use a direct sample probe to introduce sample into the mass spectrometer Electron ionization EI or chemical ionization CI ionize sample molecules upon entering the mass spectrometer The ion optics focus and accelerate the resulting sample ions into the mass analyzer where they are filtered according to their mass to charge ratios An ...

Page 38: ... window which is available by choosing Start All Programs Xcalibur Instrument Configuration Refer to Xcalibur Help for a description of TriPlus configuration options You also use the data system to set up the TriPlus autosampler to inject samples Choose Start All Programs Xcalibur Xcalibur and click Instrument Setup to open the Instrument Setup window Then click the TriPlus icon to open the TriPlu...

Page 39: ...able by choosing Start All Programs Xcalibur Instrument 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 Click the TRACE GC Ultra icon to open the TRA...

Page 40: ...n probe DIP has a temperature controlled heated capillary tube that slowly vaporizes solid samples You can use the DIP for rapid analysis of solids or trace components in solid matrices such as forensic samples or tissue Figure 7 Direct sample probe and controller Transfer Line The transfer line is the interface between the GC and mass spectrometer The transfer line heats the capillary column as i...

Page 41: ... 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 High sensitivity and resolution m z 10 to 3000 mass range EI and CI ionization modes Positive and negative ion polarity modes MS and MS MS scan modes Full scan SIM SRM iSRM QED MS AutoSIM and data dependent scan types The mass spectrometer include...

Page 42: ...fe to turn on the ion gauge The Vacuum LED is off if the turbomolecular pump is not at speed The Vacuum LED illuminates green whenever the pressure in the analyzer chamber as measured by the ion gauge is at or below the value required to enable high voltages to the mass analyzer See Table 2 Figure 9 Front panel LEDs of the mass spectrometer The Communication LED illuminates yellow when the mass sp...

Page 43: ...ss spectrometer gas chromatograph and autosampler See Figure 10 You must use the main power circuit breaker located on the back of the electronics module to restore power to the mass spectrometer gas chromatograph and autosampler Figure 10 Front panel System Power Off button The main power circuit breaker switch labeled Main Power is located on the power panel at the back of the electronics module...

Page 44: ... Figure 12 In the Service Mode position the switch removes power to all components of the vacuum system including the forepump turbomolecular pump and turbomolecular pump controller The switch in the Operating Mode position supplies power to all vacuum system components of the mass spectrometer The System Reset button is also located on the mass spectrometer power panel Pressing the System Reset b...

Page 45: ...on between the System Control PCB and the data system PC Figure 12 Right side power panel of the mass spectrometer 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 on page 3 P u m...

Page 46: ...r 26 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific Figure 13 Ion source of the TSQ Quantum XLS Magnets and magnet yoke Filament EI CI Source PCB Heater ring Ion source block Q00 quadrupole lens assembly L1 L2 L3 lens assembly ...

Page 47: ...losed EI ion volume has a smaller ion exit hole than the EI ion volume This results in a higher pressure of analyte and greater sensitivity but less dynamic range The CI ion volume is closed on the analyzer end except for a small ion exit hole and a relatively small electron entrance hole In the CI mode it is important to maintain a relatively high reagent gas pressure The ion source block holds t...

Page 48: ...ent and its reflector are maintained at a negative potential relative to the ion volume The electron lens prevents positive ions from traveling up the electron beam In turn this prevents positive ions from leaving the ion volume through the electron entrance hole The difference in potential between the filament and the ion volume determines the electron energy Two permanent magnets are held in a m...

Page 49: ...ool to insert or remove ion volumes See Figure 16 The forepump evacuates the inlet valve The ball valve is a ball with a hole in it and it is located between the vacuum manifold and the inlet valve block The ball valve is open when the hole in the ball is aligned with the opening between the vacuum manifold and the inlet valve The ball valve lever opens and closes the ball valve When the ball valv...

Page 50: ...enses L11 and L12 The Q0 quadrupole is a square array of square profile rods that acts as an ion transmission device See Figure 17 An rf voltage applied to the rods gives rise to an electric field that guides the ions along the axis of the quadrupole 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...

Page 51: ...c TSQ Quantum XLS and TSQ Quantum GC User Guide 31 Figure 18 Cross sectional view of the transfer line ion source and Q0 quadrupole of the TSQ Quantum XLS Ion source ion volume Lens L3 Q0 quadrupole Transfer line Capillary column Q00 quadrupole Lens L2 Lens L1 ...

Page 52: ...as it passes through the lens 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 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 analyzer on the TSQ Quantum XLS and TSQ Quantum GC mass spectrometer consists...

Page 53: ...aligned hyperbolic profile round rods Q1 or Q3 are shown in Figure 20 Quartz spacers act as electrical insulators between adjacent rods Figure 20 Q1 or Q3 quadrupole Q2 is a square profile quadrupole rod assembly Q2 always acts as an ion transmission device The Q2 quadrupole rods are bent through a 90 degree arc In addition to reducing the footprint of the instrument this prevents the transmission...

Page 54: ...plied 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 22 Figure 22 Polarity of the rf and dc voltages applied to the rods of the Q1 and Q3 mass analyzers The ac voltage applied to the quadrupole rods is of constant frequency 1 123 MHz The ac voltage applied to the rods varies from 0 to 10000 V P P and the dc vo...

Page 55: ...The first and third quadrupole rod assemblies Q1 and Q3 quadrupoles can act as mass analyzers or as ion transmission devices When both rf and dc voltages are applied Q1 and Q3 function as mass analyzers When only rf voltage is applied they act as ion transmission devices In the ion transmission mode the quadrupole rod assemblies allow ions in a wide window of mass to charge ratios to pass The squa...

Page 56: ...and the process is repeated The potentials on the quadrupole rods can be changed rapidly and precisely The rf and dc voltages in the mass spectrometer can be scanned over the full mass range of the system m z 10 to 3000 in 0 6 s The precision quadrupole rods of the mass spectrometer provide excellent sensitivity peak shape resolution and high mass transmission Collision Cell and CID Efficiency In ...

Page 57: ...compensate for this the data system allows you to specify a mass dependent collision energy ramp With a mid range collision gas pressure fragmentation efficiency might vary from 15 percent to 65 percent for various compounds As the collision gas pressure increases the fragmentation efficiency for all compounds approaches 100 percent due to multiple collisions The collection efficiency decreases ho...

Page 58: ...s have three lens sets See Figure 21 on page 34 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 as L4 or exit lens All of the lenses have circular holes in their centers through which the ion beam passes The lens assemblies also retain the three rod assemblies to ensure accurate...

Page 59: ...em See Figure 24 This system produces a high signal to noise ratio and allows for voltage polarity switching between positive ion and negative ion modes of operation The ion detection system includes a 15 kV conversion dynode and a channel electron multiplier The ion detection system is located at the rear of the vacuum manifold behind the mass analyzer The conversion dynode is a concave metal sur...

Page 60: ... proportional to the number of secondary particles striking the cathode Typically the electron multiplier is set to a gain of about 3 105 that is for each ion or electron that enters 3 105 electrons exit in MS mode and 2 106 in MS MS mode The electrometer circuit converts the current that leaves the electron multiplier via the anode to a voltage and the data system records the voltage The ion dete...

Page 61: ...The inlet gasses hardware includes the following components Vent Valve Collision Gas Flow Control Valves Calibration Compound and CI Reagent Gas Flow Control Figure shows a functional block diagram of the vacuum system and inlet gasses hardware Figure 25 Functional block diagram of the vacuum system and inlet gasses hardware Collision cell Collision gas divert valve Collision gas valve Argon gas p...

Page 62: ...e main vacuum manifold is divided into two chambers by a baffle See Figure 26 The high vacuum port of the turbomolecular pump evacuates the region inside the first chamber called the analyzer region to less than 10 5 Torr The turbomolecular pump then discharges into the forepump through the foreline The region inside the second chamber called the Q0 quadrupole region is evacuated to 1 mTorr by the...

Page 63: ...Torr The forepump evacuates the argon in the collision cell when CID is turned off 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 Turbomolecular pump Ion gauge O ring Collision cell ch...

Page 64: ...an draws air in from the front of the instrument cools the pump Power to the turbomolecular pump shuts off if the foreline pressure as measured by the Convectron gauge is too high or if the turbomolecular temperature is too high Forepump An Edwards E2M30 forepump or roughing pump establishes the vacuum necessary for the proper operation of the turbomolecular pump The forepump also evacuates the in...

Page 65: ...is related to the pressure in the vacuum manifold The ion gauge is also involved in vacuum protection Vent Valve The vent valve located in the area of Q2 allows the vacuum manifold to be vented to air that has been filtered through a sintered nylon filter The vent valve is a solenoid operated valve which is controlled by the Vent Delay PCB When the solenoid is energized the vent valve closes If th...

Page 66: ...hat control the operation of the mass spectrometer are distributed among various PCBs and other modules located in the tower in the embedded computer and on or around the vacuum manifold of the mass spectrometer The Power Entry Module provides mass spectrometer power control a contact closure interface vent valve control an Ethernet 100 base T connection from the System Control PCB to the data sys...

Page 67: ...tion system electronic assemblies provide high voltage to the electron multiplier and conversion dynode of the ion detection system They also receive the electron multiplier output current signal convert it to a voltage by the electrometer circuit and pass it to the embedded computer The ion detection system electronic assemblies include the following Electron multiplier power supply Conversion dy...

Page 68: ...y Ethernet port data system to local area network High performance video graphics card CDRW drive DVD drive 1280 1024 resolution color monitor Keyboard and mouse For more information about the computer refer to the appropriate manuals Data System Mass Spectrometer GC Interface The data system computer contains a 100 base T Ethernet adapter called the primary Ethernet adapter that is dedicated to d...

Page 69: ...r Guide 49 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 ...

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Page 71: ...wer circuit breaker on the rear of the electronics module and not the System Power Off switch Y To turn off the mass spectrometer in an emergency Contents Shutting Down the System in an Emergency Placing the System in Standby Mode Shutting Down the System Completely Starting Up the System after a Complete Shutdown Resetting the Mass Spectrometer Resetting the Data System Turning Off Selected Mass ...

Page 72: ...such as overnight or over weekends it does not need to be shut down completely When you are not going to operate the system for 12 hours or more you can leave the system in standby mode Y To place the TSQ Quantum XLS or TSQ Quantum GC system in standby mode 1 Wait until data acquisition if any is complete 2 From the TSQ EZ Tune window choose Control Standby or click the On Standby button to put th...

Page 73: ... the data system power on 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 For a short period of time such as overnight or over weekends you can place the system in standby mode See Placing the System in Standby Mode Y To shut down...

Page 74: ...rometer is turned off All LEDs on the front panel of the mass spectrometer are off A capacitor on the Vent Delay PCB provides power to the vent valve for two to four minutes to allow the turbomolecular pump to spin down After the capacitor discharges power to the vent valve solenoid shuts off When power to the vent valve solenoid shuts off the vent valve opens and the vacuum manifold vents to filt...

Page 75: ... on off switch 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 Restoring Power to the TSQ Quantum XLS or TSQ Quantum GC system Starting Up the GC Starting Up the Data System Starting Up the Mass Spectrometer Starting Up the Autosampler autosampler is optional Setting Up Conditions f...

Page 76: ...Windows startup procedure on the monitor and press CONTROL ALT DELETE when you are prompted to do so To complete the startup procedure click OK or enter your password if you have one in the Logon Information dialog box Starting Up the Mass Spectrometer Y To start the mass spectrometer 1 Turn on the flow of argon at the tank if it is off 2 Make sure that the mass spectrometer main power circuit bre...

Page 77: ...the Communication LED on the front panel illuminates yellow to indicate that the data system and the mass spectrometer have started to establish a communication link After several more seconds the Communication LED illuminates green to indicate that the data system and the mass spectrometer have established a communication link Software for the operation of the mass spectrometer is then transferre...

Page 78: ...ou 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 2 Ensure that the argon pressure is within the operational limits argon 135 70 kPa 20 10 psig 3 In the TSQ EZ Tune wind...

Page 79: ... panel of the mass spectrometer are off except the Power LED After several seconds the Communication LED illuminates yellow to indicate that the data system and the mass spectrometer are starting to establish a communication link After several more seconds the Communication LED illuminates green to indicate that the data system and the mass spectrometer have established a communication link Softwa...

Page 80: ...r in the Off condition Place the electronics service switch in the Service Mode position The electronics service switch turns off all components in the mass spectrometer other than the 24 V power supply forepump turbomolecular pump Vent Delay PCB and fans Place the vacuum service switch in the Service Mode position The vacuum service switch turns off all vacuum system components including the 24 V...

Page 81: ...age Off Off Off Off Off Ion source filament Off Off Off Off Off Ion source heater On On Off Off Off Ion source lenses Off Off Off Off Off Argon collision gas Off Off Off Off Off Vent valve Closed Closed Closed Open after 2 to 4 min Open after 2 to 4 min Turbomolecular pump On On On Off Off Forepump On On On Off Off Vent Delay PCB On On On On Off Embedded computer On On Off On Off Turbomolecular pu...

Page 82: ... of mass spectrometer components and voltages Sheet 2 of 2 Mass spectrometer component Standby Off Electronics service switch in Service Mode position Vacuum service switch in Service Mode position MS Main power circuit breaker switch in Off position ...

Page 83: ... the mass spectrometer Record the ion signal intensity of FC 43 see Figure 32 just after you tune and calibrate the mass spectrometer Periodically check the FC 43 ion signal Re tune and calibrate the mass spectrometer if the FC 43 ion signal falls below 50 of the tuned value Also re tune and calibrate after switching between EI and CI modes or between positive and negative polarity modes Table 5 l...

Page 84: ...mode In this example the mass spectrometer is in positive polarity mode If necessary toggle the polarity button 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 Table 5 Typically observed FC 43 peaks in EI positive polarity mode m z 69 m z 100 m ...

Page 85: ...ttings 6 Click the Calibration Gas button in the EZ Tune toolbar to turn on the flow of calibration gas into the ion source 7 Click the Filament button in the EZ Tune toolbar to turn on the filament 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 on page ...

Page 86: ...ibrating Running Auto Tune and Calibration Run the tune and calibration procedure after you obtain a good FC 43 ion signal Y To tune and calibrate your mass spectrometer automatically in the EI positive ion mode 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 th...

Page 87: ...ors occur during the automatic tuning and calibration procedure go to step 6 If the automatic tuning and calibration procedure finishes without errors go to step 7 6 If errors occur during the automatic tuning and calibration procedure restore the previous mass spectrometer device settings and perform the tuning and calibration procedure again by completing the following steps a To restore the pri...

Page 88: ...f you have already tuned and calibrated the instrument successfully in the negative ion mode click No Do not copy the positive ion mode parameters to the negative ion mode If you have not tuned and calibrated the instrument in the negative ion mode click Yes 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...

Page 89: ...ws a In the File Name box enter a name for your tune method file b Click Save to save the tune method file The mass spectrometer is now tuned and calibrated in the positive ion mode 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 f...

Page 90: ...ing 5 00 New Setting 0 86 10 56 32 Maximum Intensity 1 93e 06 10 56 32 15 Improvement 10 56 32 Optimizing Lens 1 2 for ion 69 00 m z 10 56 38 Previous Setting 21 90 New Setting 5 00 10 56 38 Maximum Intensity 2 43e 06 10 56 38 41 Improvement 10 56 38 Optimizing Lens 2 1 for ion 69 00 m z 10 56 45 Previous Setting 8 45 New Setting 3 92 10 56 45 Maximum Intensity 2 56e 06 10 56 45 17 Improvement 10 ...

Page 91: ...evious Setting Optimum Setting Mass 69 00m z 235 Improvement Mass 501 97m z 281 Improvement Mass 218 99m z 57 Improvement Optimizing Lens 4 for Q1MS 50 40 30 20 10 0 Lens 4 Voltage V 0 20 40 60 80 100 y t i s n e t n I e v i t a l e R May 9 2007 Previous Setting Optimum Setting Mass 69 00m z 60 Improvement Optimizing Lens 1 1 for Q1MS 10 8 6 4 2 0 Lens 1 1 Voltage V 0 20 40 60 80 100 y t i s n e t...

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Page 93: ...ns describe how to change the ionization mode Removing the Ion Volume Y To remove the ion volume 1 Install the guide bar a With the guide ball track facing left insert the guide bar into the entry housing See Figure 37 b Push the guide bar in as far as it will go then rotate it 90 clockwise to lock the guide bar in the entry housing Contents Removing the Ion Volume Installing the Ion Volume Tools ...

Page 94: ...losed Figure 38 shows the inlet valve lever is down for closed b Loosen the inlet valve knob counter clockwise and remove the inlet valve plug The inlet valve plug prevents air from entering the vacuum manifold in case the inlet valve is inadvertently opened c Turn the I R tool to the unlock position which indicates the I R tool is in position to accept the ion volume I R tool Guide ball Guide bal...

Page 95: ... 38 Inlet valve components 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 Inlet valve knob Inlet valve plug Entry housing Inlet valve lever down is closed up is open ...

Page 96: ...sert the guide ball into the guide ball hole b Slide the I R tool forward into the inlet valve until the guide ball is at the guide bar s first stop see Figure 40 c 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 First stop of guide bar I R tool Inlet valve knob ...

Page 97: ...repump evacuates the inlet valve Wait until the safe to insert probe message appears and then click OK Figure 41 Safe to insert the probe message 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 guide bar I R tool ...

Page 98: ...ol Figure 44 when viewed through the window of the ion source manifold should not be visible Figure 43 I R tool inserted into the inlet valve b Turn the I R tool handle counterclockwise to put the I R tool into lock position Listen for a click which indicates that the handle is fully engaged in the lock position and is holding the ion volume c Withdraw the I R tool with the ion volume attached unt...

Page 99: ...l Figure 44 Ion volume ion volume holder and I R tool 10 To clean the ion volume use the instructions in Cleaning Stainless Steel Parts on page 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 CAUTION Do not withdr...

Page 100: ...e inlet valve plug Remove the inlet valve plug The inlet valve plug prevents air from entering the vacuum manifold in case the inlet valve is inadvertently opened 5 Choose Start All Programs Thermo Instruments TSQ TSQ Tune to open the EZ Tune window 6 Click the Probe button in the EZ Tune toolbar The Insert Probe message appears See Figure 39 7 Inset the I R tool into the inlet valve a Insert the ...

Page 101: ...n Slide the I R tool back into the vacuum manifold until the end of the I R tool just touches the ion volume Test that the I R tool does not go into the inlet valve completely which indicates that the ion volume is seated properly 12 Remove the I R tool a Withdraw the I R tool until the guide ball reaches the first stop see Figure 42 b Close the inlet valve by pulling the inlet valve lever down se...

Page 102: ...Thermo Scientific 14 Replace the inlet valve plug Orient the plug to indicate whether an EI or CI ion volume is installed 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 ...

Page 103: ...nce procedures be methodical always wear clean lint free gloves when handling the components of the ion source always place the components on a clean lint free surface and never overtighten a screw or use excessive force Table 6 Maintenance procedures Sheet 1 of 2 Mass spectrometer component Procedure Frequency Procedure location Ion source Cleaning the ion volume As needed Page 87 Ion source Clea...

Page 104: ...oil Every 4 months or if pump oil is cloudy and discolored Manufacturer s documentation Ion detection system Replacing the electron multiplier assembly If noise in spectrum is excessive or proper electron multiplier gain cannot be achieved Electronic modules Replacing an electronic module If electronic module fails PCBs Replacing a PCB If PCB fails The frequency of cleaning the components of the m...

Page 105: ...ounts of samples and solvents you introduce into the system In general the closer a component is to the sample introduction point the more rapidly the component becomes dirty For example you clean the ion volume more often than other parts If you just want to change or clean the ion volumes you do not need to shut down the system Most parts can be removed and disassembled by hand Make sure you hav...

Page 106: ...86 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific Figure 46 Ion source assembly of the TSQ Quantum XLS exploded and assembled views ...

Page 107: ...87 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific Figure 47 Ion source assembly of the TSQ Quantum GC exploded and assembled views ...

Page 108: ...ion source lenses Y To clean the ion source lenses 1 Shut down and vent the system See Shutting Down the System Completely on page 53 2 Remove the ion source See Removing the TSQ Quantum XLS Ion Source on page 89 3 Remove the ion source lens assemblies from the ion source and disassemble it See Removing the L1 L2 L3 Lens Assembly and the Q00 Quadrupole Lens Assembly on page 91 4 Clean the lenses a...

Page 109: ...ures to 30 C and allow them to cool before continuing b Once the oven injector and transfer line are cool turn off the gas chromatograph c Loosen the transfer line nut See Figure 64 on page 123 d 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 Tools Needed Gloves cleanroom grade ...

Page 110: ...ion source assembly loosen the two thumbscrews that secure the ion source assembly to the Q0 quadrupole mount 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 Q0 quadrupole mount Lens L1 L2 L3 connector EI CI Source PCB connector Transfer line Thumbscrew Thumbscrew CAUTION Burn Hazar...

Page 111: ... lens assembly You must remove and disassemble the L1 L2 L3 lens assembly to clean the lenses A retainer clip fastens the L1 L2 L3 lens assembly and the Q00 quadrupole lens assembly to the ion source block To remove the ion source lens assemblies 1 Wearing clean lint and powder free gloves unscrew the threaded hexagonal standoff and remove the retainer clip that secures the lens assembly to the io...

Page 112: ...e ion source Disassembling the L1 L2 L3 Lens Assembly Y To disassemble the L1 L2 L3 lens assembly 1 Remove the lens retainer clip by pinching the ends with your fingers or a pair of tweezers See Figure 50 2 Remove the lenses and spacers from the lens holder 3 Place the components on a clean surface Ion source Retainer clip Threaded standoff Q00 quadrupole lens assembly L1 L2 L3 lens assembly ...

Page 113: ...the L1 L2 L3 Lens Assembly Ensure that the lenses are clean and dry before you reassemble the lens assembly Lens holder Lens L3 Spacer Lens L2 Spacer Lens L1 Lens retainer clip Note To clean the ion source lenses follow the procedure in Cleaning Stainless Steel Parts on page 113 To clean the remaining parts follow the procedure in Cleaning Non Stainless Steel or Hybrid Part on page 115 ...

Page 114: ...quadrupole lens assembly 3 Use the retainer clip and threaded standoff to secure the lens assemblies to the ion source Reinstalling the TSQ Quantum XLS Ion Source Y To reinstall the ion source into the vacuum manifold 1 Wearing clean lint and powder free gloves place the ion source onto the magnet yoke 2 Position the ion source in the vacuum manifold and ensure the following The transfer line is s...

Page 115: ...oes not restore system performance clean the ion source lenses Y To clean the ion source lenses 1 Shut down and vent the system See Shutting Down the System Completely on page 49 2 Remove the ion source See Removing the TSQ Quantum XLS Ion Source on page 89 3 Remove the ion source lens assembly from the ion source and disassemble it See Removing the L1 L2 L3 Lens Assembly and the Q00 Quadrupole Le...

Page 116: ...tinuing b Once the oven injector and transfer line are cool turn off the gas chromatograph c Loosen the transfer line nut See Figure 64 on page 123 d 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 4 Undo the two latches that secure the lid of the ion source vacuum manifold and o...

Page 117: ...ource assembly to the Q0 quadrupole 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 Q0 quadrupole mount Lens L1 L2 L3 connector EI CI Source PCB connector Transfer line Thumbscrew Thumbscrew Lens L4 connector CAUTION Burn H...

Page 118: ...e ion source block To remove the ion source lens assembly 1 Wearing clean lint and powder free gloves unscrew the threaded hexagonal standoff and remove the retainer clip that secures the lens assembly to the ion source block See Figure 2 Pull the lens assembly out of the ion source 3 Place the ion source and lens assembly on a clean surface Figure 52 Lens assembly removed from the ion source Disa...

Page 119: ... assembly separated into L1 L2 L3 lens assembly left and L4 lens assembly right 2 Disassemble the L1 L2 L3 lens assembly a 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 L4 lens assembly L1 L2 L3 lens assembly ...

Page 120: ... L1 L2 L3 lens assembly exploded and assembled views 3 Disassemble the L4 lens assembly a 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 Lens holder Lens L3 Spacer Lens L2 Spacer Lens L1 Lens retainer clip ...

Page 121: ...lens assembly See Figure 54 a Reinstall the lenses and spacers in the lens holder in the order and orientation shown in Figure 54 b 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 Insert the L4 lens assembly into t...

Page 122: ...ns L4 assembly See Figure 48 5 Reinsert the capillary column into the ion source a Using the I R tool remove the ion volume See Removing the Ion Volume on page 69 b Push the column in until you can see it through the inlet valve c Pull the column back just far enough that you cannot see it d Tighten the transfer line nut and transfer line union e Using the I R tool install the ion volume See Insta...

Page 123: ...e area with lint free cloth 2 Shut down and vent the TSQ Quantum XLS mass spectrometer See Shutting Down the System Completely on page 53 3 Remove the ion source See Removing the TSQ Quantum XLS Ion Source on page 89 4 Wearing clean lint and powder free gloves remove the ion source from the magnet yoke Tools Needed Filament P N 120320 0030 Gloves cleanroom grade P N 23827 0008 and 23827 0009 Lint ...

Page 124: ...ner 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 9 Inspect and install a new filament P N 120320 0030 in the 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 Note Now is a good time to clean the ion source b...

Page 125: ...art the system See Starting Up the System after a Complete Shutdown on page 55 Replacing the Filament of the TSQ Quantum GC Ion Source The number of ions produced in the ion source is approximately proportional to the filament emission current If ion production is lacking you might have to replace the filament If the measured emission current is substantially less than the value that the emission ...

Page 126: ...ource to replace the filament 5 Unscrew the threaded standoff and remove the retainer clip that secures the heater ring and lens assembly to the ion source block See Figure 56 6 Pull the heater ring and lens assembly out of the ion source block 7 Remove the retainer clip that secures the filament and centering ring to the ion source block CAUTION Shock Hazard Unplug the TSQ Quantum GC before proce...

Page 127: ...e into the vacuum manifold See Reinstalling the TSQ Quantum XLS Ion Source on page 94 14 Restart the system See Starting Up the System after a Complete Shutdown on page 51 Disassembling and Reassembling the TSQ Quantum XLS Ion Source Completely Disassemble the ion source completely to clean the ion source block or to replace the EI CI Source PCB See Figure 58 for the location of the ion source com...

Page 128: ... Remove the ion source from the magnet yoke Figure 58 TSQ Quantum XLS ion source disassembled 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 CAUTION Shock Hazard Unplug the TSQ Quantum XLS mass spectrometer before proceeding Filament retainer clip Filament Ion source block...

Page 129: ...ng holes in the ion source block b Reinstall the three base studs 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 The gap allows the ceramic centering ring to properly position and align the electron lens hole with the ion volume 2 Press the heater rin...

Page 130: ...he ion source components Y 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 See Shutting Down the System Completely on page 49 3 Wearing clean lint and powder free gloves remove the ion source See Removing the TSQ Quantum XLS Ion Source on page 89 4 Remove the ion source from the magnet yoke Tool...

Page 131: ... the cartridge heaters down and the EI CI Source PCB up b Press down on the ion source block to separate it from the EI CI Source PCB 9 Remove the retainer clip that secures the filament and centering ring to the ion source block 10 Remove the filament and centering ring from the ion source block Filament retainer clip Filament Ion source block Lens assembly Heater ring EI CI Source PCB Base studs...

Page 132: ... gently press the leads into the connectors Normally there is a small gap about 0 016 in between the filament and the connectors The gap allows the ceramic centering ring to properly position and align the electron lens hole with the ion volume 2 Press the heater ring and lens assembly onto the ion source block 3 Use the retainer clip and threaded standoff to secure the lens assembly to the ion so...

Page 133: ...hing swab at its lowest speed to increase cleaning efficiency as well as decrease the time required to clean the items To prevent personal injury be sure to keep the Dremel tool away from possible hazards such as standing water or flammable solvents Tools Needed Acetone reagent grade or other suitable polar solvent Aluminum oxide abrasive number 600 P N 32000 60340 Applicators cotton tipped P N 00...

Page 134: ...he parts in a beaker containing deionized water b Place the beaker and contents in an ultrasonic bath for five minutes c If the water is cloudy after sonicating pour off the water add fresh water and place the beaker and its contents in an ultrasonic bath again for five minutes Repeat until the water is clear 5 Sonicate the parts in acetone a Using forceps place the parts in a beaker containing ac...

Page 135: ...aning efficiency as well as decrease the time required to clean the items To prevent personal injury be sure to keep the tool away from possible hazards such as standing water or flammable solvents 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 Clean dry gas De ionized ...

Page 136: ...e clean dry gas to blow the acetone off the parts Maintaining the Forepump Inspecting adding purging and changing the forepump oil are all that is required to maintain the forepump Forepump oil is a translucent light amber color which you must check often During normal operation oil must always be visible in the oil level sight glass between the MIN and MAX marks If the oil level is below the MIN ...

Page 137: ...be added However there are many factors other than a decrease in the calibration compound that can cause a shortage of calibration gas ions As a rule add calibration compound once a year Y To add calibration compound 1 Shut down and vent the mass spectrometer See Shutting Down the System Completely on page 53 2 Lower the GC oven and transfer line temperatures to 30 C and allow them to cool before ...

Page 138: ...n compound a Draw up no more than 0 1 mL of calibration compound into a clean syringe b Insert the syringe in the calibration compound vial until it comes in contact with the white frit at the bottom of the vial c Inject no more than 0 1 mL of calibration compound into the white frit The frit absorbs the calibration compound so if the calibration compound is pooled calibrant covers the top of the ...

Page 139: ...ion compound vial P N 96000 40013 into the module a Hold the vial vertically and place the nut on the neck of the vial b Place the 1 4 in ferrule over the neck of the vial and into the nut c Connect the vial to the calibration valve fitting with the nut and ferrule 10 Reinstall the cover to the calibration compound vial compartment 11 Position the GC next to the mass spectrometer 12 Restart your s...

Page 140: ...in the TSQ Quantum XLS Accessory Kit The ball valve seal consists of a Teflon spool and two O rings See Figure 62 Figure 62 Components of the ball valve seal and inlet valve 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 63 Tools Needed Ball valve seal kit P N 119265 0003 Frequency If the ball valve seal leaks ai...

Page 141: ...er of the ball valve seal extraction tool forward 5 Remove the seal and tool 6 Pull the plunger back to disengage the seal Figure 63 Ball valve seal extraction tool and ball valve seal not engaged left and engaged right Y To install the ball valve seal 1 Obtain the ball valve seal kit P N 119265 0003 from the Accessory Kit 2 Assemble the ball valve seal by installing the two O rings onto the Teflo...

Page 142: ...ss spectrometer See Shutting Down the System Completely on page 53 b Lower the oven injector and transfer line temperatures to 30 C and allow them to cool before continuing c Once the oven injector and transfer line are cool turn off the gas chromatograph 2 Remove the column from the transfer line See Figure 64 a Unscrew the transfer line nut b Remove the column from the transfer line Tools Needed...

Page 143: ...llary Column Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide 123 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 ...

Page 144: ...n 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 Tools Needed Capillary column Gloves cleanroom grade P N 23827 0008 and 23827 0009 Injector ferrule for 0 25 mm column P N 290 134 88 Leak detector hand held electronic GL Sciences Inc model LD 228 or equivalent Lint free tissue Magnifying glass Methanol or ...

Page 145: ...leaks at all the fittings in the GC c Repeat column evaluation and leak check procedures until no leaks can be found 6 Condition the capillary column according to the manufacturer s instructions New columns must be conditioned before inserting them in the mass spectrometer 7 Connect the column to the transfer line a Shut down and vent the mass spectrometer See Shutting Down the System Completely o...

Page 146: ... inlet valve v Pull the column back just far enough that you cannot see it vi Tighten the transfer line nut and transfer line union vii Using the I R tool replace the ion volume See Installing the Ion Volume on page 80 8 Condition the transfer line ferrule Graphite Vespel ferrules like the transfer line ferrule require conditioning to ensure a leak tight seal a Raise the oven temperature to the ma...

Page 147: ...uide 127 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 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 ...

Page 148: ......

Page 149: ... circuits pass or fail the tests If there is a problem with the instrument electronics the system diagnostics can often locate the problem The system diagnostics do not diagnose problems that are not electrical in nature For example they do not diagnose poor sensitivity due to misaligned or dirty components or to improper tuning Therefore it is important that the person running the diagnostics be ...

Page 150: ...are failure and running the diagnostics is appropriate If the answer is yes to either of the last two questions above the problem is probably mechanical not electrical Reverify that alignment configurations and cable connections are correct before you call the Thermo Fisher Scientific Field Service Engineer Keep careful notes documenting the nature of the problem and the corrective steps you have ...

Page 151: ...ical 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 It also delivers a steady stream of mass spectral data during acquisition Why does the MS have communication issues Some communication issues are due to me...

Page 152: ...oftware is not properly configured Verify the correct settings in Instrument Configuration Issue Acquisition does not begin as expected Possible causes solutions 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 inco...

Page 153: ...Verify consistency between method and instrument configuration COM1 is not configured properly Verify COM port configuration Issue Unable to initialize the autosampler Possible causes solutions The autosampler is not turned on Turn on autosampler The autosampler is not configured properly in Xcalibur Check Instrument Configuration The cable between the GC and autosampler is disconnected Verify con...

Page 154: ...apillary column has not been properly conditioned Condition the capillary column 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 Issue Excessive injection port septum bleed Typical m z 207 429 355 281 Possible causes solutions The septum is worn out or damaged Replace the sept...

Page 155: ...t peak from the area of interest in the chromatogram Filament and Lens Control Issues The lifetime of a filament depends on its exposure to oxygen and solvent vapors The filament assembly protects the filament and increases its lifetime for many months Xcalibur diagnostics test the filament for continuity and current regulation Testing the filament for continuity before each acquisition ensures th...

Page 156: ...lutions The power supply to the lens has a fault Contact Thermo Fisher Scientific Technical Support There is a fault with the lens drivers Contact Thermo Fisher Scientific Technical Support Heated Zone Issues The ion source and transfer line are heated zones The ion source heater is controlled by the mass spectrometer and the transfer line heater is controlled by the Aux1 heated zone of the TRACE ...

Page 157: ...the L1 L2 L3 Lens Assembly on page 93 One or more heater cartridges on the EI CI Source PCB is defective Replace the EI CI Source PCB See Disassembling and Reassembling the TSQ Quantum XLS Ion Source Completely on page 107 TSQ Quantum XLS or Disassembling and Reassembling the TSQ Quantum GC Ion Source Completely on page 110 TSQ Quantum GC The ion source temperature sensor RTD is defective Replace ...

Page 158: ... 10 5 Torr with argon collision gas on and 2 10 6 Torr with Ar collision gas off The most reliable way to find vacuum leaks is to spray a gas around the vacuum manifold and look for the characteristics ions in full scan EI mode Argon produces m z 40 Alternatively you can use compressed electronic dusting spray containing an HFC For example Falcon Dust Off and MicroCare Micro Blast contain tetraflu...

Page 159: ...strument operating conditions can cause linearity problems Additionally certain compounds do not give a desired linear response due to chromatographic activity A well maintained instrument provides good linear response over a wide range of concentrations for most compounds Like any instrument however the TSQ Quantum XLS and TSQ Quantum GC has a saturation point Perform routine injector and column ...

Page 160: ... Technical Support Issue The TSQ Quantum XLS powers on but trips the circuit breaker Possible causes solutions The Power Module is faulty Contact Thermo Fisher Scientific Technical Support The forepump causes the circuit breaker to trip Check forepump replace it if necessary Sensitivity Issues If you observe a drop in instrument sensitivity you should determine if the sensitivity drop was sudden o...

Page 161: ...e emission current is set too low Check the setting listed for the emission current Choose Tune Manual and select the Controls tab The ground connection between the electrometer PCB and anode feedthrough is faulty Contact Thermo Fisher Scientific Technical Support There is a problem with the filament or lens control See Filament and Lens Control Issues on page 135 for more information The EI CI So...

Page 162: ...act Thermo Fisher Scientific Technical Support The injection port liner or capillary column is contaminated Replace the injection port liner and trim the capillary column Issue Poor sensitivity in CI mode Possible causes solutions An EI ion volume is installed Install a CI ion volume as described in Changing Ionization Modes on page 73 The small hole in the CI ion volume is plugged Use a dental pi...

Page 163: ...mation Dust has collected in the electron multiplier or on the conversion dynode Contact Thermo Fisher Scientific Technical Support Tuning Issues You can suspect a tuning problem when Xcalibur Auto Tune Calibration fails Auto Tune Calibration performs several functions and issues or error messages indicate different problems Diagnostics can usually uncover a tuning problem Issue Cannot find Calibr...

Page 164: ...e Poor high m z ion intensity because of bad ion source lens settings Run Auto Tune Calibration See Tuning and Calibrating on page 63 Helium pressure in the ion source is too high or low Set flow to 1 0 mL per minute for most applications There is a vacuum leak Find and repair any leaks Be sure to check the transfer line fitting in the GC oven See High Vacuum Issues on page 138 for more informatio...

Page 165: ...ifferent ion volumes They may not be used interchangeably Change the ion volume as described in Changing Ionization Modes on page 73 The ion volume is absent or incorrectly positioned Verify that the ion volume is positioned correctly There is a filament or lens control problem See Filament and Lens Control Issues on page 135 for more information The electron multiplier is faulty Contact Thermo Fi...

Page 166: ...7 Diagnostics and Troubleshooting Replacing PCBs and Power Supplies 146 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific ...

Page 167: ...s the settings that the TSQ Quantum XLS or TSQ Quantum GC mass spectrometer uses during an experiment Use the Instrument Setup view to create the instrument method Y To create an instrument method 1 On the Xcalibur Home Page click the Instrument Setup icon to open the Instrument Setup view 2 Click the TSQ icon in the viewbar 3 Choose TSQ Regular Method to open the regular method Scan Editor page 4...

Page 168: ...m XLS and TSQ Quantum GC User Guide Thermo Scientific 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 ...

Page 169: ...de 149 Figure 66 EI CI page of Instrument Setup 7 Enter or select the following settings Number of States 1 State at Start of Run On Calibration Gas Setting Off Use DIP DEP Probe 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 ...

Page 170: ...as one sample Y To create a sequence 1 On the Xcalibur Home Page click the Sequence Setup icon to open the Sequence Setup view see Figure 67 2 Enter the name and path of the instrument method In this example it is C Xcalibur methods DIP test 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 showi...

Page 171: ...ith the guide ball track facing left insert the guide bar into the entry housing See Figure 16 on page 29 b Push the guide bar in as far as it goes Rotate it 90 clockwise to lock the guide bar in the entry housing 5 Prepare the inlet valve a Make sure the inlet valve is closed with the inlet valve lever down as shown in Figure 16 on page 29 b Loosen the inlet valve knob counter clockwise and remov...

Page 172: ...n the Xcalibur Home Page click the Sequence Setup icon to open Sequence Setup if it is not already open b 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 ...

Page 173: ...Use column Click the area if necessary f Click any Yes in the Start Instrument column to clear all start instruments g Click OK to save your settings and close the Change Instruments In Use dialog box Running the Sequence You acquire data by running the sequence Xcalibur saves the acquired data in a raw file Y To run the sequence 1 In the Run Sequence dialog box see Figure 68 on page 152 click OK ...

Page 174: ...uide ball on the DIP probe into the guide ball hole on the guide bar b Slide the probe forward into the inlet valve until the guide ball is at the guide bar s first stop See Figure 71 c Tighten the inlet valve knob clockwise to ensure a leak tight seal 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 c...

Page 175: ...message 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 73 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 ...

Page 176: ...ic Figure 74 Acquisition Ready message 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 75 and Figure 76 Figure 75 Perfluorotetracosane mass spectrum at 0 56 minute retention time ...

Page 177: ...etracosane chromatogram Examining the Raw Data in Qual Browser You can use Qual Browser to display the mass spectrum at various times in the chromatogram Y To examine the raw data 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 77 ...

Page 178: ...es the first stop on the guide bar Figure 71 2 Close the inlet valve by pushing the lever down 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 CAUTION Close the inlet valve first Otherwise the system vents to the atmosphere Do not withdraw the probe beyond the ...

Page 179: ...ve the guide bar by rotating it 90 counter clockwise and sliding it out of the entry housing 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 ...

Page 180: ......

Page 181: ... Kit Contents Accessory Kit Chemicals Kit Table 7 Accessory Kit P N 70111 62077 Sheet 1 of 2 Description Function Part number Fitting ferrule SWG 1 8 in brass set 00101 08 00009 Fitting connection 1 4 to 1 8 in 00101 01709 Fitting connection 1 4 to 1 8 in 00101 01712 Fitting ferrule SWG front 3 8 in brass 00101 11500 Ferrule 0 4mm ID 1 16 00101 18100 Restek capillary grade hydrocarbon trap For rem...

Page 182: ...1 00012 Cable start probe Contact closure cable between the direct sample probe and the mass spectrometer 70111 63627 Cable start GC Contact closure cable between the GC and the mass spectrometer 70111 63626 Forceps 10 in stainless steel For handling ion volumes and clean components 76360 0400 Cable 10 base T crossover 15 ft shielded 76396 0052 Table 7 Accessory Kit P N 70111 62077 Sheet 2 of 2 De...

Page 183: ...ote 63 running 66 tune and calibration report 69 calibration compound adding 117 flow control description 46 mass spectrum displaying 64 observed peaks 64 on off 64 spectrum positive EI mode 66 calibration compound vial location figure 118 removing and reinstalling 118 calibration gas valve description 46 capillary column conditioning 125 installing 124 removing 122 removing ion source Caution 89 ...

Page 184: ...rument method 147 2 creating a sequence 150 3 preparing the probe and inlet valve 151 4 preparing the mass spectrometer 151 5 running the sequence 153 6 examining the data 157 perfluorotetracosane 147 direct insertion probe DIP perfluorotetracosane example procedure 147 direct sample probe and inlet valve 151 direct exposure probe DEP 20 direct insertion probe DIP 20 inserting into inlet valve fig...

Page 185: ...m 48 configuring 19 functional description 19 leak check 125 photo 2 power outlet 24 startup 55 56 troubleshooting communication problems 133 guide bar figure 29 74 intalling 73 H hydrocarbon trap 161 I inlet gasses hardware calibration compound 46 CI gas valve 46 collision gas valve 45 description 41 functional block diagram 41 inlet valve and direct sample probe 151 Caution 79 components figure ...

Page 186: ...3 iSRM scan type 13 L leak check GC 125 leak checking 138 LEDs Communication LED 22 Communication LED mass spectrometer reset 59 Communication LED mass spectrometer startup 57 Ethernet Link OK 24 25 Forepump On 24 Power LED 22 Power LED mass spectrometer reset 59 Power LED mass spectrometer startup 57 Pump On location figure 25 Scan LED 23 System LED 23 System LED mass spectrometer reset 59 System...

Page 187: ...l pump 44 MS main power circuit breaker mass spectrometer components On Off status 60 MS MS scan modes Neutral Loss 9 Parent 8 Product 7 N Neutral Loss scan mode discussed 9 example figure 11 illustration figure 10 O octafluoronaphthalene 162 Off condition mass spectrometer components On Off status 60 offset voltage quadrupole 37 oxygen trap 161 P Parent 9 Parent scan mode discussed 8 illustration...

Page 188: ...ctional description 33 quadrupole offset voltage 37 quadrupoles mass analysis 33 Q0 description 30 Q1 and Q3 33 RF and dc fields 34 RF and dc fields figure 34 35 Qual Browser direct sample probe data 157 reviewing data 157 quantitation enhanced data dependent MS QED MS scan type 14 R rear power panel location figure 52 reference SRM reactions 14 regulatory compliance iii removed 98 Replaceable 161...

Page 189: ... conditions setting 58 switch 24 System Control PCB description 46 System LED figure 22 mass spectrometer reset 59 mass spectrometer startup 57 system power off button emergency shutdown 23 location figure 52 system reset button description 24 location figure 24 mass spectrometer reset 59 system shutdown emergency procedure 51 System Tune and Calibration workspace figure 66 T tables Accessory Kit ...

Page 190: ...uum LED and analyzer region pressure 22 description 22 figure 22 vacuum manifold description 42 location figure 43 side cover plate description 43 vacuum pumps forepump 44 turbomolecular pump 44 vacuum service switch description 24 location figure 25 On Off status of mass spectrometer components 60 vacuum system collision gas valve 45 Convectron gauge 45 description 41 forepump 44 functional block...

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