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7

Diagnostics and Troubleshooting

Troubleshooting

Thermo Scientific

TSQ Quantum XLS Series User Guide

117

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 the Xcalibur data system. Check

Instrument Configuration.

• The cable between the GC and autosampler is disconnected. Verify connection.

• The autosampler instrument configuration is not set to the correct port. Verify

connection and configuration.

Issue:

Unable to

download methods to

the autosampler.

Possible cause/solution

• There is a discrepancy between instrument method and configuration. Verify consistency

between instrument method and instrument configuration.

Contamination Issues

Chemical noise is always present in any mass spectrometer. As a result, the high sensitivity of
the mass spectrometer can cause new users to confuse background with a contamination
problem. Additionally, the spectra shown in Xcalibur Tune and Real-Time Display are
auto-normalized, which can make the background level appear high.

Some chemical noise does occur, such as septum bleed after a series of injections, vial sample
bleed (which occurs if more than one injection is made from a sample vial), and siloxane peaks
that appear in the chromatogram at regular intervals from focusing at the head of the column
or in the injector.

Other possible contamination sources include hydrocarbon contamination of the carrier gas,
pump oil, or instrument cleaning solvents.

Always wear clean, lint- and powder- free gloves when handling ion source and mass analyzer
components, and ensure that the carrier gas filter, carrier gas lines, and gas regulators are free
of contamination and leaks.

Issue:

Excessive

chemical background

due to a column bleed

(

m/z

429, 355, 281).

Possible causes/solutions

• The capillary 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.

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Summary of Contents for TSQ Quantum XLS

Page 1: ...TSQ Series TSQ Quantum XLS Series User Guide 70111 97225 Revision A December 2011 ...

Page 2: ... use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specificat...

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Page 5: ...um XLS and TSQ Quantum XLS Ultra EMC Directive 2004 108 EC EMC compliance has been evaluated by TUV Rheinland of North America Inc Low Voltage Directive 2006 95 EC This device complies with Low Voltage Directive 2006 95 EC and harmonized standards EN 61010 1 2001 IEC 61010 1 2002 UL 61010A 1 2004 CAN CSA 22 2 61010 1 2004 Changes that you make to your system may void compliance with one or more of...

Page 6: ...c could impair any protection provided by the instrument Notice on the Susceptibility to Electromagnetic Transmissions Your instrument is designed to work in a controlled electromagnetic environment Do not use radio frequency transmitters such as mobile phones in close proximity to the instrument THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITION...

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: ...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 HSRM 13 Intelligent Selected Reaction Monitoring iSRM 13 Quantitation Enhanced Data Dependent MS QED MS 14 AutoSIM 14 Data Types 14 Profile Data Type 14 Centroid Data Type 15 Mass Charge Range 1...

Page 10: ...estoring Power to the TSQ Quantum XLS Series System 54 Starting Up the GC 54 Starting Up the Data System 54 Starting Up the Mass Spectrometer 54 Starting Up the Autosampler 56 Setting Up Conditions for Operation 56 Resetting the Mass Spectrometer 57 Resetting the Data System 57 Turning Off Selected Mass Spectrometer Components 58 Chapter 4 Tuning and Calibrating 61 Displaying the FC 43 Mass Spectr...

Page 11: ...g 114 Communication Issues 114 Contamination Issues 117 Filament and Lens Control Issues 119 Heated Zone Issues 120 High Vacuum Issues 121 Linearity Issues 123 Power Supply Issues 124 Sensitivity Issues 124 Stability Issues 127 Tuning Issues 128 Replacing Fuses 130 Replacing PCBs and Power Supplies 130 Appendix A Using the Direct Sample Probe 131 Creating an Instrument Method 131 Creating a Sequen...

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Page 13: ...e provides step by step instructions for cleaning and maintaining your mass spectrometer Y To suggest changes to documentation or to Help Complete a brief survey about this document by clicking the link below Thank you in advance for your help Related Documentation In addition to this guide Thermo Fisher Scientific provides the following PDF document and Help for the TSQ Quantum XLS Series systems...

Page 14: ...line are hot Allow them to cool to room temperature before touching them WARNING Shock Hazard Unplug the product name mass spectrometer before proceeding WARNING Material and Eye Hazard Wear impermeable laboratory gloves and eye protection when performing cleaning procedures CAUTION Highlights hazards to property or the environment IMPORTANT Highlights information necessary to prevent damage to so...

Page 15: ...ortal ts contactus Y To copy manuals from the Internet Go to mssupport thermo com agree to the Terms and Conditions and then click Customer Manuals in the left margin of the window Y To suggest changes to documentation or to Help Fill out a reader survey online at www surveymonkey com s PQM6P62 Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com Phone 800 ...

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Page 17: ...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 The specific process used to ionize the sample is known as the ionization mode The ion optics transmit the ions produced in the ion source into the mass analyzer where they are filtered according to their mass to charge ratio The polarity of...

Page 18: ...ies User Guide Thermo Scientific Figure 1 TSQ Quantum XLS Ultra mass spectrometer TriPlus autosampler and TRACE GC Ultra gas chromatograph Figure 2 TSQ Quantum XLS mass spectrometer TriPlus autosampler and TRACE GC Ultra gas chromatograph ...

Page 19: ... of mass analysis you can use the mass spectrometer to elucidate the structures of pure organic compounds and the structures of the components within mixtures Furthermore in a second stage of mass analysis the mass 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 As a result the TSQ Qua...

Page 20: ...de 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 This...

Page 21: ...urce 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 Because the information obtained from a positive ion mass spectrum is different from and complementary to the information from a negative ion spectrum the ability to obtain both positive...

Page 22: ...ransmission devices The Q2 rod assembly operates exclusively with rf voltage As a result 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 ions b Pas...

Page 23: ...rent 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 collision cell...

Page 24: ...tion 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 obtaine...

Page 25: ...e over mass ranges of the same width The respective mass ranges however are offset by a selected mass so that the product mass analyzer scans a selected number of mass units lower than the parent mass analyzer As a result the Neutral Loss scan mode has two stages of mass analysis In the first stage the parent mass analyzer separates ions formed in the ion source by mass to charge ratio Then the io...

Page 26: ...fset 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 is obtained from Q1 the parent ion whereas data for the ion intensity axis is obtained from Q3 the product ion being monitored You can perform experiments that use the Neutral Loss scan mode neutral loss experiments when a ...

Page 27: ... 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 compound you can set ...

Page 28: ...mation about an analyte than does SIM but a full scan does not yield the sensitivity that SIM or SRM 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 SIM or SRM scan types To use SIM or SRM you must know what ions or reactions you are looking for before you can perform an ex...

Page 29: ...y 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 Not only would an interfering compound 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 fragment to form a p...

Page 30: ... 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 You can perform retention time correction with QED MS 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 t...

Page 31: ...ultiple sampling intervals This sum is displayed versus the integral center of mass of the sampling intervals In general for faster scan speed use the centroid scan data type for data acquisition Data processing is also much faster for centroid data Mass Charge Range The TSQ Quantum XLS and TSQ Quantum XLS Ultra mass spectrometers can operate in a mass charge range of 10 to 3000 Da and 10 to 1500 ...

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Page 33: ...trometer 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 ionizes 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 ion detection syst...

Page 34: ...icrosoft Windows taskbar by choosing Start All Programs Thermo Foundation 2 0 Instrument Configuration For a description of TriPlus configuration options refer to the Xcalibur Help You also use the data system to set up the TriPlus autosampler to inject samples Choose Start All Programs Thermo Xcalibur Xcalibur and click Instrument Setup to open the Instrument Setup window Then click the TriPlus i...

Page 35: ...dows taskbar by choosing Start All Programs Thermo Foundation 2 0 Instrument Configuration For a description of TRACE GC Ultra configuration options refer to the Xcalibur Help The TSQ Quantum XLS Series data system computers can directly control the TRACE GC Ultra Choose Start All Programs Thermo Xcalibur Xcalibur and click Instrument Setup to open the Instrument Setup window Click the TRACE GC Ul...

Page 36: ...as 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 8 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 it passes from...

Page 37: ... the mass analyzer Several important features of the TSQ Quantum XLS Series mass spectrometers are as follows High sensitivity and resolution m z 10 to 3000 mass range for the TSQ Quantum XLS and m z 10 to 1500 mass range for the TSQ Quantum XLS Ultra EI and CI ionization modes Positive and negative ion polarity modes MS and MS MS scan modes Full scan SIM SRM iSRM QED MS AutoSIM and data dependent...

Page 38: ...urbomolecular pump is nearly at speed 80 percent of its operating speed of 750 MHz and it is safe 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 10 Fro...

Page 39: ...ter is on and is scanning ions The System Power Off button located on the front of the electronics module turns off power to the mass spectrometer gas chromatograph and autosampler See Figure 12 To restore power to the mass spectrometer gas chromatograph and autosampler you must use the main power circuit breaker located on the back of the electronics module Figure 12 Front panel System Power Off ...

Page 40: ...er 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 button takes the 5 V logic to ground and causes the embedded co...

Page 41: ...k OK LED is green when the System Control PCB is communicating with the data system computer The LED is off when there is no communication between the System Control PCB and the data system computer Figure 14 Right side power panel of the mass spectrometer Qualified Service Personnel Only Electronics Vacuum PumpOn ...

Page 42: ...s molecules to form ions Three exchangeable ion volumes and ion volume holders are available for use in the ion source See Figure 16 The choice of ion volume depends on the ionization mode The open EI ion volume is open on the analyzer end with a relatively large electron entrance hole The closed EI ion volume has a smaller ion exit hole than the EI ion volume This results in a higher pressure of ...

Page 43: ... lens The filament is a rhenium wire that is electrically heated to produce electrons by thermionic emission The reflector repels electrons emitted by the filament away from the filament toward the ion volume The filament 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 prev...

Page 44: ... insert or remove ion volumes See Figure 17 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 valve is c...

Page 45: ...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 The Q0 quadrupole is split into two sections See Figure 18 The smaller heated Q0 quadrupole assembly attaches to the ion source which heats it with the cartridge heaters The rods of the heated Q0 quadrupole make electr...

Page 46: ...the center that the ion beam can pass through Together they act as a two element cone lens You can apply an electrical potential to the lens to accelerate or decelerate ions as they approach the lens and focus the ion beam 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...

Page 47: ...ncy Quadrupole Offset Voltage Mass Analyzer Lenses Quadrupole Rod Assemblies The three rod assemblies used in the mass spectrometer are numbered from the ion source end of the manifold and are designated Q1 Q2 and Q3 Q1 and Q3 are quadrupoles that enable high resolution scans without signal loss Q1 and Q3 are square arrays of precision machined and precision aligned true hyperbolic quadrupoles cal...

Page 48: ...l is the chamber that encloses Q2 where collision induced dissociation can take place if the argon collision gas is present See Figure 22 Figure 22 Collision cell Q2 quadrupole and lenses Rf and dc Fields Applied to the Quadrupoles In a quadrupole rod assembly because rods opposite each other in the array connect electrically you can consider the four rods as two pairs of two rods each Ac and dc v...

Page 49: ...f and dc voltage applied to one rod pair and the dashed line represents the combined rf and dc voltage applied to the other rod pair The ratio of rf voltage to dc voltage determines the ability of the mass spectrometer to separate ions of different mass to charge ratios The first and third quadrupole rod assemblies Q1 and Q3 quadrupoles can act as mass analyzers or as ion transmission devices When...

Page 50: ...ns with a specific mass to charge ratio and unstable oscillations to all others At any given instant one particular set of rf and dc voltage values is being applied to the mass analyzer rods Under these conditions only ions of one mass to charge ratio for example m z 180 are maintained within bounded oscillations as their velocity carries them through the mass analyzer During this same time all ot...

Page 51: ...le rods A variable rf voltage charges the rods which creates an electrostatic field that gives stable oscillations to ions in a wide window of mass to charge ratios The collision cell surrounds Q2 and is usually pressurized from about 1 10 3 to 4 10 3 Torr with argon collision gas The collision cell is where collision induced dissociation CID takes place CID is a process in which an ion collides w...

Page 52: ...om its optimum value because fewer and fewer collisions take place Quadrupole Offset Voltage The quadrupole offset voltage is a dc potential applied to the quadrupole rods in addition to the ramping dc voltage The offset voltage applied to the two rod pairs of the assemblies is equal in magnitude and equal in sign Because the quadrupole offset voltage accelerates or decelerates ions it sets the TK...

Page 53: ... applied to Q2 and vice versa L3x lens set To focus the ion beam The three lenses between Q1 and Q2 and those between Q2 and Q3 together form a three element aperture lens The first and third lenses are generally set to similar or identical values and the central lens is set to a value different either higher or lower from the other two The voltage applied to each of the lenses can vary from about...

Page 54: ... of the conversion dynode one or more secondary particles are produced These secondary particles can include positive ions negative ions electrons and neutrals When positive ions strike a negatively charged conversion dynode the secondary particles of interest are negative ions and electrons When negative ions strike a positively charged conversion dynode the secondary particles of interest are po...

Page 55: ...portional 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 detectio...

Page 56: ...for the inlet gases includes the following components Vent Valve Collision Gas Flow Control Valves Calibration Compound and CI Reagent Gas Flow Control Figure 26 shows a functional block diagram of the vacuum system and inlet gasses hardware Figure 26 Functional block diagram of the vacuum system and inlet gases hardware Collision cell Collision gas divert valve Collision gas valve Argon gas port ...

Page 57: ...n 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 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 also evacuates the ion source region When CID is turned on th...

Page 58: ...er region of the vacuum manifold The turbomolecular pump mounts onto the top of the vacuum manifold Figure 27 The turbomolecular pump has two pumping inlets A high vacuum inlet at the top of the rotor stack which evacuates the analyzer chamber An interstage inlet about halfway down the rotor stack which evacuates the ion source and Q0 quadrupole chambers Ion gauge O ring Turbomolecular pump Collis...

Page 59: ...itch not by the electronics service switch Convectron Gauges A Convectron gauge measures the pressure in the inlet valve and the foreline which connects the turbomolecular pump and the forepump A second Convectron gauge measures the pressure of argon collision gas in the collision cell The Convectron gauge uses a Wheatstone bridge with a temperature dependent resistor to measure pressure down to a...

Page 60: ... regulated by a proportional valve that is controlled by the data system You can set the collision gas pressure 0 to 5 mTorr in the Define Scan dialog box of the EZ Tune window Ions enter the Q2 collision cell collide with the argon collision gas and then because of the collision dissociate into smaller fragments See Collision Cell and CID Efficiency on page 35 Argon enters the mass spectrometer t...

Page 61: ...e protection circuit linked to vent valve control A system reset button Status LEDs Service ports The right side power panel shown in Figure 14 on page 25 is part of the Power Entry Module The Power Entry Module accepts line power filters it and provides it to various components of the mass spectrometer The Power Module includes these components Main power circuit breaker switch Surge suppressor L...

Page 62: ...nvert 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 dynode power supply Electrometer PCB Acquisition DSP The Analyzer Control PCB contains circuitry for controlling and monitoring the operation of the ion source ion optics mass analyzer and ion detecti...

Page 63: ...ase T Ethernet adapter called the primary Ethernet adapter that is dedicated to data system mass spectrometer GC communication This primary Ethernet adapter communicates with the mass spectrometer and GC modules via a 10 100 base T Ethernet switch The Ethernet adapter on the mass spectrometer resides on the System Control PCB A twisted pair Ethernet cable connects the primary Ethernet adapter of t...

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Page 65: ...in power circuit breaker on the back 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 ...

Page 66: ...cientific Figure 28 System Power Off button on the front of the electronics module Figure 29 Power panel on the back of the electronics module System Power Off button Electronics module Power In GC Power Out Quantum Power Out A S Power Out V 230 50 60 Hz 2A MAX V 230 50 60 Hz 10A MAX V 230 50 60 Hz 16A MAX V 230 Hz 30A MAX ...

Page 67: ...when the mass spectrometer is in Standby mode The System LED on the front panel of the mass spectrometer illuminates yellow when the system is in standby 3 Leave the mass spectrometer power on 4 Leave the GC power on with column flow 5 Leave the autosampler power on 6 Leave the data system power on Shutting Down the System Completely Shut down the TSQ Quantum XLS Series system completely only when...

Page 68: ...ace the main power circuit breaker switch in the Off position the following occurs All power to the mass spectrometer 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 ...

Page 69: ...g the on off switch Starting Up the System after a Complete Shutdown Starting the TSQ Quantum XLS Series system after it has been shut down requires completion of these tasks Restoring Power to the TSQ Quantum XLS Series 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 for Operation Not...

Page 70: ... 2 Observe the Windows startup procedure on the monitor At the prompt press CTRL ALT DELETE 3 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 breaker switch on the right side power panel...

Page 71: ...ass 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 transferred from the data system to the mass spectrometer After three minutes the System LED illuminates yellow ...

Page 72: ...r operation 1 Before you begin data acquisition with your TSQ Quantum XLS Series system allow the system to pump down for at least one hour Operation of the system with excessive air and water in the vacuum manifold can cause reduced sensitivity tuning problems and reduced lifetime of the electron multiplier 2 Ensure that the argon pressure is within the operational limits argon 135 70 kPa 20 10 p...

Page 73: ...meter 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 Software for the operation of th...

Page 74: ...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 power supply forepump turbomolecular pump Vent Delay PCB and f...

Page 75: ... source filament Off Off Off Off Off Ion source heater On Off 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 pump controller On On On Off...

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Page 77: ...nsity of FC 43 see Figure 34 just after you tune and calibrate the mass spectrometer Periodically check the FC 43 ion signal Retune and calibrate the mass spectrometer if the FC 43 ion signal falls below 50 percent of the tuned value Also retune and calibrate after switching between EI and CI modes or between positive and negative polarity modes Table 5 lists typical peaks that are observed in the...

Page 78: ...meter is in positive polarity mode If necessary click the polarity button 3 Click the Define Scan button to display the Define Scan dialog box See Figure 33 4 In the Define Scan dialog box select or enter the following settings Scan type Full Scan Scan mode Q1MS Scan range entry mode FM LM First mass 50 Last mass 650 Scan time 0 500 Table 5 Typically observed FC 43 peaks in EI positive polarity mo...

Page 79: ...into the ion source click the Calibration Gas button in the EZ Tune toolbar 7 To turn on the filament 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 34 see Diagnostics and Troubleshooting on page 113 Cal Gas Off Cal Gas ...

Page 80: ...ing 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 the System Tune...

Page 81: ...end of the entire procedure it displays a summary If errors occur during the automatic tuning and calibration procedure go to step 5 If the automatic tuning and calibration procedure finishes without errors go to step 6 5 If errors occur during the automatic tuning and calibration procedure restore the previous mass spectrometer device settings and perform the tuning and calibration procedure agai...

Page 82: ...e positive ion tuning and calibration settings to the negative ion mode If 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 Note If you intend to perform high sensitivity negative ion mass spe...

Page 83: ...s dialog box appears 8 Save the tune method file as follows 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 EI 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 Examp...

Page 84: ...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 56 45 ...

Page 85: ... 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 n I e...

Page 86: ...ting Mass 218 99m z 117 Improvement Optimizing Lens 1 for Q3MS 45 36 27 18 9 0 Lens 1 Voltage V 0 20 40 60 80 100 Relative Intensity Feb 22 2010 Previous Setting Optimum Setting Mass 218 99m z 29 Improvement Optimizing Lens 1 1 for Q1MS 15 12 10 7 5 2 Lens 1 1 Voltage V 0 20 40 60 80 100 Relative Intensity Feb 22 2010 Previous Setting Optimum Setting Mass 218 99m z 94 Improvement Optimizing Lens 1...

Page 87: ... the maintenance tune procedure 5 After the procedure terminates you can accept the maintenance tune and save the calibration or undo the tune Creating a Quality Control QC Tune Report Use the TSQ QC quality control Report dialog box in EZ Tune to produce a report that displays tune parameters and mass spectra relevant to the performance of the mass spectrometer You can save the report as a PDF fi...

Page 88: ... 10 10 Electron Energy eV 70 69 Source Temperature C 100 100 Ion Gauge Pressure Torr 7 1e 06 Q1 Peak Width amu 0 7 Air Water Leak Check FAIL qcr20111202155106 1 ST 3 02 uS 1 NL 2 07E7 68 70 m z 218 220 m z 500 502 504 m z 0 10 20 30 40 50 60 70 80 90 100 Relative Intensity 0 10 20 30 40 50 60 70 80 90 100 Relative Intensity 0 10 20 30 40 50 60 70 80 90 100 Relative Intensity 71 213 69 030 219 021 ...

Page 89: ...ow 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 41 b Push the guide bar in as far as it can 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 needed Gloves ...

Page 90: ...Figure 42 shows the inlet valve lever is down for closed b Loosen the inlet valve knob counterclockwise 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 hole First stop ...

Page 91: ...EZ Tune toolbar The Insert Probe message appears Figure 43 Figure 43 Insert Probe message 5 Insert the I R tool into the inlet valve a Insert 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 44 c Tighten the inlet valve knob clockwise to ensure a leak tight seal Inlet valve knob Inlet valve pl...

Page 92: ...t stop on guide bar and the inlet valve knob tightened 6 Click OK The forepump evacuates the inlet valve Wait until you can safely insert the probe Figure 45 and then click OK Figure 45 Safe to insert the probe message 7 Once evacuation is complete pull the inlet valve lever up Figure 46 Inlet valve knob First stop of guide bar I R tool ...

Page 93: ...er up The inlet valve is now open 8 Remove the ion volume a Slide the I R tool into the vacuum manifold until the tip of the I R tool is fully inserted into the ion volume holder See Figure 47 The head of the arrow on the I R tool when viewed through the window of the ion source manifold should not be visible Inlet valve lever First stop of guide bar I R tool ...

Page 94: ...the ion volume attached until the guide ball reaches the first stop see Figure 46 on page 77 d Pull the lever down to close the inlet valve e Loosen the inlet valve knob by turning it counterclockwise to release the seal f 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 I R tool inserted into the vacuum manifol...

Page 95: ...volume holder and I R tool 10 To clean the ion volume use the instructions in Cleaning Stainless Steel Parts on page 98 If you are cleaning a CI ion volume be sure to clean out the small electron entrance hole Aluminum oxide can get trapped in this hole which can adversely affect sensitivity Use a dental pick or old syringe needle to clean the hole WARNING Burn Hazard Because the ion volume might ...

Page 96: ...se 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 5 Choose Start 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 43 7 Inset the I R tool into the inlet valve a Insert the guide ball into ...

Page 97: ... R tool handle to the lock position 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 46 on page 77 b Close the inlet v...

Page 98: ...t 90 counterclockwise and sliding it out of the entry housing 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 99: ... refer to the manuals that come with the GC or autosampler Contents Cleaning Ion Source Components Replacing the Filament of the Ion Source Completely Disassembling and Reassembling the Ion Source Maintaining the Forepump Adding Calibration Compound Replacing the Ball Valve Seal Removing and Installing a GC Capillary Column Tip When you perform maintenance procedures be methodical always wear clea...

Page 100: ...orepump pump oil If pump oil is cloudy Manufacturer s documentation Forepump Adding pump oil If pump oil level is low Manufacturer s documentation Forepump Changing the pump oil Every 4 months or if pump oil is cloudy and discolored Manufacturer s documentation Ion detection system Replacing the electron multiplier assemblyb If noise in spectrum is excessive or proper electron multiplier gain cann...

Page 101: ... system decreases significantly from your benchmark test results clean the ion volume If this does not restore performance clean the lenses How often you clean the ion source depends on the types and amounts 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 The ion volume becomes ...

Page 102: ...86 TSQ Quantum XLS Series User Guide Thermo Scientific Figure 50 Ion source assembly assembled and exploded views ...

Page 103: ...urce lenses Y To clean the ion source lenses 1 Shut down and vent the system See Shutting Down the System Completely on page 51 2 Remove the ion source See Removing the Ion Source on page 88 3 Remove the ion source lens assemblies from the ion source and disassemble it See Removing the L1 L2 L3 Lens Assembly and the Heated Q0 Quadrupole Assembly on page 90 4 Clean the lenses and the spacers See Cl...

Page 104: ...nuing b Once the oven injector and transfer line are cool turn off the gas chromatograph c Loosen the transfer line nut See Figure 61 on page 108 d Pull back the column You can first mark the column s position with white correction fluid 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 man...

Page 105: ... mount 7 Pull the ion source assembly away from the Q0 quadrupole mount and slightly 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 10 Close the lid of the ion source vacuum manifold Q0 quadrupole mount Lens L1 L2 L3 connector EI CI Source PCB connector Transfer line Thumbscrew Thumbscrew ...

Page 106: ...Q0 quadrupole 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 ion source block See Figure 52 2 Remove the heated Q0 quadrupole assembly and the L1 L2 L3 lens assembly from the heater cartridges of the ion source Place them ...

Page 107: ...tweezers See Figure 53 2 Remove the lenses and spacers from the lens holder 3 Place the components on a clean surface Figure 53 L1 L2 L3 lens assembly assembled and exploded views Lens holder Lens L3 Lens spacer Lens L2 Lens spacer Lens L1 Lens retainer clip Note To clean the ion source lenses follow the procedure in Cleaning Stainless Steel Parts on page 98 To clean the remaining parts follow the...

Page 108: ...on source through their corresponding holes in the heated Q0 quadrupole assembly Verify the correct orientation of the guide pin hole and the retainer clip groove on the heated Q0 quadrupole assembly 3 Use the retainer clip and threaded standoff to secure the lens assemblies to the ion source Reinstalling the Ion Source For the location of the ion source components see Figure 50 on page 86 Y To re...

Page 109: ...me See Installing the Ion Volume on page 80 8 Close and secure the cover to the ion source vacuum manifold Replacing the Filament of the 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 ...

Page 110: ...er ring and lens assemblies to the ion source block See Figure 54 6 Pull the heater ring and lens assemblies off of the cartridge heaters on the ion source block Place them on a clean surface 7 Remove the retainer clip that secures the filament and centering ring to the ion source block 8 Remove the filament and centering ring from the ion source block WARNING Shock Hazard Unplug the mass spectrom...

Page 111: ...e block 10 Use the retainer clip and threaded standoff to secure the lens assemblies to the ion source See Figure 54 on page 94 11 Reinstall the ion source onto the magnet yoke 12 Reinstall the ion source into the vacuum manifold and reinsert the capillary column into the ion source See Reinstalling the Ion Source on page 92 Restart the system See Starting Up the System after a Complete Shutdown o...

Page 112: ... and remove the retainer clip that secures the heater ring and lens assemblies to the ion source block 6 Pull the heated Q0 quadrupole assembly and the L1 L2 L3 lens assembly off the ion source WARNING Shock Hazard Unplug the mass spectrometer before proceeding L1 L2 L3 lens assembly 70111 60842 Heater ring 70111 22052 Centering ring 70111 22061 Ion source block 70111 22019 Heater ring and lens as...

Page 113: ...l the EI CI Source PCB a Align and insert the cartridge heaters and temperature sensor on the EI CI Source PCB with the corresponding holes in the ion source block b Reinstall the three base studs 2 Reinstall the filament and centering ring a Insert the filament into the centering ring b Align the filament leads with the EI CI Source PCB connectors and gently press the leads into the connectors No...

Page 114: ...erature sensor and the heater block 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 Deionized water Detergent Alconox Micro or equivalent Dremel rotary tool or equivalent recommended Foil aluminum Forceps P N 76360 0400 Gloves cleanroom grade P N 23827 0008...

Page 115: ...warm detergent solution a Using forceps place the parts in a beaker containing warm detergent solution b Place the beaker and contents in an ultrasonic bath for five minutes c Rinse the parts with tap water to remove the detergent 4 Sonicate the parts in deionized water a Using forceps place the parts in a beaker containing deionized water b Place the beaker and contents in an ultrasonic bath for ...

Page 116: ...leaning efficiency as well as decrease the time required to clean the items 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 Deionized water Detergent Alconox Micro or equivalent Dremel rotary tool or equivalent recommended Forceps P N 76360 0400 Gloves clea...

Page 117: ...ump 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 mark add oil If the oil is cloudy or discolored purge the oil to decont...

Page 118: ...ensity of calibration gas ions is too low You must add calibration compound however many factors other than a decrease in the calibration compound can cause a shortage of calibration gas ions As a rule add calibration compound once a year The calibration compound resides in a cylindrical vial see Figure 56 Figure 56 Calibration gas flow modules showing the calibration compound vial Y To add calibr...

Page 119: ...57 Location of the calibration compound vial compartment 3 Twist the calibration compound vial counterclockwise and remove it from the calibration gas flow module See Figure 58 Set the vial on the work table Figure 58 Calibration compound vial Calibration compound vial compartment Calibration compound vial ...

Page 120: ...top of the frit then you have too much in the vial Immediately pour out the excess calibrant according to local environmental regulations 5 Remove the syringe from the calibration compound vial 6 Reinstall the calibration compound vial to the calibration gas flow module Turn the vial clockwise to tighten it 7 Reinstall the cover to the calibration compound vial compartment CAUTION Having more than...

Page 121: ...d in the Accessory Kit The ball valve seal consists of a Teflon spool and two O rings See Figure 59 Figure 59 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 60 Tools needed Ball valve seal kit P N 119265 0003 Frequency If the ball valve seal leaks air after you in...

Page 122: ...action tool forward 5 Remove the seal and tool 6 Pull the plunger back to disengage the seal Figure 60 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 Teflon spool 3 Insert the ball valv...

Page 123: ...utting Down the System Completely on page 51 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 61 a Unscrew the transfer line nut b Remove the column from the transfer line Tools needed Gloves cleanroom grad...

Page 124: ... Guide Thermo Scientific Figure 61 GC injector and transfer line unions 3 Remove the column from the injector For instructions refer to the Columns chapter of the TRACE GC Ultra Operating Manual Column retaining nut Ferrule Capillary column Injector Transfer line nut Ferrule Transfer line end ...

Page 125: ...ow to 1 0 mL min d Turn off vacuum compensation under the Right or Left Carrier menu e Dip the column outlet in a small vial of methanol Bubbles indicate there is flow through the column 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 L...

Page 126: ...lary column according to the manufacturer s instructions You must condition new columns 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 on page 51 b Lower the GC oven temperature to 30 C and allow it to cool before continuing Note The K factor is a measure of the resistance o...

Page 127: ...e inlet valve v Pull the column back just far enough so 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 th...

Page 128: ...g a GC Capillary Column 112 TSQ Quantum XLS Series User Guide Thermo Scientific 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 129: ...e instrument electronics do have a problem the system diagnostics can often pinpoint the location Because the system diagnostics only diagnose problems that are electrical in nature for example they do not diagnose poor sensitivity due to misaligned or dirty components or to improper tuning whoever runs the diagnostics must be familiar with system operation and basic hardware theory as well as the...

Page 130: ...arrives at your site Troubleshooting The following topics discuss possible TSQ Quantum XLS Series system problems and solutions Communication Issues Communication issues likely involve links between the data system and the mass spectrometer gas chromatograph or autosampler This section does not address communication issues with other devices Communication issues can occur during the following Data...

Page 131: ...w The Ethernet cable is unplugged Verify that the Ethernet cable is connected to the Ethernet port on the mass spectrometer See Figure 14 on page page 25 The Ethernet card in the PC is not configured or is faulty Check the configuration or replace the Ethernet card if necessary The electronics service switch of the mass spectrometer is in the Service Mode position Return the electronics service sw...

Page 132: ...instrument method and configuration Verify that the sample is present The heated zone stipend is not attained See Heated Zone Issues on page 120 Issue Acquisition terminates unexpectedly Possible causes solutions The end run time in the TSQ Quantum XLS Series instrument method is incorrect Check the instrument method for the GC and the MS The data system is out of disk space Check disk space back ...

Page 133: ...em Additionally the spectra shown in Xcalibur Tune and Real Time Display are auto normalized which can make the background level appear high Some chemical noise does occur such as septum bleed after a series of injections vial sample bleed which occurs if more than one injection is made from a sample vial and siloxane peaks that appear in the chromatogram at regular intervals from focusing at the ...

Page 134: ...iners and remedy Issue Excessive hydrocarbon contamination Typical ions are m z 43 57 71 85 99 Possible causes solutions Carrier gas tubing is contaminated Isolate source of hydrocarbon contamination and remedy Replace carrier gas tubing Change carrier gas filters Issue Chemical background due to rhenium oxide m z 185 187 201 203 217 219 233 235 250 252 Possible causes solutions These series of rh...

Page 135: ...rate an error message Diagnostics test the lenses of the TSQ Quantum XLS Series mass spectrometers A flat line which represents voltage readback versus the predicted voltage ramp indicates a lens or other control fault Contamination causes lens performance to deteriorate over time the amount of time depends on what type of sample and ionization mode you use Issue Diagnostics indicate that the fila...

Page 136: ...artridges or faulty temperature sensors This manual does not discuss heated zones in the gas chromatograph Issue Excessive chromatographic peak tailing Possible causes solutions The ion source transfer line or both are not hot enough Increase the transfer line temperature so that it is at least as hot as the highest GC oven temperature Then try increasing the ion source temperature The sample anal...

Page 137: ...ossible causes solutions Aux1 zone of the GC is not configured for MS Transfer Line Configure Aux1 zone of the 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 Issue Transfer line overheats Possible cause solution The transfer line temper...

Page 138: ... Forepump powers on but will not pump down Possible causes solutions The oil level in the forepump is insufficient Check oil level add oil if necessary The foreline is leaking Check the clamps and connectors Replace the foreline hose if a hole is found The vacuum manifold is leaking The forepump is faulty Replace the forepump Issue Turbo pump shuts off during operation Possible cause solution The ...

Page 139: ...to minimize linearity problems Usually a hardware fault that affects linearity shows different issues than those that might be attributed to linearity Issue Calibration plots not sufficiently linear Possible causes solutions High end standards are too concentrated for the MS Use the split injection technique to decrease the amount of sample or lower emission current to reduce MS sensitivity The io...

Page 140: ...er 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 determine if the sensitivity drop was sudden or if it occurred gradually A sudden loss of sensitivity can be the result of sudden component failure or an unnoticed change in the analytical method Simple errors such...

Page 141: ...me properly The magnets above and below the ion source are installed incorrectly Position both magnets so that the south pole is on top Electrons will not focus into the ion volume if one magnet is upside down Dust has collected in the electron multiplier or on the conversion dynode Contact Thermo Fisher Scientific Technical Support The emission current is set too low Check the setting listed for ...

Page 142: ...ivity is unstable or shows decrease with repeated injections Possible causes solutions The GC temperature ramp does not continue to a high enough temperature to elute high boiling point compounds Multiple injections cause these compounds to accumulate in a column reducing sensitivity Extend the upper temperature or the time at upper temperature in the GC oven ramp The ion volume or lenses are cont...

Page 143: ...rate results Good operating conditions for the mass spectrometer gas chromatograph and autosampler contribute to instrument stability Sample preparation spiking errors sample injection errors and lack of routine maintenance on the instruments can cause false stability issues When hardware faults affect instrument stability investigate simple solutions first such as cleaning the ion volume and lens...

Page 144: ...0 μL max of calibration compound to calibration gas vial See Adding Calibration Compound on page 102 Issue The electron multiplier gain calibration fails Possible causes solutions The electron multiplier has not been given sufficient time to outgas since venting Allow more time to pump out The GC column flow is too high Lower it to 1 mL min The multiplier is near the end of its lifetime Multiplier...

Page 145: ...bleed Remedy the source of these low m z ions The ion volume or lenses are contaminated Clean the ion volume or lenses See Cleaning Ion Source Components on page 85 m z 131 is not base peak because the multiplier gain is too low The multiplier gain calibration may set the multiplier voltage too low for a noisy multiplier Electron multipliers older than 2 to 3 years are often noisy Contact Thermo F...

Page 146: ... 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 119 for more information The electron multiplier is faulty Contact Thermo Fisher Scientific Technical Support Replacing Fuses Replacing PCBs and Pow...

Page 147: ...e settings that the TSQ Quantum XLS Series 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 Thermo Xcalibur Roadmap 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 On the Sc...

Page 148: ...eries User Guide Thermo Scientific 5 Specify the mass spectrometer settings for this example Full Scan Scan Type list Q1MS Scan Modes MS Mode option and Positive Polarity area Figure 62 Scan Editor page of Instrument Setup 6 Click the EI CI tab to display the EI CI page see Figure 63 ...

Page 149: ... 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 b Save the instrument method as a meth file In this example we name the instrument method Dip test meth ...

Page 150: ...r Roadmap 2 On the Thermo Xcalibur Roadmap click the Sequence Setup icon to open the Sequence Setup view see Figure 64 3 Enter the name and path of the instrument method In this example it is C Xcalibur methods DIP test 4 Enter a file name and path for the raw file that contains the acquired data In this example it is C Xcalibur Data data01 Figure 64 Sequence Setup view showing one sample in the s...

Page 151: ...try housing See Figure 17 on page 28 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 17 on page 28 b Loosen the inlet valve knob counterclockwise and remove the inlet valve plug Preparing the Mass Spectrometer Y To prepare th...

Page 152: ...ose Actions Run Sequence The Run Sequence dialog box opens see Figure 65 Figure 65 Run Sequence dialog box showing instruments in use c Click Change Instruments to open the Change Instruments In Use dialog box see Figure 66 Figure 66 Change Instruments In Use dialog box showing the TSQ Quantum mass spectrometer in use and no start instruments ...

Page 153: ...he Xcalibur data system saves the acquired data in a raw file Y To run the sequence 1 In the Run Sequence dialog box see Figure 65 on page 136 click OK to start the acquisition The Xcalibur system displays a message to insert the probe Figure 67 Figure 67 Insert probe message 2 Inset the probe into the inlet valve a Insert the guide ball on the DIP probe into the guide ball hole on the guide bar b...

Page 154: ...repump evacuates the inlet valve 4 When the Safe to Open the Valve message appears Figure 69 click OK Figure 69 Safe to open the valve 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 70 Inlet valve knob First stop on guide bar Probe ...

Page 155: ...he Acquisition Ready message Figure 71 click OK The mass spectrometer is now waiting for contact closure Figure 71 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 72 and Figure 73 on page 141 Inlet valve Probe ...

Page 156: ...A Using the Direct Sample Probe Running the Sequence 140 TSQ Quantum XLS Series User Guide Thermo Scientific Figure 72 Perfluorotetracosane mass spectrum at 0 56 minute retention time ...

Page 157: ...e 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 Thermo Xcalibur Roadmap click the Qual Browser icon to open the Qual Browser window 2 Click on the chromatogram to display the mass spectrum at that retention time See Figure 74 ...

Page 158: ...the probe until the guide ball on the probe reaches the first stop on the guide bar see Figure 68 on page 138 2 Close the inlet valve by pushing the lever down 3 Loosen the inlet valve knob by turning it counterclockwise CAUTION Do not withdraw the probe beyond the point where the guide ball reaches the first stop in the guide bar Close the inlet valve first Otherwise the system vents to the atmos...

Page 159: ...ack in the guide bar 5 Store the probe in its case 6 Remove the guide bar by rotating it 90 counterclockwise 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 pu...

Page 160: ......

Page 161: ...act Thermo Fisher Scientific Austin and have your TSQ Quantum XLS Series mass spectrometer serial number ready These kits with replaceable parts and consumables are available for the TSQ Quantum XLS Series systems EI CI Ion Source Replaceable Parts Figure 75 and Figure 76 show the replaceable parts of the EI CI ion source of the TSQ Quantum XLS Series mass spectrometers Contents EI CI Ion Source R...

Page 162: ...11 22052 Centering ring 70111 22061 Ion source block 70111 22019 Heater ring and lens assemblies retainer clip 70111 22070 Threaded standoff 70111 22060 Ion volume retaining thumbscrew 70111 22059 EI CI Source PCB 70111 60848 Base studs 70111 22056 Ion volume holder 70001 20532 T Closed EI ion volume 70111 22147 Heated Q0 quadrupole assembly 70111 60843 Filament 120320 0030 Filament retainer clip ...

Page 163: ...Lens L3 119650 3423 Lens spacer 119650 0426 Lens L2 119650 3416 Lens spacer 119650 0426 Lens L1 119650 3414 Lens retainer clip 119650 0428 Table 7 Miscellaneous replaceable parts Sheet 1 of 2 Description Function Part number Calibration compound vial Holds frit and FC 43 tuning and calibration compound 120428 0002 Calibration compound frit Holds FC 43 tuning and calibration compound 120432 0001 Io...

Page 164: ...n 1 4 to 1 8 in 00101 01712 Fitting ferrule SWG front 3 8 in brass 00101 11500 Ferrule 0 4mm ID 1 16 in 00101 18100 Restek capillary grade hydrocarbon trap For removing hydrocarbons from the GC carrier gas 00106 99 00001 Restek high capacity oxygen trap For removing oxygen from the GC carrier gas 00106 99 00002 Cotton swabs For applying cleaning paste to stainless steel parts 00301 01 00015 Tubing...

Page 165: ...nents 76360 0400 Cable 10 base T crossover 15 ft shielded Communication 76396 0052 Oil vacuum pump 1 L Lubrication of forepump 00301 15101 Cable RJ45 7 ft 00302 01838 Ethernet switch 5 port Communication 00825 01 00024 Software QuanLab Forms 2 5 1 SP1 Chromatography analysis software 120395 0001 Software GC Devices 2 1 0 for Xcalibur 2 1 GC devices control software 120399 0001 Table 8 Accessory Ki...

Page 166: ......

Page 167: ...ng procedure 64 tune and calibration report 67 calibration compound flow control description 44 mass spectrum displaying 62 observed peaks 62 on off 62 spectrum positive EI mode 64 calibration compound vial location 102 103 replaceable parts 147 calibration gas valve description 44 capillary column conditioning 110 installing 109 removing 107 removing ion source Caution 88 cathode electron multipl...

Page 168: ...ent method 131 2 creating a sequence 134 3 preparing the probe and inlet valve 135 4 preparing the mass spectrometer 135 5 running the sequence 137 6 examining the data 141 7 removing the probe 142 perfluorotetracosane 131 direct exposure probe DEP 19 direct insertion probe DIP 19 direct insertion probe DIP perfluorotetracosane example procedure 131 direct sample probe and inlet valve 135 direct e...

Page 169: ...eter 21 Q0 quadrupole 29 transfer line 20 fuses mass spectrometer replacing 130 G gas chromatograph GC capillary column installing 109 removing 107 column installation 109 communication with data system 47 configuring 19 functional description 19 leak check 110 photo 2 power outlet 24 retention time correction iSRM 13 startup 53 54 troubleshooting communication problems 116 GC Devices 2 1 0 149 gu...

Page 170: ... removing 88 ion source block location figure 26 ion source chamber location figure 42 Ion Source PCB location figure xii 53 reinstalling 97 ion transmission device defined 6 rod assembly 6 ion volumes attaching and removing from I R tool 79 cleaning 87 figure 27 installing 80 location figure 81 removing 73 replaceable parts 147 ionization modes changing 73 chemical ionization CI 3 discussed 3 ele...

Page 171: ... optics 29 ion source 26 LEDs and system startup 57 maintenance procedures table 83 mass analyzer 31 Off condition 59 On Off status of components 59 Power Entry Module description 45 power outlet 24 Q0 quadrupole 29 resetting 57 RF voltage generation electronic assemblies 46 right side power panel 52 shutdown 51 Standby condition 51 59 startup 53 tuning and calibrating note 56 tuning off component...

Page 172: ...ry column 107 removing ion source 88 removing ion source lens assembly 90 removing ion volumes 73 resetting mass spectrometer 57 saving tune and calibration reports 69 starting mass spectrometer 54 system startup 53 tuning and calibrating 64 Product scan mode discussed 7 illustration figure 8 profile data type 14 pumps forepump 43 oil part number 149 turbomolecular pump 42 Q Q0 quadrupole cross se...

Page 173: ...cted ion monitoring SIM scan type 12 selected reaction monitoring SRM scan type 13 sensitivity problems troubleshooting 124 septum bleed contamination 118 sequence creating 134 direct sample probe running 137 Sequence Setup view 134 Sequence Setup opening 135 shutdown complete shutdown 51 data system 53 emergency procedure 49 emergency front panel system power off button 23 mass spectrometer 51 no...

Page 174: ...22 ion polarity modes 5 LEDs and system startup 57 mass analysis overview 3 mass range 15 mass spectrometer 21 operating conditions setting 56 overview 1 scan modes 5 scan types 12 Standby condition 51 startup 53 tuning 61 tuning and calibrating note 56 turning off components 58 TSQ Quantum XLS Series system autosampler 18 data system 46 functional block diagram figure 18 gas chromatograph 19 TSQ ...

Page 175: ...2 Vacuum LED 22 vacuum manifold 41 vacuum service switch 24 vent valve 44 vent valve description 44 LED 24 Vent Valve Closed LED 24 voltages conversion dynode 38 Q0 offset 29 quadrupole rf and dc 32 W Warnings burn hazard GC oven injector transferline 88 removing ion source 89 shock hazard removing ion source 88 WEEE compliance vii X xylene solvent peaks 118 ...

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