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TSQ Quantum XLS and TSQ Quantum GC User Guide Version A

1. 2009 Thermo Fisher Scientific Inc All rights reserved Swagelok is a trademark of the Crawford Fitting Company Dranetz is a trademark of Dranetz Technologies Inc Styrofoam is a trademark of Dow Chemical Company Teflon is a trademark of E I du Pont de Nemours amp Co Tygon is a trademark of Norton Company Dust Off is a trademark of Falcon Safety Products Micro Blast is a trademark of MicroCare Corporation Restek is a trademark of Restek Corporation Dremel Vespel Thermo Fisher Scientific Inc provides this document to its customers with a product purchase to 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 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 will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is followed properly This document is not part of any sales contract between
2. 51 11 Maximum Intensity 4 35e 05 6 Improvement Optimizing Lens 2 1 for ion 501 97 m z 46 55 Signature Page 1 of 10 70 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Thermo Scientific 4 Tuning and Calibrating Saving the Tune and Calibration Report Figure 36 Tune and calibration report parameter optimization plots Quantum Tune Master Tune and Calibration Optimizing Lens 2 for Q1MS E Previous Setting Optimum Setting 100 gt 80 z a c 9 eo E 2 2 40 a F il 20 _ Mass 501 97m z 223 Improvement 4 AWBSs 2 nent M T T T a T T 1 50 40 30 20 10 0 Lens 2 Voltage V May 9 2007 Optimizing Lens 4 for Q1MS lll Previous Setting Optimum Settin 100 _ pa s gt 80 z a 4 c 9 eo 9 4 2 40 8 E 4 20 0 Mass 69 00m z 60 Improvement T T T T T T T 1 50 40 3 20 10 0 Lens 4 Voltage V May 9 2007 Optimizing Lens 1 1 for Q3MS E Previous Setting Optimum Settin 100 E 9 gt 80 z a 4 c 9 eo amp 9 4 2 40 Ly F 4 20 0 Mass 69 00m z 6 Improvement T T T T T T T 1 10 6 4 2 0 Lens 1 1 Voltage V May 9 2007 To save the tune and calibration report Relative Intensity Relative Intensity Relative Intensity Optimizing Lens 2 for Q3MS E Previous Setting Optimum Setting e 100 80 60 40 20 9 T T T T T T T 1 50 40 30 20 10 0 L
3. For electronic failures PCBs are not repaired to the component level except in certain cases of fuses relays and so on When these exceptions occur component information can be found in the Replaceable Parts chapter viii TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific Preface Contacting Us There are several ways to contact Thermo Fisher Scientific To contact Technical Support Phone 800 685 9535 Fax 561 688 8736 E mail TechSupport C MS thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at www mssupport thermo com To contact Customer Service for ordering information Phone 800 532 4752 Fax 561 688 8731 Web site www thermo com finnigan To suggest changes to documentation or to Help Fill out a reader survey online at www thermo com lcms techpubs Sendan e mail message to the Technical Publications Editor at techpubs finnigan lcms thermofisher com Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide ix LLL m Introduction The TSQ Quantum XLS and TSQ Quantum GC are members of the TSQ Quantum family of Thermo Scientific mass spectrometers The TSQ Quantum XLS and the TSQ Quantum GC are advanced analytical instrument that includes a mass spectrometer liquid chromatograph and the Xcalibur data system See Figure 1 Contents lonization Modes on Polarity Modes Scan Modes Scan Types Data Typ
4. 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 Possible causes solutions The septum is worn out or damaged Replace the septum Small pieces of septum are in the injection port liner Replace the injection port liner condition the capillary column Possible causes solutions Phthalate contamination has occurred due to sample handling or solvent contamination Packaging materials could be the source of phthalates solate source of phthalates such as vial lids or plastic solvent containers and remedy Possible causes solutions e Carrier gas tubing is contaminated Isolate source of hydrocarbon contamination and remedy Replace carrier gas tubing Change carrier gas filters 134 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Issue Chemical background due to rhenium oxide m z 185 187 201 203 217 219 233 235 250 252 Issue Spectra are observed due to the following solvents 7 Diagnostics and Troubleshooting Troubleshooting Possible causes solutions These series of rhenium oxide ions come from oxidation of the rhenium filament wire due to the introduction of air into the ion source while the filament is on Check for air leaks and remedy See High Vacuum Is
5. Regular Method to open the regular method Scan Editor page 4 On the Scan Editor page create a one segment one scan event instrument method In this example the segment is 8 minutes long see Figure 65 Thermo Scientific TSQ Quantum XLS and TSO Quantum GC User Guide 147 8 Using the Direct Sample Probe Creating an Instrument Method 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 ES DIP test meth Instrument Setup Eile Quantum Help olsa S xe TRACE GC Ultra J TriPlus Autosampler SS Scan Event 1 STORET OUT SEU UU SAUER Scan Editor erc Method Summary Calibration Correction Method IT m Run Settings MS Acquire Time min fat 0 Current Segment f To display a chromatogram here use Quantum Open Raw File 00 05 10 15 4 25 30 Retention Time min 50 55 6 0 65 70 75 8 0 M Segment 1 Settings Segment Time min 8 10 Tune Method C calibur methods El PHIL TRAN TSQTune Hi ej Scan Events 1 E Chrom Filter Peak Width s Iv 3 0 Collision Gas Pressure mTor T5 Current Scan Event fi Er Scan Type Full Scan l m Scan Modes ET Data Type MS Mode HIME C OMS MS MS Mode C Parent C Product 7 Neutral Loss mi UD Polarity Positive C Negative zz Centroid Profile r Sc
6. 95 L21 L22 L23 figure 34 L31 L32 L33 figure 34 linearity problems troubleshooting 139 main power circuit breaker description 23 24 location figure 24 Maintaining 116 maintenance ball valve seal replacing 120 forepump 116 frequency 83 GC column installation 124 ion source filament replacing 105 ion source lenses cleaning 88 ion volumes cleaning 88 procedures table 83 mass analysis collision induced dissociation 36 discussion 34 mass analyzer Thermo Scientific defined 6 description 32 quadrupole rod assembly functional description 33 mass anaysis RF and dc fields figure 34 mass range 15 mass spectrometer and direct sample probe 151 CI gas valve 46 circuit breaker location figure 25 collision gas valve 45 diagnostics 129 electronic assemblies 46 electronics service switch location figure 25 emergency shutdown 51 front panel LEDs 22 functional description 21 fuses replacing 145 inlet gasses hardware 41 inlet valve figure 29 ion detection system 39 ion detection system electronic assemblies 47 ion gauge 45 ion optics 30 ion source 26 27 LEDs and system startup 59 maintenance procedures table 83 mass analyzer 32 Off condition 60 On Off status of components 60 Power Entry Module description 46 power outlet 24 QO quadrupole 30 resetting 58 RF voltage generation electronic assemblies 47 right side power panel 54 shutdown 53 Standby condition 52 60 startup 55 turbomolecular pump 44
7. Reassemble the L1 L2 L3 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 the L1 L2 L3 lens assembly Align the lead pins See Figure 53 Reinstalling the lon Source Lens Assembly Toreinstall the ion source lens assembly onto the ion source 1 Wearing clean lint and powder free gloves insert the lens assembly into the ion source See Figure 53 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 101 6 Maintenance Replacing the Filament of the TSQ Quantum XLS lon Source 2 Use the retainer clip and threaded standoff to secure the lens assembly to the ion source See Figure IMPORTANT For accurate temperature readings of the heater block fully screw the threaded standoff into the ion source to ensure contact between the temperature sensor with the heater block Reinstalling the lon Source 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 seated in the sampl
8. See Filament and Lens Control Issues on page 135 for more information There is an air leak Check for leaks See High Vacuum Issues on page 138 for more information There is a high vacuum problem See High Vacuum Issues on page 138 for more information There is a contamination problem See Contamination Issues on page 133 for more information Dust has collected in the electron multiplier or on the conversion dynode Contact Thermo Fisher Scientific Technical Support 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 Possible causes solutions There is a mechanical problem with the ion source or lenses Verify that an EI ion volume is installed Verify correct orientation and cleanliness of ion volume Verify cleanliness and correct operation of lenses Tune file settings are out of usable range Restore default tune settings and calibration settings Run Auto Tune Calibration See Tuning and Calibrating on page 63 The calibration gas vial is empty Add 100 pL max of calibration compound to calibration gas vial See Adding Calibration Compound on page 117 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
9. Tap water Toothbrush soft Ultrasonic cleaner Frequency As needed to clean these stainless steel parts on volumes on source block on source lenses CAUTION Material and Eye Hazard Wear impermeable laboratory gloves and eye protection when performing cleaning procedures To clean stainless steel parts 1 Remove contamination from all the surfaces you are cleaning a Use a slurry of number 600 aluminum oxide in glycerol and a cleaning brush or cotton tipped applicator Contamination appears as dark or discolored areas but often is not visible The heaviest contamination is usually found around the apertures such as the electron entrance hole on an ion volume Clean each part thoroughly even if no contamination is visible To clean the inside corners use the wooden end of an applicator cut at an angle Use a Dremel tool with the polishing 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 TSO Quantum XLS and TSO Quantum GC User Guide 113 6 Maintenance Disassembling and Reassembling the TSQ Quantum GC lon Source Completely Rinse the parts with clean water Use a clean applicator or toothbrush to remove the aluminum oxide slurry Do not let the slurry dry on the metal dried aluminum oxide is difficult to
10. 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 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 03 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 of unwanted neutral species to the detector and dramatically lowers the noise level in the data Q2 has become synonymous with the term collision cell Technically the collision cell is the chamber that encloses Q2 where collision induced dissociation can take place if the argon collision gas is present See Figure 21 TSO Quantum XLS and TSO Quantum GC User Guide 33 2 Functional Description Mass Spectrometer Figure 21 Collision cell Q2 quadrupole and lenses Lenses L21 L22 Lenses L31 L32 and and L23 L33 rf and DC Fields Applied to the Quadrupoles In a quadrupole rod assembly because rods opposite each other in the array connect electrically the four rods can be considered as two pairs of two rods each Ac and dc voltages are applied to the rods and these voltages are ramped during the scan Voltages of the same amplitude and sign are applied to the rods of each p
11. gt CH4 2e7 CH e gt CH3 e H CH CH gt CH CH4 CH3 CH4 gt C2Hs H5 4 Positive sample ions are formed by one of the following The transfer of a proton from a secondary reagent gas ion to a sample molecule e The abstraction of an electron by a reagent gas ion e An ion association reaction in which an adduct ion is formed between a reagent gas ion and a sample molecule In methane positive ion mode CI the relevant peaks observed are MH M CHs and M C Hs but mainly MH 4 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific 1 Introduction lon Polarity Modes In isobutane positive ion mode CI the main peak observed is MH In ammonia positive ion mode CI the main peaks observed are MH and M NH Negative sample ions are most commonly formed by one of the following Sample molecules capture the secondary thermal electrons present in the ion source Electron transfer from ionized reagent gas e g NH Proton abstraction Molecular ions observed in negative ion chemical ionization mass spectra are usually M or M H lon Polarity Modes Scan Modes Thermo Scientific You can operate the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers in either of two ion polarity modes positive or negative Both positively charged and negatively charged ions form in the ion source of the mass spectrometer The mass spectrometer controls whether positive ions or negative i
12. lon source ion volume Q0 quadrupole een ERT NDT NLT pe pares gt L P Transfer line Capillary column The L11 and L12 lenses are metal disks with a circular hole in the center through which the ion beam can pass Together they act as a two element cone lens An electrical potential can be applied to the lens to accelerate or decelerate ions as they approach the lens and to 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 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 of three quadrupole rod assemblies Q1 Q2 and Q2 and three lens sets The mass analyzer is discussed in detail in the following subtopics Quadrupole Rod Assemblies rf and DC Fields Applied to the Quadrupoles 32 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer Mass Analysis Collision Cell and CID Efficiency e Quadrupole Offset Voltage Mass Analyzer Lenses Quadrupole Rod Assemblies Thermo Scientific The three rod assemblies used in the mass spectrometer are numbered from the ion source end of the manifold and are designated Q1 Q2
13. on page 115 respectively 5 Reassemble L1 L2 L3 lens assembly and install it and the Q00 quadrupole onto the ion source See Reassembling the L1 L2 L3 Lens Assembly on page 93 88 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Cleaning lon Source Components 6 Reinstall the ion source into the mass spectrometer See Reinstalling the TSQ Quantum XLS Ion Source on page 94 7 Restart the system See Starting Up the System after a Complete Shutdown on page 55 Removing the TSQ Quantum XLS lon Source Remove the ion source to clean the lenses or replace the filament Tools Needed Gloves cleanroom grade P N 23827 0008 and 23827 0009 j Lint free cloth Frequency As needed to perform ion source maintenance NIS To remove the ion source CAUTION Do not remove the ion source without first pulling back the GC capillary column or else the capillary column might break 1 Shut down and vent the TSQ Quantum XLS mass spectrometer See Shutting Down the System Completely on page 53 CAUTION Shock Hazard Unplug the TSQ Quantum XLS mass spectrometer before proceeding 2 Pull back the capillary column a Lower the oven injector and transfer line temperatures to 30 C and allow them to cool before continuing CAUTION Burn Hazard The GC oven injector and transfer line are hot Allow them to cool to room temperature before touching them b Once the oven injec
14. right M L1 L2 L3 lens L4 lens assembly assembly 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 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 99 6 Maintenance Cleaning lon Source Components Figure 54 11 12 L3 lens assembly exploded and assembled views Lens retainer clip 3 Disassemble the L lens assembly a Remove the lens clip by pinching the ends with your fingers or a pair of tweezers b Remove the lens L from the lens holder c Place the components on a clean surface 100 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Cleaning lon Source Components Figure 55 4 lens assembly exploded view Lens clip Lens L4 Lens holder Note To clean the ion source lenses follow the procedure in Cleaning Stainless Steel Parts on page 113 Reassembling the lon Source Lens Assembly Ensure that the lenses are clean and dry before you reassemble the lens assembly To reassemble the ion source lens assembly 1 Wearing clean lint and powder free gloves reassemble the L4 lens assembly a Insert lens L4 into the lens holder See Figure 55 b Install the lens clip by pinching the ends with your fingers or a pair of tweezers Seat the lens clip in the lens holder 2
15. stainless steel For handling ion volumes and clean 76360 0400 components Cable 10 base T crossover 15 ft 76396 0052 shielded Table 8 Chemicals Kit P N 70111 62078 Description Function Part number Perfluorotributylamine FC 43 Tuning and calibration compound 50010 02500 Aluminum Oxide Cleaning stainless steel parts 32000 60340 Benzohexane Performance testing 120150 TEST Octafluoronaphthalene TSO Quantum XLS and TSO Quantum GC User Guide Performance testing 120150 TEST Thermo Scientific LLL m Index Symbols 133 A Accessory Kit 161 aluminum oxide 162 analyzer assembly lenses voltages applied to 39 analyzer chamber location figure 43 Analyzer Control PCB discussion 47 analyzer region vacuum manifold description 42 analyzer region vacuum manifold location 42 and 41 anode electron multiplier description 39 Auto Tune Calibration 66 automatically 66 autosampler cofiguration 18 photo 2 power outlet 24 startup 55 58 TriPlus 18 troubleshooting communication problems 133 AutoSIM scan type 14 ball valve extraction tool figure 121 extraction tool using 121 seal replacing 121 ball valve seal kit 161 benzohexane 162 C cables 162 calibrating and H SRM note 63 discussed 63 frequency note 63 Thermo Scientific running 66 tune and calibration report 69 calibration compound adding 117 flow control description 46 mass spectrum display
16. 80 maintaining forepump 116 operating the inlet valve 73 placing system in standby 52 reassembly ion source lenses 93 101 TSO Quantum XLS User Guide 167 Index Q reinstalling ion source 94 102 reinstalling ion source lenses 94 101 reinstalling Ion Source PCB 109 112 removing capillary column 122 removing ion source 89 96 removing ion source lens assembly 91 98 removing the ion volume 73 replacing filament 102 105 replacing ion source filament 102 105 resetting mass spectrometer 58 saving tune and calibration report 71 starting mass spectrometer 56 system startup 55 tuning and calibrating 66 Product scan mode discussed 7 illustration figure 8 profile scan defined 14 pumps forepump 44 turbomolecular pump 44 Q QO 30 QO quadrupole cross sectional view figure 31 description 30 figure 30 location figure 43 QI 33 Q1 quadrupole figure 33 scan modes 6 QI1MS and Q3MS scan modes 7 Q2 rod assembly figure 34 scan modes 6 Q3 quadrupole figure 33 scan modes 6 QED MS scan type 14 quadrupole 30 quadrupole mass analyzer functional description 33 quadrupole offset voltage 37 quadrupoles mass analysis 33 QO description 30 Q1 and Q3 33 RF and dc fields 34 RF and dc fields figure 34 35 Qual Browser 168 TSO Quantum XLS User Guide direct sample probe data 157 reviewing data 157 quantitation enhanced data dependent MS QED MS scan type 14 rear power panel location figure 52 reference SRM reacti
17. Convectron gauge description 45 conversion dynode description 39 figure 40 data dependent scan mode discussed 11 data system description 48 GC interface 48 instrument interface 48 LAN interface 49 personal computer 48 primary Ethernet adapter 48 shutdown 55 data types discussed 14 detector system 39 diagnostics 129 running 129 DIP example procedure 1 creating an instrument method 147 2 creating a sequence 150 3 preparing the probe and inlet valve 151 4 preparing the mass spectrometer 151 164 TSO Quantum XLS User Guide 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 figure 154 mass spectrometer preparing 151 photo 20 using 147 dynode 39 E electron ionization EI discussed 4 removing ion volume 73 electron multiplier anode description 39 description 39 figure 40 electronic assemblies description 46 ion detection system 47 Power Entry Module description 46 RF voltage generation description 47 electronics service switch description 24 location figure 24 25 mass spectrometer components On Off status 60 embedded computer description 46 resetting 58 emergency shutdown Caution 23 front panel system power off button 23 procedure 51 system power off button 51 Ethernet 48
18. 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 click OK 154 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 8 Using the Direct Sample Probe Running the Sequence Figure 72 Safe to Open Valve message Instrument Messages It is safe to open the valve with the lever Click OK when Finished il 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 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 155 8 Using the Direct Sample Probe Running the Sequence Figure 74 Acquisition Ready message Instrument Messages K ES Acquisition Ready Click OK to proceed Then Start Probe Method 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 X 1 Real Time Plot
19. File Actions View GoTo Help zxjere g Pimm aLe ee amp ue 8 Status Acquisition Queue Run Manager Acquiring Sequence C DOCUME 1 QUANTUMSLOCALS 1 Sample Name Working On Seq Row 1 Position 1 Raw File C 2 lt Calibur Data datall RAW Inst Method C lt calibur methods DIP test TS Quantum Running TRACE GC Ultra Ready to Download TriPlus Autosampler Ready to Download Status Temperature Flow Pressure General Status Standby Waiting for PREP RUN Run Elapsed time Remaining time Emergency conditions Emergency shutdown Over temperature data01 122 RT 0 56 AV 1 NL 5 52E6 T CI O4 MS 500 000 1400 000 499 530 59 20 20 704 60 Relative Abundance 818 53 49 53 868 75 968 73 1018 98 113075 422088 120684 1200 RT 0 00 8 10 100 90 80 70 60 50 40 Relative Abundance 30 156 TSO Quantum XLS and TSO Quantum GC User Guide data01 4 Time min NUM 5 10 2007 11 57 AM NOTSAVED Thermo Scientific 8 Using the Direct Sample Probe Examining the Raw Data in Qual Browser Figure 76 Perfluorotetracosane chromatogram X 1 Real Time Plot File Actions View GoTo Help T wi o zh gt mul T te aeee gu ule 9 data01 685 RT 3 16 AV 1 NL O Status Acquisition Queue T c CI Q1MS 500 000 1400 000 Run Manager 1004 Acquiring 904 Sequ
20. In general use the centroid scan data type for data acquisition for faster scan speed Data processing is also much faster for centroid data Mass Charge Range The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers can operate in a mass charge range of 10 to 3000 Da Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 15 LLL m Functional Description This chapter describes the principal components of the TSQ Quantum XLS and TSQ Quantum GC systems and their respective functions Contents Autosampler optional Gas Chromatograph Direct Sample Probes optional Transfer Line Mass Spectrometer Data System A functional block diagram of the TSQ Quantum XLS or TSQ Quantum GC system is shown in Figure 6 A sample transfer line connects the gas chromatograph GC to the mass spectrometer The autosampler and GC are installed on the left side of the mass spectrometer In analysis by GC MS a sample is injected into a GC column The sample then separates into its various components The components elute from the GC column and pass through the transfer line 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 fil
21. 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 Therefore the forepump should be connected to a fume exhaust system Consult local regulations for the proper method of exhausting the fumes from your system CAUTION Use Care When Changing Vacuum Pump Oil Treat drained vacuum pump oil and pump oil reservoirs with care Hazardous compounds introduced into the system might have become dissolved in the pump oil Always use approved containers and procedures for disposing of waste oil Whenever a pump has been operating on a system used for the analysis of toxic carcinogenic mutagenic or corrosive irritant chemicals the pump must be decontaminated by the user and certified to be free of contamination before repairs or adjustments are made by a Thermo Fisher Scientific San Jose Customer Support Engineer or before it is sent back to the factory for service TSQ Quantum XLS and TSQ Quantum GC User Guide vii Preface Solvent and Gas Purity Requirements Use the highest purity solvents available The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers are extremely sensitive to solvent impurities Liquid chromatography grade is the minimum acceptable purity Higher grade solvents are preferred Distilled water is recommended Deionized water contains chemicals and is not recommended For a wide variety of solvents
22. ROI GOR a GER WA S GER 83 Cleaning Ion Source Components ts ecdoh ice e t kc hoes ot ae eR Potens 85 Cleaning Ton Voltinesia iiss dox Ra es ER eb prp ete eee eld 88 Cleaning Lenses of the TSQ Quantum XLS Ion Source sse 88 Cleaning the Lenses of the TSQ Quantum GC Ion Source 95 Reinstalling the Ton Source taps sata ae ew PUER Eb ES 102 Replacing the Filament of the TSQ Quantum XLS Ion Source 102 Replacing the Filament of the TSQ Quantum GC Ion Source 105 Disassembling and Reassembling the TSQ Quantum XLS Ion Source Completely ooa kee te elt Roe A ole MOR t Cie aie sc Ait A ca i 107 Disassembling and Reassembling the TSQ Quantum GC Ion Source APONTE LED eti aueueraa t onte ase ableton Eyam od fitu OU duly era EN ed 110 Cleaning Stainless Steel Parts 55s eer px orca xs eec poke puc 113 Cleaning Non Stainless Steel or Hybrid Part 0 0 00 000 00 115 Maintaining th Forepump taa se sau tee oe th MERE ER eRe e eae ES 116 Adding Calibration Compound X sese ey een cea 117 Replacing the Ball Valve Seal aa WA iiis Bais eter erbe E ed 120 Removing and Installing a GC Capillary Column 0 122 Removing a GC Capillary Column o oo ceterae Poo ia 122 Installing a GC Capillary Column 322 xor nee eee ER oae S 124 Diagnostics and Troubleshooting Lsuslslsuuesseeeseeese 129 TSQ Quantum XLS System Diagnostics llle 129 TrouNfes NONO 6a ducss ees
23. Shutdown Startup and Reset Starting Up the System after a Complete Shutdown Restoring Power to the TSQ Quantum XLS or TSQ Quantum GC system To restore power to the TSO Quantum XLS or TSO Quantum GC system Place the main power circuit breaker located on the rear of the electronics module Figure 28 in the On position Starting Up the GC To start the GC Follow the startup procedure described in the manual that came with the GC Verify that the gas chromatograph is on and there is carrier gas flowing through the column into the mass spectrometer Starting Up the Data System To start the data system 1 Turn on the monitor computer and printer 2 Observe the 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 To start the mass spectrometer CAUTION Ifyou turn on the mass spectrometer without column flow air can damage the GC column This large air leak into the TSQ Quantum GC also causes the ion source to require cleaning 1 Turn on the flow of argon at the tank if it is off IMPORTANT The data system must be running before you start the mass spectrometer The mass spectrometer will not operate until it receives software from the data system 2 Make sure that the mass spectrometer main power circuit b
24. TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 8 Using the Direct Sample Probe Preparing the Probe and Inlet Valve Preparing the Probe and Inlet Valve To prepare the probe and inlet valve 1 Connect the direct sample probe controller to the mass spectrometer by contact closure with the probe start cable P N 70111 63627 in TSQ Quantum XLS or TSQ Quantum GC Accessory Kit 2 Create a probe method on the controller Refer to the probe manual This example uses the following DIP settings Initial temperature 50 C Initial time 5 s Ramp rate 100 C min Final temperature 200 C Ramp hold time 200 s 3 Load sample on the probe 4 Install the guide bar a With 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 remove the inlet valve plug Preparing the Mass Spectrometer To prepare the TSO Quantum XLS for the experiment 1 Choose Start gt All Programs gt Thermo Instruments gt TSQ gt TSQ Tune to open the EZ Tune window if it is not already open IMPORTANT The TSQ EZ Tune window must be open for the mass spectrometer to
25. Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision A March 2010 Software version Xcalibur 2 1 TSQ 2 3 For Research Use Only Not for use in diagnostic procedures Thermo SCIENTIFIC Regulatory Compliance Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with applicable domestic and international regulations When the system is delivered to you it meets all pertinent electromagnetic compatibility EMC and safety standards as described in the next section or sections by product name Changes that you make to your system may void compliance with one or more of these EMC and safety standards Changes to your system include replacing a part or adding components options or peripherals 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 been evaluated by TUV Rheinland of North America Inc EN 55011 1998 1999 2002 EN 61000 4 3 2
26. Vacuum Forepump V 230 50 60 Hz 15 0 A Max V 230 50 60 Hz 50 A Max System Reset O Hapdi O Vent Valve Closed O Ethernet Link OK O Ethernet 100 Base T 30V Max Start In Tl Refer to Manual Qualified D Service Personnel Only El Cl lon Source Thermo Scientific 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 TSO Quantum XLS and TSO Quantum GC User Guide 25 2 Functional Description Mass Spectrometer Figure 13 lon source of the TSQ Quantum XLS Magnets and magnet yoke EI Cl Source PCB lon source block Heater ring 000 quadrupole lens assembly L1 L2 L3 lens assembly 26 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer Figure 14 lon source of the TSQ Quantum GC Magnets and magnet yoke EI Cl Source PCB lon source Filament block Heater ring L1 L2 L3 and L4 lens assembly The ion volume located in the center of the ion source is the site where electrons interact with sample or r
27. XLS and TSO Quantum GC User Guide 43 2 Functional Description Mass Spectrometer Turbomolecular Pump A Leybold TW220 150 15S double inlet turbomolecular pump provides the vacuum for the ion source QO quadrupole region and analyzer region of the vacuum manifold The turbomolecular pump mounts onto the top of the vacuum manifold Figure 26 The turbomolecular pump has two pumping inlets e 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 QO quadrupole chambers The turbomolecular pump is controlled by a Leybold TDS controller and powered by a 24 V dc 250 W power supply The mass spectrometer circuit breaker switch and the vacuum service switch but not the electronics service switch turn power for the turbomolecular pump off and on A fan 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 inlet valve and the collision cell The pump has a maximum displacement of 650 L min and maintains a minimum pressure of approximately 1 Pa 0 01 Torr The forepump is
28. aerei aco oed do e e el oto et a d C DA GS RD 161 Chemicals Kitir idco A re eh VD pU DE RUE d en 162 Index oracle s dp gentaciAs Pe Ud a E lonis pia did tiu itd 163 iv TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific LL mm Preface The Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC systems are members of the TSQ Quantum family of mass spectrometers This TSQ Quantum XLS and TSQ Quantum GC User Guide contains a description of the modes of operation and principle hardware components of your TSQ Quantum XLS or TSQ Quantum GC system In addition this manual provides step by step instructions for cleaning and maintaining your mass spectrometer Related Documentation In addition to this 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 humans property or the environment Each CAUTION notice is accompanied by an appropriate CAUTION symbol IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Note Hig
29. box showing the TSQ Quantum mass spectrometer in use and no start instruments Change Instruments In Use TriPlus Autosampler TRACE GC Ultra TSQ Quantum Cancel Help d Click any Yes in the In Use column to clear all instruments other than the TSQ Quantum e Ensure that the TSQ Quantum has a Yes in the In 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 Note You must have the TSQ EZ Tune or QuickQuan application running so that Xcalibur can display instrument methods Torun the sequence 1 In the Run Sequence dialog box see Figure 68 on page 152 click OK to start the acquisition Xcalibur displays the Insert Probe message Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 153 8 Using the Direct Sample Probe Running the Sequence Figure 70 Insert Probe message Instrument Messages Insert probe and tighten seal Click OK to proceed or Cancel to abort ad operation DK Cancel 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 Slide the probe forward into the inlet valve until the guide ball is at the guide bar s first stop See
30. breaker located on the rear of the electronics module You can turn on the system power only with the main power circuit breaker on the rear of the electronics module and not the System Power Off switch Toturn off the mass spectrometer in an emergency CAUTION Press the System Power Off button located on the front of the electronics module See Figure 27 The System Power Off button turns off all power to the mass spectrometer including the vacuum pumps gas chromatograph and autosampler Although removing power abruptly does no harm to any component within the system under normal conditions do not shut down the system with the System Power Off button For the recommended procedure see Shutting Down the System Completely on page 53 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 51 3 System Shutdown Startup and Reset Placing the System in Standby Mode Figure 27 System Power Off button on the front of the electronics module rsa ovantum GC System Power Off button Figure 28 Power panel on the rear of the electronics module Main Power Power In GC Power Out Quantum Power Out A S Power Out V 230 V 230 50 60 Hz 10A MAX 50 60 Hz 2A MAX Placing the System in Standby Mode If you are not going to use the TSQ Quantum XLS or TSQ Quantum GC system for a short period of time such as overnight or over weekends it does not need to be shut down completely When you are not going to operate the system fo
31. detection system Replacing the electron If noise in multiplier assembly spectrum is excessive or proper electron multiplier gain cannot be achieved Electronic modules Replacing an electronic If electronic module module fails PCBs Replacing a PCB If PCB fails The frequency of cleaning the components of the mass spectrometer depends on the types and amounts of samples and solvents that are introduced into the instrument Cleaning of the Q0 Q1 Q2 and Q3 quadrupoles is rarely if ever required A Thermo Fisher Scientific Field Service Engineer must perform this maintenance procedure 84 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Cleaning lon Source Components Contents Cleaning Ion Source Components Replacing the Filament of the TSQ Quantum XLS Ion Source Replacing the Filament of the TSQ Quantum GC Ion Source Disassembling and Reassembling the TSQ Quantum XLS Ion Source Completely Disassembling and Reassembling the TSQ Quantum GC Ion Source Completely Maintaining the Forepump Adding Calibration Compound Replacing the Ball Valve Seal Removing and Installing a GC Capillary Column Cleaning lon Source Components An important part of maintaining your TSQ Quantum XLS or TSQ Quantum GC mass spectrometer is making sure that the ion source components are clean Follow the cleaning procedures in this section to clean stainless steel and non stainless stee
32. gas CI reagent gas calibration compound and air during venting into the mass spectrometer The inlet gasses hardware includes the following components Vent Valve Collision Gas Flow Control Valves e 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 Calibration Calibration Giisagent CI reagent compound compound Air 1 Ive gas valve gas port vial va filter p mS l l l Gas chromatograph pene lon source Q0 quadrupole Analyzer Collision chamber chamber chamber cell 4 x 10 5 Torr 3 x 10 6 Torr Convectron gauge Dual inlet turbomolecular pump Convectron gauge Collision gas Exhaust divert valve o Lo Forepump Argon gas port Collision gas valve Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide n 2 Functional Description Mass Spectrometer Vacuum Manifold The vacuum manifold encloses the ion source ion optics mass analyzer and ion detection system assemblies The vacuum manifold is a thick walled aluminum chamber with two removable side cover plates with openings on the front sides and top and various electrical feedthroughs and gas inlets The main vacuum manifold is divided into two chambers by a baffle Se
33. initiate the probe insertion sequence 2 Ensure that the TSQ Quantum XLS or TSQ Quantum GC mass spectrometer is the only instrument in use and that there are no start instruments Thermo Scientific TSQ Quantum XLS and TSO Quantum GC User Guide 151 8 Using the Direct Sample Probe Preparing the Mass Spectrometer if it is not already open opens see Figure 68 Run Sequence m Acquisition Options Start Instrument TRACE GC Ultra TSQ Quantum M Start When Ready ert Instrument Method Start Up Browse Shut Down Browse Programs Pre Acquisition Browse Post Acquisition Browse r Run Synchronously IV Pre Acquisition V Post Acquisition l After Sequence Set System On C Standby C Off OK Cancel 152 TSO Quantum XLS and TSQ Quantum GC User Guide Figure 68 Run Sequence dialog box showing instruments in use User QUANTUM Run Rows fi Priority Sequence m Processing Actions Quan Qual ja Reports Programs Create Guan Summary On the Xcalibur Home Page click the Sequence Setup icon to open Sequence Setup In Sequence Setup choose Actions gt Run Sequence The Run Sequence dialog box Help Click Change Instruments to open the Change Instruments In Use dialog box Thermo Scientific 8 Using the Direct Sample Probe Running the Sequence Figure 69 Change Instruments In Use dialog
34. magnet yoke on a clean lint free cloth 10 Close the lid of the ion source vacuum manifold Removing the L1 L2 L3 Lens Assembly and the 000 Quadrupole Lens Assembly Thermo Scientific The ion source includes the L1 L2 L3 lens assembly and the Q00 quadrupole 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 ion source block See Figure 49 2 Remove the Q00 quadrupole lens assembly and the L1 L2 L3 lens assembly from the heater cartridges of the ion source Place them on a clean surface TSO Quantum XLS and TSO Quantum GC User Guide 91 6 Maintenance Cleaning lon Source Components Figure 49 L1 L2 L3 lens assembly and Q00 quadrupole lens assembly removed from the ion source Q00 quadrupole lens assembly L1 L2 L3 lens assembly lon source Retainer clip Threaded standoff Disassembling the L1 L2 L3 Lens Assembly itN 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
35. mode See Placing the System in Standby Mode To shut down the TSO Quantum XLS or TSQ Quantum GC system completely 1 Cool the GC transfer line and ion source GC oven 30 C Injector off Transfer line off Jon source 30 C Note If you do not plan to change the column or perform maintenance on the gas chromatograph you do not have to lower the injector temperature 2 From the TSQ EZ Tune window choose Control Standby or click the On Standby button to put the mass spectrometer in standby 3 Place the electronics service switch located on the right side power panel in the Service Mode Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide 53 3 System Shutdown Startup and Reset Shutting Down the System Completely Figure 29 Right side power panel of the mass spectrometer Operating Mode Operating Mode D QD System Reset Q hil O Vent Valve Closed O Ethernet Link OK QO Ethernet 100 Base T OO Main Power Power In V 230 50 60 Hz 150 A Max Service Mode Electronics Service Mode Vacuum Forepump V 230 50 60 Hz 50 A Max l ior Qualified Service Personnel Only 30V Max Start In A Mode position Place the vacuum servi
36. of the data system to the Ethernet switch which is connected to the Ethernet connector on the power panel of the mass spectrometer and to the GC 48 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Data System Data System Local Area Network Interface The data system computer contains a secondary Ethernet adapter This secondary Ethernet adapter is not involved in data system mass spectrometer or GC communications You can use this secondary Ethernet adapter to access your local area network Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide 49 LLL MM System Shutdown Startup and Reset Many maintenance procedures for the TSQ Quantum XLS and TSQ Quantum GC systems require that the mass spectrometer be shut down completely In addition you can place the mass spectrometer in Standby mode if the system is not to be used for 12 hours or more Contents Shutting Down the System in an Emergency e 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 Spectrometer Components Shutting Down the System in an Emergency You can turn off all power to the mass spectrometer gas chromatograph and autosampler by pressing the System Power Off button located on the front of the electronics module or the main power circuit
37. or does not have the appropriate stationary phase for your application Change the GC column See Removing and Installing a GC Capillary Column on page 122 The GC column does not extend far enough past the end of the transfer line tip If the end of the column is inside the tip an excessive amount of GC effluent will contact the inside wall of the tip Follow the procedure described in Installing a GC Capillary Column on page 124 Possible causes solutions e No contact between the ion source temperature sensor and the heater block For accurate temperature readings of the heater block fully screw the threaded standoff into the ion source to ensure contact between the temperature sensor and the heater block See Reassembling 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 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 Possible cause solution The ion source tem
38. panel system power off button 23 mass spectrometer 53 non emergency 53 side cover plate vacuum manifold description 43 solvent ions masses 135 solvents purity requirements viii spectrometer 14 square 33 stability problems troubleshooting 143 stainless steel cleaning 113 Standby condition mass spectrometer components On Off status 60 placing system in 52 startup 55 autosampler 58 gas chromatograph GC 56 operating 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 Thermo Scientific Index T location figure 24 mass spectrometer reset 59 system shutdown emergency procedure 51 System Tune and Calibration workspace figure 66 T tables Accessory Kit 161 Chemicals Kit 162 mass spectrometer components on off status 60 mass spectrometer maintenance procedures 83 maximum allowed pressures 57 summary of scan modes 6 the 46 TRACE GC Ultra gas chromatograph configuration 19 photo 2 transfer line capillary column removing 123 cross sectional view figure 31 figure 21 functional description 20 location figure 89 96 union figure 123 TriPlus autosampler cofiguration 18 photo 2 troubleshooting autosampler communication 133 communication 131 contamination 133 filament and lens control 135 gas chromatograph communic
39. remove Sonicate the parts in a 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 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 five minutes c Ifthe 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 Sonicate the parts in acetone a Using forceps place the parts in a beaker containing acetone b Using forceps transfer the parts to a beaker containing fresh acetone c Place the beaker and contents in an ultrasonic bath again for five minutes Blow dry the parts immediately Use clean dry gas to blow the acetone off the parts Using forceps place the parts in a beaker cover the beaker with aluminum foil and put the beaker in the oven Dry the parts in an oven set at 100 C for 30 minutes Allow the parts to cool before putting them back together 114 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Disassembling and Reassembling the TSQ Quantum GC lon Source Completely Cleaning Non Stainless Steel or Hybrid Part e The
40. results from fragmented ions Fragmentation efficiency depends directly on the stability of the ion and indirectly on the mass of the ion The more stable the ion the less likely a given collision will fragment the ion Typically low mass ions require a higher collision energy to dissociate than high mass ions To 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 however due to scattering Overall CID efficiency The product of the collection efficiency and the fragmentation efficiency The overall CID efficiency exhibits a maximum with intermediate pressure As the pressure is increased beyond the optimum value more and more collisions take place the probability of scattering increases and fewer and fewer ions pass through the collision cell This results in the collection efficiency decreasing The fragmentation efficiency also decreases as the pressure is decreased from its optimum value because fewer and fewer collisions take place Quadrupole Offset Voltage Thermo Scientific The quadrupole offset voltage is a dc potential applied to the quadrupole rods in addition to the ramping dc vo
41. scan MS MS product ion scan to confirm the identity of the analyte 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 current at only these selected masses AutoSIM scans can be performed on any full scan in any scan mode but not on data dependent scans You can acquire and display mass spectral data intensity versus mass to charge ratio with the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers in one of two data types Profile data type Centroid data type In the profile data type you can see the shape of the peaks in the mass spectrum Each atomic mass unit is divided into many sampling intervals The intensity of the ion current is determined at each of the sampling intervals The profile data type displays the intensity at each sampling interval with the intensities connected by a continuous line In general use the profile scan data type when you tune and calibrate the mass spectrometer so that you can easily see and measure mass resolution 14 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 1 Introduction Mass Charge Range Centroid Data Type The centroid data type displays the mass spectrum as a bar graph and sums the intensities of each set of multiple sampling intervals This sum is displayed versus the integral center of mass of the sampling intervals
42. the European Union s Waste Electrical amp Electronic Equipment WEEE Directive 2002 96 EC It is marked with the following symbol Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union EU Member State and these companies should dispose of or recycle this product See www thermo com WEEERoHS for further information on Thermo Fisher Scientific s compliance with these Directives and the recyclers in your country WEEE Konformit t Dieses Produkt muss die EU Waste Electrical amp Electronic Equipment WEEE Richtlinie 2002 96 EC erf llen 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 entsorgt werden kann Mehr Information ber die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific ber die Verwerter und weitere Hinweise die n tzlich sind um die Produkte zu identifizieren die unter diese RoHS Anweisung fallen finden sie unter www thermo com WEEERoHS Conformit DEEE Ce produit doit tre conforme la directive europ enne 2002 96 EC des D chets d Equipements Electriques et Electroniques DEEE Il est marqu par le symbole suivant Thermo Fisher Scientific s est associ avec une ou plusieurs compagnies de recyclage dans chaque tat membre de l union europ enne
43. third rod assemblies Q1 and Q3 are quadrupoles and the second rod assembly Q2 is a square profile quadrupole Rod assemblies can operate in either of two capacities Asion transmission devices As mass analyzers If only RF voltage is applied a rod assembly serves as an ion transmission device that passes all ions within a large range of mass to charge ratios that is virtually all ions present When you apply both RF and dc voltages to a rod assembly the separation of ions of different mass to charge ratios occurs This separation allows the rod assembly to serve as a mass analyzer On the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers the quadrupole rod assemblies can operate with rf and dc voltages or with only rf voltage That is Q1 and Q3 can act either as mass analyzers or ion transmission devices 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 Table 1 Summary of scan modes Scan mode 01 quadrupole 02 collision cell 03 quadrupole QIMS Scan Pass all ions Pass all ions 03MS Pass all ions Pass all ions Scan Product Set Fragment ions then pass Scan all fragments Parent Scan Fragment ions then pass all Set fragments
44. vacuum manifold 42 vacuum service switch location figure 25 vacuum system 41 vent valve 45 mass spectrometer circuit breaker location figure 25 mechanical 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 Thermo Scientific Index N Neutral Loss scan mode discussed 9 example figure 11 illustration figure 10 0 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 figure 8 Perfluorotetracosane 157 personal computer features 48 phthalate contamination 133 power cord forepump Caution 44 Power Entry Module description 46 Power LED description 22 figure 22 mass spectrometer reset 59 mass spectrometer startup 57 power supply problems troubleshooting 140 pressure maximim allowed table 57 probe button 75 procedures adding calibration compound 117 changing ionization modes 73 cleaning ion source components 85 cleaning ion source lenses 88 95 cleaning ion volumes 88 cleaning stainless steel parts 113 complete system shutdown 53 conditioning capillary columns 125 disassembling ion source lens assembly 92 98 displaying FC 43 spectrum 64 dissassembling ion source completely 107 110 emergency shutdown 51 GC leak checking 125 installing capillary column 124 installing the ion volume
45. 002 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 EN 61000 4 11 1994 A1 2001 CISPR 11 1998 FCC Class A CFR 47 Part 15 TSQ Quantum GC EMC Directive 89 336 EEC as amended by 92 31 EEC and 93 68 EEC EMC compliance has been evaluated by TUV Rheinland of North America Inc EN 55011 1998 1999 2002 EN 61000 4 3 2002 EN 61000 3 2 1995 Al 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 EN 61000 4 11 1994 A1 2001 CISPR 11 1998 FCC Class A CFR 47 Part 15 Low Voltage Safety Compliance Compliance with safety issues is declared under Thermo Fisher Scientific sole responsibility This device complies with Low Voltage Directive 73 23 EEC and harmonized standard EN 61010 1 2001 Changes that you make to your system may void compliance with one or more of these EMC and safety standards Changes to your system include replacing a part or adding components options or peripherals 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 auth
46. 3 lens assembly See Figure 49 2 Insert the three heater cartridges of the ion source through their corresponding holes in the Q00 quadrupole lens assembly Verify the correct orientation of the guide pin hole and the retainer clip groove on the Q00 quadrupole lens assembly 3 Use the retainer clip and threaded standoff to secure the lens assemblies to the ion source IMPORTANT For accurate temperature readings of the heater block fully screw the threaded standoff into the ion source to ensure contact between the temperature sensor with the heater block Reinstalling the TSQ Quantum XLS lon Source 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 seated in the sample inlet aperture in the ion source The guide pin on the QO quadrupole mount inserts into the guide pin groove on the Q00 lens assembly The two thumbscrews are aligned with the screw holes in the QO quadrupole mount See Figure 48 3 Secure the ion source to the QO quadrupole mount by alternately tightening each thumbscrew one half turn at a time Make sure there is no play in the ion source 4 Align and reconnect the 8 pin connector to the lead pins on the EI CI Source PCB See Figure 48 5 Align the 3 pin connector such that the side with the beveled edge is clo
47. 712 Fitting ferrule SWG front 3 8 in 00101 11500 brass Ferrule 0 4mm ID x 1 16 00101 18100 Restek capillary grade hydrocarbon For removing hydrocarbons from the GC 00106 99 00001 trap carrier gas Restek high capacity oxygen trap For removing oxygen from the GC carrier 00106 99 00002 gas Cotton swabs For applying cleaning paste to stainless 00301 01 00015 steel parts Tubing 1 8 in copper pre cleaned Gas lines 00301 22701 Ball valve seal kit replacement For replacing the ball valve seal in the inlet 119265 0003 valve Thermo Scientific TSQ Quantum XLS and TSO Quantum GC User Guide 161 Chemicals Kit 9 Replaceable Parts and Consumables Table 7 Accessory Kit P N 70111 62077 Sheet 2 of 2 Description Lens alignment tool Function For aligning ion source lenses 1 2 and 3 Part number 120271 0001 Filament assembly For replacing a failed filament in the ion source 120320 0030 Nitrile gloves medium For handling clean parts that are under 23827 0008 vacuum Nitrile gloves large For handling clean parts that are under 23827 0009 vacuum Syringe 10 uL 80mm For adding calibration compound 36502019 Tee union 1 8 in 00101 01 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
48. B to dc voltages that are applied to the lenses TSO Quantum XLS and TSO Quantum GC User Guide 4 2 Functional Description Data System Data System The data system controls and monitors the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers The data system also processes data that the mass spectrometer acquires The data system is composed of the following Computer Hardware Computer Hardware Data System Mass Spectrometer GC Interface Data System Local Area Network Interface The data system computer has the following major features Intel Pentium IV processor High capacity hard disk drive Recordable rewriteable CD drive Primary Ethernet port data system to mass spectrometer Secondary Ethernet port data system to local area network High performance video graphics card CDRW drive DVD drive 1280x1024 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 data system mass spectrometer GC communications 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
49. Completely on page 49 CAUTION Shock Hazard Unplug the TSQ Quantum XLS mass spectrometer before proceeding 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 bay Filament retainer clip Figure 58 TSO Quantum XLS ion source disassembled 000 quadrupole Filament lens assembly Heater ring Centering ring O lon source block L1 L2 L3 lens assembly Heater ring and lens assemblies retainer clip EI CI Source PCB Base studs 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 108 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Thermo Scientific 10 11 6 Maintenance Disassembling and Reassembling the TSQ Quantum XLS lon Source Completely CAUTION Do not pull the EI CI Source PCB out of the ion source block This might damage the EI CI Source PCB Remove the EI CI Source PCB a Place the ion source on a clean surface with 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 Remove the retainer clip that secures the filament and centering ring to the ion source block Remove the filament and centering ring from the
50. 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 fans Place the right side power panel circuit breaker switch in the Off position Placing the right side power panel circuit breaker switch in the Off position removes all power to the mass spectrometer including the vacuum system Press the System Power Off button Pressing the System Power Off button removes all power to the mass spectrometer gas chromatograph and autosampler Table 4 summarizes the on off status of mass spectrometer components voltages and gas flows 60 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 3 System Shutdown Startup and Reset Turning Off Selected Mass Spectrometer Components Table 4 On Off status of mass spectrometer components and voltages Sheet 1 of 2 Standby Off Electronics Vacuum service MS Main power vectors J O ment gwen ea position position position Electron multiplier Off Off Off Off Off Conversion dynode Off Off Off Off Off Mass analyzer rf voltage Off Off Off Off Off Mass analyzer dc offset voltage Off Off Off Off Off QO ion optics rf voltage Off Off Off Off Off QO ion optics dc offset voltage Off Off Off Off Off Ion source filament Off Off Off Off Off Ion source h
51. Ec ER FOU E bebe a EXER EE 131 Communication Issues 6 6 6 cence eee eee 131 Contamination Issues 0 eee cc eee eee 133 Filament and Lens Control ssu s cair teal ieee Rs pedet 135 Heated Zone Issues nnno Bn wae ak eee Boa d adve be ration a e qve 136 High Vaconmts Istes ie sie derriere pore bbb c EU a 138 Linearity Issues etos 202k cna eg eren eere dee Press Rr aret eels 139 Power Supply Issues iio eek i bok st aec Re olo doro od Teo ea e dnb 140 Sensitivity Issues ie ves eos e E emus iD beens yee Fes 140 Stability Esse eA EEA Ex CET MER ee Gti SES 143 RETA S Iss s i a e X DRE VIEN OI UE OS A Bee ES SEGA eS pO 143 Pebphcnio dCDuSeo street Qd tiva tust een ge cst 145 Replacing PCBs and Power Supplies 21 pis rer o TRE RE 146 Using the Direct Sample Probe Lusseueseeseeeeees 147 Creating an Instrument Method 121 deed ES Tu ER e ded cd 147 Creating a Sequence sc cs ker x a ere Roh acte e e cree at Re erae 150 Preparing the Probe and Inlet Valve v dawn te Ep Ret eR PER en 151 Preparing the Mass Spectrometer i d lesu eon Pei aide een ee 151 Running The Sequencers cda ated eerte rien at wo eiaa eei ii eel ed dui A 153 Examining the Raw Data in Qual Browser 00 157 Removing hed tobe ers cope tod Nae wee eq xat Done cuve Maher t 158 TSO Quantum XLS and TSO Quantum GC User Guide iii Contents Chapter9 Replaceable Parts and Consumables Lusuueseeeeeeeee 161 Accessory Kits teneret
52. Ethernet Link OK LED 25 F FC 43 adding 117 mass spectrum displaying 64 observed peaks 64 on off 64 part number 162 spectrum positive EI mode 66 Thermo Scientific ferules 161 filament description 28 location figure 26 27 104 106 on off 64 part number 102 105 problems troubleshooting 135 replaceable parts 162 replacing 102 105 filters 46 fittings 161 forepump description 44 maintainence 116 power cord Caution 44 forpump power outlet figure 25 front panel LEDs Communication 22 description 22 figure 22 Power 22 Scan 23 System 23 Vacuum 22 front panel system power off button figure 23 full scan type 12 functional description autosampler 18 data system 48 direct sample probes 20 gas chromatograph GC 19 inlet valve 29 ion optics 30 mass analyzer 32 mass spectrometer 21 QO quadrupole 30 transfer line 20 TSQ Quantum GC 17 fuses mass spectrometer replacing 145 G gas chromatograph GC capillary column installing 124 capillary column removing 122 column installation 124 communication with data system 48 configuring 19 functional description 19 leak check 125 photo 2 Thermo Scientific Index G power outlet 24 startup 55 56 troubleshooting communication problems 133 guide bar figure 29 74 intalling 73 H hydrocarbon trap 161 inlet gasses hardware calibration compound 46 CI gas valve 46 collision gas valve 45 description 41 functional block diagram 41 inlet v
53. Fuses should be replaced by a Thermo Fisher Scientific Field Service Engineer Possible causes solutions The power cord is disconnected Verify that the power cord is plugged in Voltage is not coming from the electrical outlet Verify that the electrical outlet is operational The Power Module is faulty Contact Thermo Fisher Scientific Technical Support 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 If you observe a drop in instrument sensitivity you should 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 as a plugged autosampler syringe or too low sample level in the sample vial can give the appearance of instrument failure Gradual drops in sensitivity are usually the result of ion volume or lens contamination and are easily remedied by cleaning the ion volume or lenses The electron multiplier influences sensitivity and has a limited lifetime Eventually the electron multiplier must be replaced Improper GC maintenance is another cause of diminished sensitivity It is important to establish a routine maintenance program for the GC See the TRACE GC Maintenance Manual for more information on establishing a main
54. IMBETERL AIC EHESAS AHEAD YET RTF EER DGUHGREIRB IEL MRED THMORMLTFEY EMH A EAM LEST HME CRA LAUT EV TY gt BUS EDRED EIE STRUCT SV USER ERAAN PELTOA HEB Y ET BEE FRANE PARE ER MRE LU O 23 EE RR5NE RAE MALTA EWONE MEDSBL FMEHALTFSV M WAS ROKMMIMADOL HO TH ORF SBLTOTHSV AI MED HADES SBM CL AF ALMETSBSIL KORE EMOTE PRIS BIER CFD REPORT AK L CARE 8017 5 fe DRIED OE Y CERDO 4RVS do 5 VTEBERISSO FRSE SAIC L TILA MALTESE RSTRfEBR ORRERA ZA TORRBAETS OL ERLE T Xf HRB COMMA CU 538813 Ev 2 TUVO e BUCT amp U RSeMRtSFMME lt DA SEIS SEE BPRRIEL i534 0 rIv2knv n ZZn4ko0T2 h W WR bkt v4 cCCHe ESL ARE G2 RERARARPERKRARHESHRRKRER EHEZH gt LAA RERA ERER o EOS EGER E E E NS ELT RH th 3o th 77 HF PCB A HE E LEG RERA TEREA AREE AR o EMH Eo KERAN ADECER WRTTSIESESX Bt HR Bi FT NUR BEF o Hh 6 5 T1500 ALKA EE o KR EA RAE REA AR gt HB LD ORE RSE ER RRA RRA Ee AREE ESI BSR RS KM HMM ESM X KEBR RAARBBELBANPHRRERe KH RE i EE ARR UR A PAR AT AP Ro Wt Sc REE ARE la WERE ZS HEAD AE ERR AMRA PT LKR a a E Contents Lupi RET v Related Documentation 000 ccc cee tenet eens v Safety and Sp cial Notices pse dide odes d Cl o dedo e bs o Ao apes v Safety Precautions 142 end e ERR nir nio a ee EE Roa dob M band abc e vii Solvent and Gas Purity Requirements is eco bbs abe sb ur FR viii Service Phil sophy osre ue a6 p al OR Rey G
55. L3 lens assembly and the Q00 quadrupole lens assembly extract the ions formed in the ion source and transmit them to the ion optics The lens L2 voltage is mass dependent The rods of the Q00 quadrupole contact the rods of the QO quadrupole and share their rf and dc voltages In positive ion mode the lenses are adjusted to a negative potential and in negative ion mode the lenses are adjusted to a positive potential The arrangement of the lenses and their spacers enables quick and efficient pump out of the ion source 28 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Inlet Valve Thermo Scientific 2 Functional Description Mass Spectrometer The inlet valve which is attached to the front of the vacuum manifold is a vacuum sealed valve that allows you to change ion volumes or insert the direct exposure probe without venting the mass spectrometer to atmosphere You use the insertion removal I R tool 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 valve is closed it prevents the vacuum manifold from venting to atmosphere Figure 16 Inlet valve R tool guide bar and ball
56. Neutral Loss Scan Fragment ions then pass all Scan fragments aScan full scan or transmission of selected ions PPass all ions or fragments pass ions or fragments within a wide range of mass to charge ratios Fragment ions collisions with argon gas cause ions to fragment dSet set to pass ions of a single mass to charge ratio or a set of mass to charge ratios A rod assembly is a regular array of metal rods Refer to Mass Analyzer on page 32 for a discussion of the rod assemblies used on the TSQ Quantum XLS instrument 6 TSO Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific 1 Introduction Scan Modes 01MS and O3MS Scan Modes In the QIMS and Q3MS scan modes only one stage of mass analysis is performed The mass spectrum obtained is equivalent to the mass spectrum obtained from an instrument with a single mass analyzer In the one stage of analysis ions formed in the ion source enter the analyzer assembly One of the mass analyzers Q1 or Q3 is scanned to obtain a complete mass spectrum The other rod assemblies Q2 and Q3 or Q1 and Q2 respectively act as ion transmission devices In the QI MS scan mode Q1 is used as the mass analyzer in the Q3MS scan mode Q3 is used as the mass analyzer Product Scan Mode Thermo Scientific Product scan mode performs two stages of analysis In the first stage ions formed in the ion source enter Q1 which is set to transmit ions of one mass to charge ratio Ions
57. Off On 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 129 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 65 4 Tuning and Calibrating Running Auto Tune and Calibration Figure 32 EZ Tune EZ Workspace showing the FC 43 mass spectrum in El positive polarity mode before tuning and calibrating J Thermo TSQ EZ Tune EZ Workspace El FC 43 El Tune FC 43 EI Calib TSQCalib W Emission Current 48 9892 v5 T ia ele gods Se ee TSQ Quantum XLS w Fotepump Pressure 0 0033 A c uu i MN S 1417 FULL Q1MS crosi 267 lon Signal 400 219 10 95 90 85 80 75 70 55 60 55 50 45 Relative Abundance 40 35 30 551 76 57618 613 77 Ready NUM 11 17 2009 11 41 AM 56 of AdbeRdr920 i Thermo TSQ EZ Tune Running Auto Tune and Calibration Run the tune and calibration procedure after you obtain a good FC 43 ion signal To tune and calibrate your mass spectrometer automatically in the El 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 gt System Tune and Calibration to display the System Tune and Calibration dialog box 66 TSQ Quantum XLS and TSQ Quantum GC
58. SQ Quantum XLS and TSQ Quantum GC User Guide 7 1 Introduction Scan Modes Figure2 Illustration of Product scan mode Q2 RF Only A Q1 Set I Q3 Scanning Parent Scan Mode The Parent scan mode also uses two stages of analysis In the first stage ions formed in the ion source are introduced into the parent mass analyzer which is scanned to transmit parent ions sequentially into the collision cell In the second stage of analysis in the collision cell parent ions can fragment to produce product ions by unimolecular decomposition 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 obtained in the Parent scan mode parent mass spectrum data for the mass to charge ratio axis are obtained from Q1 the parent ions whereas data for the ion intensity axis are obtained from Q3 from monitoring the product ion The Parent scan mode is illustrated in Figure 3 8 TSO Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific 1 Introduction Scan Modes Figure3 Illustration of the Parent scan mode Q2 HF Only Ar Q1 Scanning Q3 Set 4e Experiments that employ the parent s
59. TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Replacing the Filament of the TSQ Quantum XLS lon Source See Figure 46 on page 86 and Figure 56 on page page 104 for the location of the ion source components Tools Needed Filament P N 120320 0030 Gloves cleanroom grade P N 23827 0008 and 23827 0009 Lint free cloth Frequency If filament fails To replace the ion source filament 1 Prepare a clean work area by covering the 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 CAUTION Shock Hazard Unplug the T Q Quantum XLS mass spectrometer before proceeding 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 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 103 6 Maintenance Replacing the Filament of the TSQ Quantum XLS lon Source Figure 56 Disassembling the TSQ Quantum XLS ion source to replace the filament Filament retainer clip Filament Heater ring and lens assemblies Heater ring and lens 2 assemblies retainer clip lon source block and EI CI Source PCB Threaded standoff 5 Unscrew the threaded standoff and remove the retainer clip that secures the heater ring and lens assemblies to the ion source block See Figure 56 6 Pul
60. Tuning and Calibrating O1 Tuning Q1MS at mass 69 00 m z Opening resolution Adjusting resolution The adjusted resolution is 13 33 at the width 0 78 Coarse resolution done Quick calibration The adjusted calibration of mass 69 0 is 0 88 Averaging Stopping Curve Q1 Quadrupole Offset set to 0 85 for all reswidths Optimizing Lens 2 for ion 69 00 m z Previous Setting 7 00 New Setting 0 80 Maximum Intensity 1 04e 06 322 Improvement Optimizing Lens 4 for ion 69 00 m z Previous Setting 10 00 New Setting Maximum Intensity 1 61le 06 60 Improvement Optimizing Lens 1 1 for ion 69 00 m z Previous Setting 5 00 New Setting 0 86 Maximum Intensity 1 93e 06 5 Improvement Optimizing Lens 1 2 for ion 69 00 m z Previous Setting 21 90 New Setting 5 00 Maximum Intensity 2 43e 06 41 Improvement Optimizing Lens 2 1 for ion 69 00 m z Previous Setting 8 45 New Setting 3 92 Maximum Intensity 2 56e 06 7 Improvement Tuning Q1MS at mass 501 97 m s Opening resolution Adjusting resolution The adjusted resolution is 14 38 at the width 0 78 Coarse resolution done Quick calibration The adjusted calibration of mass 502 0 is 0 16 Averaging Stopping Curve O1 Quadrupole Offset set to 2 00 for all reswidths Optimizing Lens 2 for ion 501 97 m z Previous Setting 7 00 New Setting 2 70 Maximum Intensity 2 97e 05 223 Improvement Optimizing Lens 1 2 for ion 501 97 m z Previous Setting 50 14 New Setting
61. User Guide Thermo Scientific 4 Tuning and Calibrating Running Auto Tune and Calibration Figure 33 System Tune and Calibration dialog box System Tune and Calibration Compound FC43 Pos lons 218 986 501 971 Algorithm Tune amp C TuneB Open optimization graph of Start Save Report Help 3 In the Compound list select FC43 pos ions This automatically selects the positively charged FC 43 ions to be used for automatic tuning and calibrating 4 Select Tune A as the tune algorithm Note Tune A is the first choice of tune algorithm if there is a regular EI or CI ion volume installed in the ion source Tune B is the first choice of tune algorithm if there is a closed EI ion volume installed 5 Click Start to start the automatic tuning and calibration procedure The Status box displays real time messages about the system tune and calibration so that you can monitor the progress of each sub procedure After a sub procedure is complete the result is reported for example whether it passed or failed At the end of the entire procedure it displays a summary ferrors occur during the automatic tuning and calibration procedure go to step 6 f 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 agai
62. ack 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 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 73 5 Changing lonization Modes Removing the lon Volume Figure 37 Insertion removal I R tool and guide bar I R tool Guide ball Guide ball hole First stop Guide ball Guide bar Bayonet lock track 2 Prepare the inlet valve and I R tool for insertion a Make sure the inlet valve is closed 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 as zm which indicates the I R tool is in position to accept the ion volume 74 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 5 Changing lonization Modes Removing the lon Volume Figure 38 Inlet valve components Inlet valve knob Inlet valve L r a a plug B Entry housing Inlet valve lever BENE down is closed up is open 3 Choose Start gt All Programs gt Thermo Instruments gt TSQ gt TSQ Tune to open the EZ Tune window 4 Click the Probe d button in the EZ Tune toolbar The Insert Probe message appea
63. age is enabled and the system is in the On state High voltage is enabled if the pressure of the analyzer chamber is below the values listed in Table 2 The Scan LED flashes blue whenever the mass spectrometer 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 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 CAUTION In an emergency to shut off all power to the mass spectrometer gas chromatograph and autosampler press the System Power Off button located at the front of the instrument Figure 10 Front panel System Power Off button System c e System Power Off io The main power circuit breaker switch labeled Main Power is located on the power panel at the back of the electronics module See Figure 11 In the Off O position the circuit breaker removes all power to the mass spectrometer gas chromatograph and autosampler In the On position power is supplied to the mass spectrometer gas chromatograph and autosampler In the standard operational mode the circuit breaker is kept in the On position Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 23 2 Functional Description Mass Spectrometer Figure 11 Rear power panel of the el
64. air 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 03 mass analyzers RF voltage dc voltage RF voltage 180 out of phase dc voltage 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 voltage varies from 0 to 840 V Voltages of the same amplitude and sign are applied to each rod pair However the voltages applied to the other rod pair are equal in amplitude but opposite in sign 34 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer Because the frequency of this ac voltage is in the radio frequency range it is referred to as rf voltage In Figure 23 the solid line represents the combined rf 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 both rf and dc voltages are applied Q1 and Q3 function as mass analyzers When only rf voltage is applied they act as ion tran
65. airs In product type experiments a parent ion is selected as usual but generally only one product ion is monitored SRM experiments are normally conducted with the product scan mode As does SIM SRM provides 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 fragment to form a product ion of the same mass to charge ratio as the selected product ion from the target compound Highly Selective Reaction Monitoring H SRM Highly selective reaction monitoring H SRM is SRM performed at higher resolution 0 4 u FWHM versus 0 7 u FWHM for SRM Intelligent Selected Reaction Monitoring iSRM Thermo Scientific In intelligent selected reaction monitoring iSRM experiments the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers perform multiple primary selected reaction monitoring SRM scans for each analyte parent ion of interest The mass spectrometer uses for quantification the sum of the intensities of an analytes primary SRM scans You specify a trigger threshold for each primary SRM scan If the intensities of all the listed primary SRM reactions for an analyte are above their trigger thresho
66. alibrating 58 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 3 System Shutdown Startup and Reset Resetting the Mass Spectrometer Resetting the Mass Spectrometer If communication between the mass spectrometer and data system computer is lost it might be necessary to reset the mass spectrometer using the System Reset button on the right side power panel Pressing the System Reset button creates an interrupt in the embedded computer This causes the embedded computer to restart in a known default state See Figure 29 on page 54 for the location of the System Reset button The procedure given here assumes that the mass spectrometer and data system computer are both powered on and operational If the mass spectrometer data system computer or both are off go to Starting Up the System after a Complete Shutdown on page 55 To reset the mass spectrometer Press the System Reset button located on the right side power panel Make sure the Communication LED is extinguished before releasing the System Reset button When you press the Reset button the following occurs An interrupt on the embedded computer causes the CPU to reboot All LEDs on the front 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 th
67. alve and direct sample probe 151 Caution 79 components figure 75 description 29 figure 29 guide bar 29 Insert Probe message 75 insertion removal I R tool inserting 76 ion volumes installing 80 lever removing 82 plug orientation 82 procedure 74 Safe to Insert Probe message 77 Insert Probe message figure 75 insertion removal I R tool figure 29 74 inserting 76 ion volumes removing and installing 79 lock position 78 unlock position 74 withdrawal Caution 79 Instrument Configuration window opening 18 19 instrument method creating 147 intelligent selected reaction monitoring SRM 13 ion detection system conversion dynode 39 description 39 electron multiplier 39 electron multiplier gain 40 electronic assemblies 47 ion gauge description 45 location figure 43 TSO Quantum XLS User Guide 165 Index L ion optics description 30 ion polarity modes discussed 5 ion source cleaning 102 105 cleaning components 85 cross sectional view figure 31 description 25 dissassembling completely 107 110 electrical connections 89 96 exploded view figure 86 87 figure 26 27 filament replacing 102 105 filament replacing 102 105 ion source lenses reinstalling 94 101 Ion Source PCB location figure 108 111 lens assembly disassembling 92 98 lens assembly removing 91 98 lenses cleaning 88 95 lenses reassembling 93 101 less assembly exploded view 93 100 location figure 89 96 re
68. an Parameters Scan Range First Mass m z 500 000 i Last Mass m z 1400 000 Scan Time s 0258 H 1 Peak width FWHM 0 70 Micto Scans Set Mass mz po Q3 Peak Width FWHM 0 70 Collision Energy V fi 5 Energy Ramp eV 0 Copy SeanE vent Paste ScanEvent 6 Click the ET CI tab to display the EI CI page see Figure 66 148 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific 8 Using the Direct Sample Probe Creating an Instrument Method Figure 66 El CI page of Instrument Setup EJ DIP test meth Instrument Setup BE Eile Quantum Help Dag S x SeanEditor El CI Method Summary be p Filament Settings TSO Quantum Number of States f State at Start of Run On On To display a chromatogram here use Quantum Open Raw File TRACE GC Ultra ml ex TriPlus REESE Emission Current wa 200 0 1 2 3 State Duration min 10 Retention Time min Calibration Gas Setting oit x Cl Method CI Gas Flow 20 CI Gas Type Methane v Use DIP DEP Probe p E e a el pim 7 Enter or select the following settings Number of States 1 State at Start of Run On Calibration Gas Setting Off e Use DIP DEP Probe vw This example is an EI experiment with a 200 uA emission current 8 Save the instrument method a Choose File gt Save As to open the Save As dialog
69. ance and Troubleshooting Manual for instructions 4 Perform a column evaluation Refer to the Column chapter of the TRACE GC Ultra Operating Manual for instructions Refer to the K Factor Quick Reference card for expected K factors for various column diameters column lengths and carrier gases Note The K factor is a measure of the resistance of the column A K factor that is too low might indicate a leak in the system while a K factor that is too high might indicate a blockage 5 Perform an automatic column leak check a Runan automatic leak check Refer to the Column chapter of the TRACE GC Ultra Operating Manual for instructions b Ifthe report indicates a leak look for leaks and use the leak detector to fix leaks at all the fittings in the GC c Repeat column evaluation and leak check procedures until no leaks can be found CAUTION Do not raise the oven temperature until you are sure the system is leak free At temperatures above 100 C oxygen exposure will destroy the column 6 Condition the capillary column according to the manufacturer s instructions New columns must be conditioned before inserting them in the mass spectrometer CAUTION Do not insert the column into the transfer line during the co The material released from the column during the conditioning column bleed will contaminate the ion source You must then clean the ion source CAUTION Never exceed the column manufacturers maximum operating temper
70. and TSO Quantum GC User Guide 127 MEN Diagnostics and Troubleshooting The TSQ Quantum XLS and TSQ Quantum GC system diagnostics can test many components of the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers If there is a problem with the instrument electronics the diagnostics can often locate the problem Replacing a faulty PCB or assembly can usually correct the problem After the PCB or assembly is replaced the diagnostic tests are rerun to verify the instrument is functioning properly Contents TSQ Quantum XLS and TSQ Quantum GC System Diagnostics Troubleshooting Replacing a Fuse Replacing PCBs and Power Supplies TSQ Quantum XLS and TSQ Quantum GC System Diagnostics The TSQ Quantum XLS and TSQ Quantum GC system diagnostics are used to test the major electronic circuits within the instrument and indicate whether the circuits pass or fail the tests 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 familiar with system operation and basic hardware theory as well as the details of the diagnostics IMPORTANT Typically only a Thermo Fisher Scientific Field Service Engineer runs diagnostic tests
71. and consumables visit www FisherLCMS com The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers use argon as a collision gas The argon must be high purity 99 995 The required gas pressure is 135 70 kPa 20 10 psig Thermo Fisher has found that particulate filters are often contaminated and are therefore not recommended Service Philosophy Servicing the TSQ Quantum XLS and TSQ Quantum GC systems consists of performing procedures required to maintain system performance standards 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 performance Only a Thermo Fisher Scientific Customer Support Engineer can perform services not described in this manual Level of Repair Thermo Fisher Scientific s service philosophy for the TSQ Quantum XLS and TSQ Quantum GC systems calls for troubleshooting to the lowest part assembly printed circuit board PCB or module listed in the Replaceable Parts chapter of this manual For mechanical failures A mechanical assembly typically is to be repaired to the level of the smallest item listed in the Replaceable Parts chapter of this manual
72. ansfer line ferrule 0 4 mm ID P N A0101 18100 Wrench open ended 5 16 in Wrench two open ended 7 16 in Wrench open ended 6 mm Frequency As needed Refer to the TRACE GC Ultra Operating Manual and the TRACE GC Ultra Maintenance and Troubleshooting Manual for additional GC column installation information To install a GC capillary column CAUTION Burn Hazard The injector oven and transfer line might be hot Allow them to cool to room temperature before touching them Note Wear clean lint and powder free gloves when you handle the column and injector ferrule 1 Connect the column to the injector Refer to the Column chapter of the TRACE GC Ultra Operating Manual for instructions Refer to the TRACE GC Ultra Quick Reference card for the column depth length for your injector 2 Set up the gas chromatograph a b C Turn on the gas chromatograph Set the oven and injector temperatures to 30 C Set the injector flow to 1 0 mL min Turn off vacuum compensation under the Right or Left Carrier menu 124 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Removing and Installing a GC Capillary Column e Dip the column outlet in a small vial of methanol Bubbles indicate there is flow through the column f Allow the column to purge for at least 10 minutes 3 Perform a manual column leak check Refer to the Ensuring Tightness chapter of the TRACE GC Ultra Mainten
73. ata Dependent Scan Mode The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers use the information in a data dependent scan mode experiment to make automatic decisions about the next step of the experiment without input from a user In data dependent scan mode you specify criteria to select one or more ions of interest on which to perform subsequent scans such as MS MS You can approach the setup of data dependent experiments in either of two ways e f 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 e f you have little information about your compound you can set up the parameters of a data dependent experiment so that if the intensity of the ion signal is above a specified threshold the mass spectrometer generates product spectra Later you can decide if the information is useful Because a data dependent scan needs to use a target ion from a previous scan the first scan event cannot be a data dependent scan Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 11 1 Introduction Scan Types Scan Types Full Scan You can operate the TSQ Quantum XLS and TSQ Quantum GC systems with a variety of scan types The mos
74. ated components as described in Cleaning Ion Source Components on page 85 The multiplier is set too low Run multiplier gain calibration in Auto Tune Calibration as described in Tuning and Calibrating on page 63 An electron multiplier older than 2 3 years may be too noisy for the multiplier gain calibration to accurately set the voltage The electron multiplier might need to be replaced Contact Thermo Fisher Scientific Technical Support The wrong type of ion volume is installed EI and CI require different 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 yP 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 Fisher Scientific Technical Support CAUTION Fuses protect the various circuits by opening the circuits whenever overcurrent occurs On the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers a failed fuse indicates a failed board or electronic module that must be replaced by a Thermo Fisher Scientific Field Service Engineer Replacing PCBs and Power Supplies CAUTION The TSQ Quantum XLS and TSQ Quantum GC mass spectrometer electronic assemblies are close packed to minimize the size of the system Due to the compl
75. ated in the chromatogram Typical forepressure readbacks are 30 to 40 mTorr in EI mode and typical manifold pressure ion gauge readback is 2 x 105 Torr with argon collision gas on and 2 x 10 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 Offgand MicroCare Micro Blast contain tetrafluoroethane which produces ions at m z 69 and 83 Issue Forepump will Possible causes solutions not turn on The forepump is off Check the forepump switch The vacuum service switch is in the Off position Place the vacuum service switch in the operating position The forepump power cable from the TSQ Quantum XLS or TSQ Quantum GC is not connected Connect the power cable The forepump is faulty Replace the forepump Issue Forepump Possible causes solutions powers on but will not f pump down 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 cover is leaking The forepump is faulty Replace the forepump 138 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 7 Diagnostics and Troubles
76. ation 133 heated zones 136 high vacuum 138 leak checking 138 linearity 139 power supplies 140 sensitivity 140 stability 143 tuning 143 TSQ Quantum GC autosampler 18 calibrating 63 data system 48 data types 14 diagnostics 129 front panel LEDs 22 functional block diagram figure 17 functional description 17 TSO Quantum XLS User Guide 169 Index V gas chromatograph 19 ion polarity modes 5 LEDs and system startup 59 mass range 15 mass spectrometer 21 operating conditions setting 58 overview 1 photo 2 scan modes 5 scan types 12 shutdown 55 Standby condition 52 53 startup 55 tuning 63 TSQ Tune Master Application diagnostics 129 tune and calibration report figure 70 saving 69 tuning discussed 63 frequency note 63 running 66 tune and calibration report 69 tuning problems troubleshooting 143 turbomolecular pump description 44 V Vacuum 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 diagram figure 42 ion gauge 45 leak checking 138 maximim allowed pressures 57 170 TSO Quantum XLS User Guide powering off 24 problems troubleshoo
77. ature 7 Connect the column to the transfer line a Shut down and vent the mass spectrometer See Shutting Down the System Completely on page 53 b Lower the GC oven temperature to 30 C and allow it to cool before continuing Thermo Scientific TSQ Quantum XLS and TSO Quantum GC User Guide 125 6 Maintenance Removing and Installing a GC Capillary Column CAUTION Burn Hazard The GC oven and transfer line might be hot Allow them to cool to room temperature before touching them Do not touch the injector when it is hot Wearing clean lint and powder free gloves unwind about one turn of the capillary column shown in Figure 64 from the column outlet end Wipe about 450 mm 18 in of the column with a tissue soaked in methanol Note Sliding a septum on the column before the transfer line nut helps you measure the proper distance between the nut and the end of the column The column should extend approximately 1 to 2 mm past the end of the transfer line Insert the column through the transfer line nut and ferrule Wipe the column again with a tissue soaked in methanol Score and break the end of the column with a scoring wafer With the magnifying glass check for an even flat cut Repeat if necessary Insert the column into the transfer line i Open the lid of the ion source vacuum chamber so that you can get a better view of the column ii Using the I R tool remove the ion volume See Removing the Ion V
78. because certain tests can overwrite system parameters Before calling a Thermo Fisher Scientific Field Service Engineer to run diagnostics consider the following Did the system fail when you were running samples Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 129 7 Diagnostics and Troubleshooting TSO Quantum XLS and TSO Quantum GC System Diagnostics Did problems occur after you performed maintenance on the instrument data system or peripherals Did you change the configuration of the system cables or peripherals just before the problem occurred If the answer is yes to the first item above there is the possibility of a hardware 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 taken If you are not successful in correcting the problem you can e mail this information to Field Service engineer Field Service can then do a preliminary evaluation of the problem before the Field Service engineer arrives at your site 130 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 7 Diagnostics and Troubleshooting Troubleshooting Troubleshooting The
79. box Thermo Scientific TSQ Quantum XLS and TSO Quantum GC User Guide 149 8 Using the Direct Sample Probe Creating a Sequence b Save the instrument method as a meth file In this example we name the instrument method Dip test meth Creating a Sequence A sequence contains sample information one sample per row In this example the sequence has one sample Note If the sequence has more than one sample Xcalibur prompts you to reload the probe after each sample 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 showing one sample in the sequence X Open Sequence Setup Home Page T EES File Edit Change Actions View GoTo Help ajue Cua as Ba o TASS ev c Status Acquisition Queue 1 Unknown data01 C xCalibur Data C Xcaliburymethods DIP test 1 Sample Type File Name Path Inst Meth Position Inj Vol Comment Run Manager Ready To Download Sequence Sample Name Working On Position Raw File Inst Method TSQ Quantum Ready to Download TRACE GC Ultra Ready to Download TriPlus Autosampler Ready to Download 150
80. c 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 Source PCB is faulty allowing emission current to leak to ground Contact Thermo Fisher Scientific Technical Support Reagent gas is leaking into the analyzer suppressing EI signal Check for presence of CI reagent ions in spectrum Replace CI Gas Flow Module if necessary Possible causes solutions The syringe injection port liner and column depth in injector are incorrectly matched See TRACE GC Ultra Operators Manual for the correct combination Sample delivery is insufficient due to a plugged syringe needle Clean or replace the syringe The injection port liner is contaminated Clean or replace the injection port liner Graphite or septa particles contaminate the injection port Clean the injection port The injector or septum is leaking Replace septum and perform leak check on the GC The capillary column is at the end of its life span Replace the capillary column TSO Quantum XLS and TSO Quantum GC User Guide 141 7 Diagnostics and Troubleshooting Troubleshooting Method development problems are present Contact Thermo Fisher Scientific Technical Support Issue Sensitivity is Possible causes solutions unstable or shows decrease with repeated injections The GC temperature ramp does not continue to a high enough temperature to elute high boiling point
81. can mode parent experiments can be used in structure and fragmentation studies as well as in survey analyses of mixtures In general parent experiments detect all compounds that decompose to a common fragment The experiments are useful for the rapid detection of a series of structural homologs that have a common fragment ion for example m z 149 for the phthalates Neutral Loss Scan Modes Thermo Scientific In the Neutral Loss scan mode the two mass analyzers Q1 and Q3 are linked together so that they are scanned at 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 ratio Then the ions are introduced sequentially into the collision cell In the second stage of analysis ions admitted to the collision cell can fragment further by metastable ion decomposition or by CID to produce product ions The product mass analyzer then separates these product ions by mass to charge ratio Neutral Loss scan mode is illustrated in Figure 4 Examples of compounds with a common neutral loss fragment appear in Figure 5 TSQ Quantum XLS and TSQ Quantum GC User Guide 9 1 Introduction Scan Modes To de
82. ce switch located on the right side power panel in the Service Place the mass spectrometer main power circuit breaker switch located on the right side power panel in the Off position When you place 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 off When power to the vent valve solenoid shuts off the vent valve opens and the vacuum manifold vents to filtered air You can hear a hissing sound as the air passes through the air filter After about two minutes the pressure of the vacuum manifold reaches atmospheric pressure 6 Unplug the power cord for the mass spectrometer CAUTION Allow heated components to cool before servicing them 54 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 3 System Shutdown Startup and Reset Starting Up the System after a Complete Shutdown Note If you plan to perform routine or preventive system maintenance on the mass spectrometer only you can leave the argon data system GC and autosampler on In this case the shutdown procedure is complete However if you do not plan to operate your system for an exte
83. components on a clean surface 92 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Cleaning lon Source Components Figure 50 11 12 L3 lens assembly exploded and assembled views Lens holder Lens L3 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 Reassembling the L1 L2 L3 Lens Assembly Ensure that the lenses are clean and dry before you reassemble the lens assembly Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 93 6 Maintenance Cleaning lon Source Components To reassemble the L1 L2 L3 lens assembly 1 Wearing clean lint and powder free gloves reinstall the lenses and spacers in the lens holder in the order and orientation shown in Figure 50 starting with lens L3 2 Reinstall the lens clip by pinching the ends with your fingers or a pair of tweezers and seating it in the lens holder 3 Insert the lens alignment tool in the TSQ Quantum XLS Accessory Kit into the lens assembly and align the lenses Reinstalling the lon Source Lens Assemblies To reinstall the ion source lens assemblies onto the ion source 1 Wearing clean lint and powder free gloves insert the three heater cartridges of the ion source through their corresponding holes in the L1 L2 L
84. 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 contaminated Clean the ion volume and lenses as described in Cleaning Ion Source Components on page 85 The ion source temperature is too low and causes the ion source to contaminate too quickly Clean ion volume and lenses as described in Cleaning lon Source Components on page 85 and then raise ion source temperature There is a problem with the filament emission current control See Filament and Lens Control Issues on page 135 for more information The electron multiplier is faulty Contact Thermo Fisher Scientific Technical Support The injection port liner or capillary column is contaminated Replace the injection port liner and trim the capillary column Issue Poor Possible causes solutions sensitivity in CI mode Stability Issues An El 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 pick or old syringe needle to clear it The filament is not aligned Remove the ion volume and check if the ion burn is centered around the small electron entrance hole Be sure the filament is properly inserted into the connector Carefully bend the filament wire to better align it with the ion vo
85. connected to the turbomolecular pump by a section of reinforced PVC tubing The power cord of the forepump is plugged into the outlet labeled Forepump on the power panel see Figure 12 on page 25 This outlet supplies power to the pump and is controlled by the main power circuit breaker switch and vacuum service switch not by the electronics service switch CAUTION Always plug the forepump power cord into the outlets labeled Forepump on the right side power panel of the mass spectrometer Never plug it directly into a wall outlet 44 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Convectron Gauges lon Gauges Vent Valve 2 Functional Description Mass Spectrometer 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 fraction of a milli Torr The voltage present at the top of the bridge depends on how fast the resistor can radiate heat which is related to the pressure The pressure measured by the Convectron gauge is monitored by vacuum protection circuitry on the Source PCB which in turn is monitored by the embedded computer on the System Control PCB The vacuum protection circuitry detects whether the foreline pressure is too high f
86. ctrometer 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 system PC a mechanical pump failure protection circuit linked to vent valve control a system reset button status LEDs and service ports The right side power panel shown in Figure 12 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 the following components Main power circuit breaker switch Surge suppressor Line filter Electronics service switch Vacuum service switch The brains of the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers are the System Control PCB The System Control PCB and embedded computer include the following PowerPC processor Serial Peripheral Interconnect SPI bus I O coprocessor Super Harvard Architecture Computer Sharc bus 46 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Thermo Scientific 2 Functional Description Mass Spectrometer Scan generator DSP Acquisition processor DSP nterbus bridge 100 base T Ethernet port The rf voltage generati
87. d chemical ionization gas 20 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer Figure 8 Transfer line GC end Inlet for calibration gas and Cl gas Mass spectrometer ion source end Mass Spectrometer The TSQ Quantum XLS mass spectrometer provides sample ionization and mass analysis of samples introduced from a gas chromatograph or direct insertion probe The mass spectrometer uses a triple quadrupole mass analyzer with an ion source external to the mass analyzer Several important features of the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers are as follows e High sensitivity and resolution e m z 10 to 3000 mass range e 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 includes the following components Controls and Indicators EI CI Ion Source e on Optics Mass Analyzer Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 21 2 Functional Description Mass Spectrometer e on Detection System Vacuum System and Inlet Gasses Hardware Electronic Assemblies Data System Controls and Indicators Five light emitting diodes LEDs are located at the upper right side of the front panel of the mass spectrometer See Figure 9 The Power LED illuminates green whenever power is supplie
88. d to the vacuum system and electronic assemblies of the mass spectrometer The Vacuum LED illuminates yellow when the turbomolecular pump is nearly at speed 8096 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 9 Front panel LEDs of the mass spectrometer Eo rH Power Vacuum Communication d E catu System Scan Table 2 Maximum allowed pressure to turn on high voltages Carrier gas Ar collision gas Maximum pressure Torr He Off 6 x 10 He On 5 x 10 H5 Off 5x10 H5 On 1 x 10 The Communication LED illuminates yellow when the mass spectrometer and the data system are trying to establish a communication link The Communication LED illuminates green when the Ethernet communication link between the mass spectrometer and the data system has been made 22 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer The System LED illuminates yellow whenever the mass spectrometer is in Standby that is high voltage is not supplied to the ion source mass analyzer or ion detection system but the mass spectrometer power is on The System LED illuminates green whenever the high volt
89. d transfer line temperatures to 30 C and allow them to cool before continuing CAUTION Burn Hazard The GC oven injector and transfer line are hot Allow them to cool to room temperature before touching them 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 open the lid 96 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Cleaning lon Source Components 5 Disconnect the connectors from the lead pins at the EI CI Source PCB lens L1 L2 L3 assembly and lens L4 assembly See Figure 48 Figure 51 TSQ Quantum GC ion source installed Q0 quadrupole mount Lens L4 connector Lens L1 L2 L3 connector EI CI Source PCB Oe I Thumbscrew A x RES H Transfer line Thumbscrew CAUTION Burn Hazard The ion source might be hot Allow the ion source to cool to room temperature before touching it Note Wear clean lint and powder free gloves when you handle the ion source 6 While holding the ion source assembly loosen the two thumbscrews that secure the ion source assembly to the Q0 quadrupole 7 Pull the ion source assembl
90. dby Mode 0c cece eee eee ee eee 52 Shutting Down the System Completely cee ee ene 53 Starting Up the System after a Complete Shutdown sees 55 Restoring Power to the TSQ Quantum XLS or TSQ Quantum GC system Uf ooo Re ARES E a a p AE 55 Stain M the GC udo Sop para dre cn eh RU EUER DEGERE GI IRR CR e N 56 Starting Up the Data Syste exo a s bibe KP DRE Le E be dos 56 Starting Up the Mass Spectrometer Wace lov soo Ever pee ae ERU Nes 56 Starting Up the Autosampler icai ELLE EE TED he aaa 58 Setting Up Conditions for Operation lt 0 issus ned arre ee ee 58 Resetting the Mass Spectrometer oss ete Ee po edd dones 58 Resetting the Data Systemic ai 1o aee Lee apeadacbearbd d ates adhe 59 Turning Off Selected Mass Spectrometer Components 00 004 60 Tuning and Calibrating 00 c cece eee eee eee eee eens 63 Displaying the EC 45 Mass Spectrum ii ico ch eh eee ede ees 64 Running Auto Tune and Calibration cease Soo caren ce eee Celer 66 Saving the Tune and Calibration Report 255 952 ie cise bia adi aves 69 Changing lonization Modes 0 ccc cece cece eee eee eens 73 Removing the Ion Volume Lis cons dies dan tn ee oce ec eee 73 Installing the Ion Volume fs tt noe t nd oA eats 04 ota MN et duct 80 ii TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Thermo Scientific Chapter 6 Chapter 7 Appendix 8 Contents Malntenallee oci ceu an ione ORC x tae a wna
91. e 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 software transfer is complete The System LED illuminates either green to indicate that the instrument is functional and the high voltages are on or yellow to indicate that the instrument is functional and it is in standby Resetting the Data System Thermo Scientific If possible use the Windows shutdown and restart procedure to shut down and restart the data system so that Windows can properly close programs and save changes to files To reset the data system by using the Windows shutdown and restart procedure 1 Choose Start Shut Down from the Windows task bar The Shut Down Windows dialog box appears 2 Select Restart and click OK to start the Windows shutdown and restart procedure 3 Observe the Windows shutdown and restart procedure on the monitor Press CTRL ALT DELETE when you are prompted to do so To complete the shutdown and TSO Quantum XLS and TSO Quantum GC User Guide 59 3 System Shutdown Startup and Reset Turning Off Selected Mass Spectrometer Components restart procedure click OK or enter your password if you have one in the Logon Information dialog box Note The communications link between the data system and the mass spectrom
92. e 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 Torr The turbomolecular pump then discharges into the forepump through the foreline The region inside the second chamber called the QO 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 evacuates the ion source region 42 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer Figure 26 Vacuum manifold interior Turbomolecular pump O ring lon gauge Sn a l E ENUAN LI T 4 im L TIS TNS _ Baffle lon gauge Collision cell Analyzer Q0 quadrupole lon source chamber chamber chamber chamber When CID is turned on the collision cell chamber inside the analyzer chamber has a user controlled argon pressure of between 1 and 4 mTorr 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 QO ion optics mass analyzer and ion detection system Two electrically conductive O rings provide a vacuum tight seal between the side cover plates and the vacuum manifold Thermo Scientific TSO Quantum
93. e bar 158 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 8 Using the Direct Sample Probe Removing the Probe 5 Store the probe in its case 6 Remove 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 Thermo Scientific TSQ Quantum XLS and TSO Quantum GC User Guide 159 LLL AM Replaceable Parts and Consumables This chapter contains TSQ Quantum XLS and TSQ Quantum GC part numbers for replaceable parts and consumables To ensure proper results in servicing the TSQ Quantum XLS or TSQ Quantum GC mass spectrometer order only the parts listed or their equivalent Contact Thermo Fisher Scientific San Jose and have your TSQ Quantum XLS or TSQ Quantum GC serial number ready These kits with replaceable parts and consumables are available for the TSQ Quantum XLS and TSQ Quantum GC Contents Accessory Kit Chemicals Kit Accessory 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 01
94. e inlet aperture in the ion source The two thumbscrews are aligned with the screw holes in the Q0 quadrupole mount See Figure 48 3 Secure the ion source to the Q0 quadrupole mount by alternately tightening each thumbscrew one half turn at a time Make sure there is no play in the ion source 4 Reconnect the connectors to the lead pins on the EI CI Source PCB lens L1 L2 L3 assembly the orientation is not important and lens L 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 Installing the Ion Volume on page 76 6 Close and secure the cover to the ion source vacuum manifold Replacing the Filament of the TSQ Quantum XLS lon 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 current is set to or if the measured emission current decreases over time then the filament has failed or is failing and requires replacement 102 TSO Quantum XLS and
95. e to check the transfer line fitting in the GC oven See High Vacuum Issues on page 138 for more information An excess amount of low m z ions such as hydrocarbons or column 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 Fisher Scientific Technical Support There is poor high m z intensity and poor resolution of low m z ions because the conversion dynode is faulty Contact Thermo Fisher Scientific Technical Support The injection rf is not calibrated Run Auto Tune Calibration as described in Tuning and Calibrating on page 63 There is a problem with the filament or lens control See Filament and Lens Control Issues on page 135 for more information 144 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 7 Diagnostics and Troubleshooting Replacing a Fuse Reagent gas is leaking into the analyzer suppressing EI signal Check for the presence of CI Reagent ions in spectrum Replace the CI Reagent Gas Flow Module if necessary Issue Weak signal Possible causes solutions Replacing a Fuse The ion volume or ion source lenses are dirty Clean the contamin
96. eagent gas molecules to form ions Three exchangeable ion volumes and ion volume holders are available for use in the ion source See Figure 15 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 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 the ion volume in its center Samples are introduced from the GC capillary column through an aperture on the side of the ion source block and then into the ion volume Gases for calibration or chemical ionization enter the ion volume through a gas inlet tube Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 2 2 Functional Description Mass Spectrometer Figure 15 EI left closed El center and CI right ion volumes and holders lon volume holder Electron entrance hole lon exit hole GC effluent Cl gas calibration gas front entrance hole Electron exit hole Cartridge heaters heat the ion source block and lens assemblies to minimize the rate at which deposits form on the ions source block ion volume and lens as
97. eater 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 Open after 2 to 4 min 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 Off Power supply electron multiplier Off Off Off On Off and conversion dynode Power supply 8 kV Off Off Off On Off PS1 power supply 24 V On On On Off Off PS2 power supply 5 15 On On Off Off Off 24 V dc PS3 power supply 36 On On Off Off Off 28 V dc Fan turbomolecular pump On On On Off Off Fan above manifold On On On Off Off Fan center wall On On On Off Off Convectron gauge foreline On On On On Off Convectron gauge collision cell On On Off On Off Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide 61 Table 4 On Off status of mass spectrometer components and voltages Sheet 2 of 2 Mass spectrometer component Ion gauge Standby At On Off o On Electronics service switch in Service Mode position Off Vacuum service switch in Service Mode position Off MS Main power circuit breaker switch in Off position Off ee i Tuning and Calibrating Tune parameters are instrument parameters that affect the intensity of the ion signal Calibration parameters are instrument parameters that affect the mass accuracy and resoluti
98. ectronics module Main Power Power In GC Power Out Quantum Power Out A S Power Out OBB V 230 V 230 V 230 50 60 Hz 16A MAX 50 60 Hz 10A MAX 50 60 Hz 2A MAX The mass spectrometer main power circuit breaker switch labeled Main Power is located on the mass spectrometer power panel in the lower corner of the right side panel of the mass spectrometer See Figure 12 In the Off position the circuit breaker removes all power to the mass spectrometer including the vacuum pumps In the On position power is supplied to the mass spectrometer In the standard operational mode the circuit breaker is kept in the On position The electronics service switch labeled Electronics is located next to the main power circuit breaker on the mass spectrometer power panel Figure 12 In the Service Mode position the switch removes power to all components of the mass spectrometer other than the vacuum system The Operating Mode position supplies power to all non vacuum system components of the mass spectrometer The vacuum service switch labeled Vacuum is located next to the electronics service switch on the mass spectrometer power panel 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 b
99. elerates the particles into the electron multiplier The electron multiplier includes a cathode and an anode The cathode of the electron multiplier is a lead oxide funnel like resistor The high voltage ring applies a potential of up to 2 5 kV to the cathode The exit end of the cathode at the anode is near ground potential The anode of the electron multiplier is a small cup located at the exit end of the cathode The anode collects the electrons produced by the cathode The anode screws into the anode feedthrough in the base plate TSO Quantum XLS and TSO Quantum GC User Guide 39 2 Functional Description Mass Spectrometer Figure 24 lon detection system showing the electron multiplier top and conversion dynode bottom Secondary particles from the conversion dynode strike the inner walls of the electron multiplier cathode with sufficient energy to eject electrons The ejected electrons are accelerated farther into the cathode drawn by the increasingly positive potential gradient The funnel shape of the cathode causes the ejected electrons not to travel far before they again strike the inner surface of the cathode which causes the emission of more electrons A cascade of electrons is then created that finally results in a measurable current at the end of the cathode where the anode collects the electrons The current collected by the anode is proportional to the number of secondary particles striking the cathode Typical
100. ence C DOCUME 1 QUANTUMSLOCALS 1 204 Sample Name Working On Seq Row 1 Position 1 Raw File C vXCaliburND atasdata01 RAW Inst Method C Xcalibursmethods DIP test TSO Quantum Running TRACE GC Ultra Ready to Download 104 E TriPlus Autosampler Dna oan an Sa n SS OO Ready to Download 500 600 700 800 900 1000 1100 1200 1300 1400 miz 704 604 504 404 Relative Abundance 30 4 204 gt RT 0 00 8 10 d Colision Cell Third Quad Dynode Vac 100 f epee Custom lon Optics First Qu 90 os AC TIC MS data01 80 Lens 1 V 25 2 Lens 2 V 6 9 Lens 3 V 25 3 Lens 4 V 46 3 Emission Current p 203 Electron Lens V 147 Electron Energy eV 70 70 60 50 40 Relative Abundance 30 Time min Num 5 10 2007 11 59 AM NOT SAVED 4 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 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 157 8 Using the Direct Sample Probe Removing the Probe Figure 77 Raw file displayed in Qual Browser Time 4 49 Intensity 1 70e4 008 Scan Filter none ff Qual Brows
101. ens 2 Voltage V May 9 2007 Optimizing Lens 1 1 for Q1MS lll Previous Setting 400 Optimum Setting ux awe 60 40 20 0 Mass 69 00m z 15 Improvement T T T T T T T 1 10 38 6 4 2 0 Lens 1 1 Voltage V May 9 2007 Optimizing Lens 1 2 for Q1MS li Previous Setting Optimum Settin 100 _ pa 9 80 60 40 20 Mass 501 97m z 6 Improvement Mass 218 99m z No Improvement 0 Mass 69 00m z 41 Improvement T T T T T T T T 1 250 200 150 100 50 0 Lens 1 2 Voltage V May 9 2007 1 In the System Tune and Calibration dialog box click Save Report The Save As dialog box appears 2 Enter the name and the path of the report and click Save TSQ Quantum XLS and TSQ Quantum GC User Guide 71 LLL AM Changing lonization Modes You can operate the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers in either EI or CI ionization mode Changing ionization modes requires changing ion volumes It is not necessary to shut down the mass spectrometer to change ion volumes The following sections describe how to change the ionization mode Contents Removing the Ion Volume Installing the Ion Volume Removing the lon Volume Tools Needed Gloves clean lint and powder free e nsert removal I R tool and guide bar NIS Frequency When you change ionization modes or as needed to clean the ion volume t To remove the ion volume 1 Install the guide bar a With the guide ball tr
102. er data01 RAW DEK E Eile Edit View Display Grid Actions Tools Window Help ax wm S Hel X e e e s n a mele lea e CIT mie Alc cp v m Jag Z Manuals UserstStumdata01 5 10 2007 11 54 15 AM 22 EIER tee RT 0 00 6 17 E ld data 1 28 NL 2 no fie 1005 71 33 3 14E8 amp X no file 203 148 TIC MS no file E data01 JK no file 803 amp X no file E no file ia iB ac 60 Relative Abundance a 3 I 3 08 4 01 it Ber vue uu fI b ELF D CT 0 0 0 5 1 0 1 5 20 2 5 3 0 35 40 45 5 0 55 5 0 Time min w data01 303 RT 1 39 AV 1 NL 4 08E7 T c CI Q1MS 500 000 1 400 000 530 5 618 5 630 5 Relative Abundance e 3 768 9 818 6 830 6 869 0 918 6 988 7 4919 6 1130 6 1218 8 1247 0 1295 3 500 500 700 800 900 1000 1100 1200 1300 1400 miz Removing the Probe t bd To remove the probe Withdraw the probe until the guide ball on the probe reaches the first stop on the guide bar Figure 71 Close the inlet valve by pushing the lever down CAUTION Close the inlet valve first Otherwise the system vents to the atmosphere Do not withdraw the probe beyond the point where the guide ball reaches the first stop in the guide bar Loosen the inlet valve knob by turning it counter clockwise Continue withdrawing the probe completely from the inlet valve by sliding it through the guide ball track in the guid
103. er determines the optimum quadrupole offset voltage for Q1 and for Q3 Mass Analyzer Lenses The TSQ Quantum XLS and TSQ Quantum GC mass analyzers have three lens sets See Figure 21 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 L 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 and automatic axial alignment of the rod assemblies The L2x lens set between Q1 and Q2 and the L3x lens set between Q2 and Q3 serve these functions To minimize the amount of collision gas that enters the mass analyzers Q1 and Q3 from the collision cell Q2 Lenses L22 and L21 on one side of Q2 and lenses L32 and L33 on the other side of Q2 act as baffles For high mass transmission it is important to maintain a low pressure in the mass analyzers To retain the collision gas Lenses L23 and L3 form two of the walls of the collision cell so they tend to hold the collision gas in the collision cell The collision gas escapes however through the same lens holes through which the ion beam passes To shield Q1 from the rf voltage applied to Q2 and vice versa L2x lens set and to shield Q3 from the rf voltage applied to Q2 and vice versa L3x lens set To focus the ion bea
104. es Mass Charge Range 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 Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide 1 1 Introduction Figure 1 TSQ Quantum GC mass spectrometer TriPlus autosampler and TRACE GC Ultra gas chromatograph T50 vawTuM GC The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers include an electron ionization chemical ionization EI CI ion source ion optics a triple stage mass analyzer and an ion detection system all of which are enclosed in a vacuum manifold Ionization of the sample takes place in the ion source 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 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 mode The mass spectrometer triple stage mass analyzer performs either one or two stages of mass analysis The mass spectr
105. et ce produit devrait tre collect ou recycl par celles ci Davantage d informations sur la conformit de Thermo Fisher Scientific ces directives les recycleurs dans votre pays et les informations sur les produits Thermo Fisher Scientific qui peuvent aider la d tection des substances sujettes la directive RoHS sont disponibles sur www thermo com WEEERoHS CAUTION Symbol p OPP f CAUTION Electric Shock This instrument uses high voltages that can cause personal injury Before servicing shut down the instrument and disconnect the instrument from line power Keep the top cover on while operating the instrument Do not remove protective covers from PCBs Chemical This instrument might contain hazardous chemicals Wear gloves when handling toxic carcinogenic mutagenic or corrosive or irritant chemicals Use approved containers 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 in the above categories Also this symbol appears on the instrument to refer the user to instructions in this manual When the safety of a procedure is questionable contact your l
106. eter should automatically reestablish after you reset the data system When this occurs the Communication LED on the front panel of the mass spectrometer illuminates yellow and then green If the system is unable to reestablish the communications link press the System Reset button on the power panel of the mass spectrometer Turning Off Selected Mass Spectrometer Components There are different ways that you can turn off some or all of the mass spectrometer components Turn off individual mass spectrometer components from the TSQ EZ Tune window Turning off individual mass spectrometer components might be necessary when you are troubleshooting or when you are running certain diagnostic procedures Place the mass spectrometer in Standby mode Standby is the normal condition to leave the mass spectrometer in when it is not in use Choose Control Standby or toggle the On Standby button from the TSQ EZ Tune window to place the mass spectrometer in standby Place the mass spectrometer in the Off condition The Off condition is similar to Standby except all high voltage components of the mass spectrometer are turned off Choose Control gt Off from the TSQ EZ Tune window to place the mass spectrometer 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
107. etween 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 Press the heater ring and lens assembly onto the ion source block Use the retainer clip and threaded standoff to secure the lens assembly to the ion source See Figure 58 IMPORTANT For accurate temperature readings of the heater block fully screw the threaded standoff into the ion source to ensure contact between the temperature sensor with the heater block Reinstall the ion source into the vacuum manifold See Reinstalling the TSQ Quantum XLS Ion Source on page 94 Restart the system See Starting Up the System after a Complete Shutdown on page 51 112 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Disassembling and Reassembling the TSQ Quantum GC lon Source Completely Cleaning Stainless Steel Parts e Thermo Scientific Tools Needed e 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 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 and 23827 0009 Glycerol reagent grade Lint free cloth Protective eyewear
108. exity of removing and reinstalling the mass spectrometer electronic assemblies only a Thermo Fisher Scientific Field Service Engineer can replace electronic assemblies Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 145 7 Diagnostics and Troubleshooting Replacing PCBs and Power Supplies 146 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific LLL m Using the Direct Sample Probe With the direct sample probes direct insertion probe and direct exposure probe you can introduce compounds directly into the ion source without GC column separation This chapter covers step by step a direct insertion probe DIP experiment using perfluorotetracosane CF4 CF5 55CF5 molecular weight 1238 18 melting point 190 C You can perform a similar experiment using your compound Contents Creating an Instrument Method Creating a Sequence Preparing the Probe and Inlet Valve Preparing the Mass Spectrometer Running the Sequence Examining the Raw Data in Qual Browser Removing the Probe Creating an Instrument Method An instrument method contains 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 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
109. following topics discuss possible TSQ Quantum XLS and TSQ Quantum GC 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 transfer between the mass spectrometer and the data system Mass spectrometer gas chromatograph and autosampler current status readbacks nstrument control method downloading and uploading Start stop pause and initialize functions Error messages How does the MS communication work The flow of digital information in the TSQ Quantum XLS and TSQ Quantum GC systems is bi directional the data system downloads analytical methods to the instrument and activates functions to start stop shut down start up and initialize The TSQ Quantum XLS and TSQ Quantum GC systems report their readiness state current tasks various voltages heated zones and pressure readings 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 mechanical faults for instance a cable might be unplugged or a device might be turned off In other cases the instrument method could be incorrect for TSQ Quantum XLS or TSQ Quantum GC system operations Less common communication issue
110. ght be attributed to linearity Issue Calibration plots Possible causes solutions not sufficiently linear TIN 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 ion volume and lenses are dirty Clean ion volume and lenses as described in Cleaning Ion Source Components on page 85 The electron multiplier setting is incorrect Run Auto Tune Calibration as described in Tuning and Calibrating on page 63 The injection port liner or capillary column is dirty Change the injection port liner and trim the capillary column Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 139 7 Diagnostics and Troubleshooting Troubleshooting The capillary column stationary phase is too thin for high concentration samples Use a higher capacity capillary column with a thicker stationary phase or use a split injection technique The capillary column is bad Replace the capillary column See Removing and Installing a GC Capillary Column on page 122 Power Supply Issues Issue TSQ Quantum XLS will not power on Issue The TSQ Quantum XLS powers on but trips the circuit breaker Sensitivity Issues Xcalibur diagnostics detect most power supply issues Power supply problems often involve a blown fuse faulty electronic components or something as simple as a disconnected cable
111. he FC 43 mass spectrum To display the FC 43 mass spectrum 1 Choose Start gt All Programs gt Thermo Instruments gt TSQ gt TSQ Tune to open the EZ Tune window 2 Choose a polarity mode In this example the mass spectrometer is in positive polarity 4 mode If necessary toggle the polarity button Positive Negative Note For EI negative polarity mode you might have to set the calibration gas flow to high S d 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 QIMS Scan range entry mode FM LM 64 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 4 Tuning and Calibrating Displaying the FC 43 Mass Spectrum First mass 50 Last mass 650 Scan time 0 500 Figure 31 Define Scan dialog box Define Scan Scan Type Full Scan HSRM SRM Scan Mode QIMS Q3MS Product Scan Parameters Scan Range Scan Time fo 500 FM LM First Mass 50 000 SetMass 150 000 cci Last Mass 650 000 Colision Energy Entry Mode g20DGas fo Apply Abort Help 5 Click Apply to apply the settings d d 6 Click the Calibration Gas button in the EZ Tune toolbar to turn on the flow of calibration gas into the ion source Cal Gas Off On D 7 Click the Filament button in the EZ Tune toolbar to turn on the filament Filament
112. he calibration gas flow module Be sure that there is less than 0 1 mL of the calibration compound in the vial 6 Add the calibration 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 frit then you have too much in the vial Immediately pour out the excess calibrant according to local environmental regulations 118 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Adding Calibration Compound 7 Remove the syringe from the calibration compound vial Figure 61 Calibration compound vial Ferrule Nut Calibration compound vial 8 Inspect the 1 4 in ferrule for damage Replace it if necessary P N 95001 20310 9 Reinstall the calibration 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 sys
113. he ion volume 1 Remove the ion volume See Removing the Ion Volume on page 73 CAUTION Burn Hazard The ion volume might be hot Allow the ion volume to cool to room temperature before touching it 2 Clean the ion volume See 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 3 Reinstall the ion volume See Installing the Ion Volume on page 80 Cleaning Lenses of the TSQ Quantum XLS lon Source If cleaning the ion volume does not restore system performance clean the ion source lenses To clean the ion source lenses 1 Shut down and vent the system See Shutting Down the System Completely on page 53 CAUTION Shock Hazard Unplug the TSQ Quantum XLS mass spectrometer before proceeding CAUTION Burn Hazard The ion source might be hot Allow the ion source to cool to room temperature before touching it 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 and the spacers See Cleaning Stainless Steel Parts on page 113 and Cleaning Non Stainless Steel or Hybrid Part
114. hlights information of general interest Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide v Preface Tip Highlights helpful information that can make a task easier vi TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Preface Safety Precautions gt gt po o Thermo Scientific Observe the following safety precautions when you operate or perform service on the mass spectrometer CAUTION Do Not Perform Any Servicing Other Than That Contained in the TSQ Quantum XLS and TSQ Quantum GC User Guide To avoid personal injury or damage to the instrument do not perform any servicing other than that contained in the TSQ Quantum XLS and TSQ Quantum GC User Guide or related manuals unless you are authorized to do so CAUTION Shut Down the Mass Spectrometer and Disconnect It From Line Power Before You Service It High voltages capable of causing personal injury are used in the instrument Some maintenance procedures require that the mass spectrometer be shut down and disconnected from line power before service is performed Do not operate the mass spectrometer with the top or side covers off Do not remove protective covers from PCBs CAUTION Respect Heated Zones Treat heated zones with respect 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 Fxhaust System
115. hooting Troubleshooting Issue Turbo pump Possible cause solution shuts off during operation The foreline pressure is too high Check for leaks in the foreline Issue Unexpected full Possible causes solutions ventilation occurs i A gross leak is present Check for leaks The system was vented through the inlet valve Close and plug the inlet valve The GC column broke at the transfer line Replace the GC column See Removing and Installing a GC Capillary Column on page 122 The foreline was cut Replace the foreline hose Issue Vacuum is faulty Possible Solutions A gross leak is present Check for leaks The pressure in the analyzer region of the vacuum manifold as measured by the ion gauge must be below the pressures listed in Table 3 on page 57 Linearity Issues Linearity issues occur when a plot of intensity versus concentration of a known compound is not linear Poor instrument 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 maintenance to minimize linearity problems Usually a hardware fault that affects linearity shows different issues than those that mi
116. iPlus autosampler from the data system computer Select the TriPlus instrument button in the Instrument Configuration window which is available by choosing Start gt All Programs gt Xcalibur gt 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 gt All Programs gt Xcalibur gt Xcalibur and click Instrument Setup to open the Instrument Setup window Then click the TriPlus icon to open the TriPlus Autosampler page Refer to the Help for instructions on running the TriPlus autosampler Refer to the documentation provided with the autosampler for maintenance procedures 18 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific 2 Functional Description Gas Chromatograph Gas Chromatograph The Thermo Scientific TRACE GC Ultra gas chromatograph GC separates a sample mixture into its chemical components by gas chromatography In gas chromatography the sample mixture is partitioned between a solid stationary phase and a mobile gas The stationary phase is adhered to the inside of a small diameter glass tube the capillary column The molecular structure of each component of the mixture determines in which order each component elutes from the GC and enters the mass spectrometer The TRACE GC Ultra gas chromatograph is shown in Figure 1 on page 2 Gas chromatography is widely used in anal
117. ific TSO Quantum XLS and TSO Quantum GC User Guide 81 5 Changing lonization Modes Installing the lon Volume 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 82 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Maintenance This chapter describes routine maintenance procedures that you must perform to ensure optimum performance of the TSQ Quantum XLS or TSQ Quantum GC mass spectrometer Optimum performance of the mass spectrometer depends on the maintenance of all parts of the instrument You are responsible for maintaining your instrument properly by performing the maintenance procedures on a regular basis Note When you perform maintenance 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 lists routine and infrequent mass spectrometer maintenance procedures For instructions on maintaining the GC or autosampler refer to the manuals that come with the GC or autosampler Table 6 Maintenance procedures Sheet 1 of 2 Mass spectrometer Procedure Procedure Freq
118. ill go and then rotate it 90 clockwise to lock the guide bar in the entry housing 4 Prepare the inlet valve for insertion a Make sure the inlet valve is closed 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 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 gt All Programs gt Thermo Instruments gt TSQ gt TSQ Tune to open the EZ Tune window 6 Click the Probe 2 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 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 8 Click OK The forepump evacuates the inlet valve Wait for the safe to insert probe message to appear Figure 41 then click OK 9 Once evacuation is complete pull the inlet valve lever up to open the inlet valve 80 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 5 Changing lonization Modes Installing the lon Volume 10 Install the ion volume a Slide the I R tool and ion volume assembly into the vacuum manifold until the ion volume assembly is fully inserted and sea
119. ing 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 96 cathode electron multiplier description 39 Cautions emergency shutdown 23 51 forepump and line power 44 I R tool removal withdrawing 79 Ion Source PCB removal 109 111 removing ion source and capillary column 89 96 replacing fuses 145 replacing PCBs and power supplies 145 centroid scan defined 15 chemical ionization CI discussed 4 gas valve description 46 methane 4 removing ion volume 73 Chemicals Kit 162 circuit breaker 23 24 cleaning aluminum parts 115 ceramic parts 115 frequency 83 ion volumes 88 lenses L1 L2 L3 L4 88 95 TSO Quantum XLS User Guide 163 Index D list table 83 stainless steel parts 113 collision cell figure 34 location figure 43 collision energy Q2 offset voltage 38 collision gas description 36 collision gas valve description 45 collision induced dissociation discussion 36 column bleed contamination 133 Communication LED description 22 figure 22 mass spectrometer reset 59 mass spectrometer startup 57 compliance regulatory iii WEEE vii computer features 48 consumables 161 contamination column bleed 133 septum bleed 133 solvent ions 135 troubleshooting 133
120. installing 94 102 removing 89 96 ion source block location figure 26 27 ion source chamber location figure 43 Ion Source PCB location figure 26 27 89 96 107 110 reinstalling 109 112 removal 109 111 removal Caution 109 111 ion transmission device defined 6 rod assembly 6 ion volumes attaching and removing from I R tool 79 cleaning 88 figure 28 installing 80 location figure 81 removing 73 ionization modes changing 73 chemical ionization CI 3 discussed 3 electron ionization EI 3 iSRM scan type 13 L leak check GC 125 166 TSO Quantum XLS User Guide 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 LED mass spectrometer startup 57 Vacuum LED 22 Vent Valve Closed 24 Vent Valve Closed figure 25 lens alignment tool 161 lens L1 L2 L3 and L location figure 26 27 lenses analyzer assembly voltages applied to 39 ion source lenses exploded view 93 100 ion source lenses reassembling 93 101 ion source lenses reinstalling 94 101 L1 L2 L3 exploded view 93 100 L1 L2 L3 L4 figure TSQ Quantum XLS 26 L1 L2 L3 L4 location figure 27 L1 L2 L3 L4 cleaning 88
121. ion source block Clean the ion source block and lenses See Cleaning Stainless Steel Parts on page 113 Clean non stainless steel parts as described in Cleaning Non Stainless Steel or Hybrid Part on page 115 To reassemble the ion source Reinstall the EI CI Source PCB and filament 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 IMPORTANT Ensure that the temperature sensor is seated snugly 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 Press the heater ring and lens assemblies onto the ion source block Use the retainer clip and threaded standoff to secure the lens assembly to the ion source See Figure 58 IMPORTANT For accurate temperature readings of the heater block fully screw the threaded standoff into the ion source to ensure contact between the temperature sensor with the heater block Reinstall the ion source into the vacuum manifold See Reinstalling the TSQ Quantum XLS Ion Source on page 94 Restart the system See Starting Up the System after a Complete Shutdown on page 51 TSO Quan
122. ir pongase en contacto con la Oficina de Asistencia Tecnica local para los productos de Thermo Fisher Scientific San Jose AVVERTENZA Shock da folgorazione l apparecchio alimentato da corrente ad alta tensione che puo provocare lesioni fisiche Prima di effettuare qualsiasi intervento di manutenzione occorre spegnere ed isolare l apparecchio dalla linea elettrica Non attivare lo strumento senza lo schermo superiore Non togliere i coperchi a protezione dalle schede di circuito stampato PCB Prodotti chimici Possibile presenza di sostanze chimiche pericolose nell apparecchio Indossare dei guanti per maneggiare prodotti chimici tossici cancerogeni mutageni 0 corrosivi irritanti Utilizzare contenitori aprovo e seguire la procedura indicata per lo smaltimento dei residui di olio Calore Attendere che i componenti riscaldati si raffreddino prima di effetturare l intervento di manutenzione Incendio Adottare le dovute precauzioni quando si usa il sistema in presenza di gas infiammabili Pericolo per la vista Gli schizzi di prodotti chimici o delle particelle presenti nell aria potrebbero causare danni alla vista Indossare occhiali protettivi quando si maneggiano prodotti chimici o si effettuano interventi di manutenzione sull apparecchio Pericolo generico Pericolo non compreso tra le precedenti categorie Questo simbolo e utilizzato inoltre sull apparecchio per segnalare all utente di consultare le istruzi
123. is too high Lower it tol mL min TSO Quantum XLS and TSO Quantum GC User Guide 143 7 Diagnostics and Troubleshooting Troubleshooting Issue Poor high mass response The multiplier is near the end of its lifetime Multipliers typically last about 2 to 3 years before they are too noisy for the gain to be set accurately Contact Thermo Fisher Scientific Technical Support The multiplier power supply is faulty Contact Thermo Fisher Scientific Technical Support The filament is the source of too much background noise See Filament and Lens Control Issues on page 135 for more information Chemical background in the manifold is elevated Remedy leaks or sources of water contamination in carrier gas See High Vacuum Issues on page 138 for more information The difference between the electron energy and the setpoint is greater than 5 V Contact Thermo Fisher Scientific Technical Support for assistance Possible causes solutions Poor high m z ion intensity because the ion source temperature is too high Reduce the ion source temperature to reduce the amount of thermal decomposition and fragmentation of your analyte 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 sur
124. it b ed n Rd i e een OPE viii Level of Repaltza a iita dici e dedos e ode aie e det de eed deg ed agi viii Contacting Us ersi erdie e Ne te e et reae da e Rae en ix Chapter Introduction yom Ap fee cece cence eee ene nrnna 1 Ionization Modes iN fee e acexo Ex ar E Siew e eg aes mee Eas 3 Electron Ionization Mode 2 1 0 cece ene eee 4 Chemical Ionization Mode 12 02 0 ccc ete ena 4 Ion Polarin MQAes i 1453445 OEC REDE ROUGE wehe Rese Diar d 5 Ment 46i b RTT 5 QIMS and Q3MS Scan Modes isses eens 7 Product Scan Mod esc ee odes ates dde Mates d bah os Pear ab d 7 Parent Scan Modes e Re RR ERA A E ERE URS paris 8 Neutral Loss Scan Modes 2 02 0 cece eee e nen esee 9 Dare Dependent Scan Made ois eer er po be e e RE E E e 11 Scan Types TEC MC 12 FU viu 12 Selected Ion Monitoring SIM sega Rh RR bER REO ERR UR ERR 12 Selected Reaction Monitoring SRM i sicspotakus pe tusesaesaseuaes 13 Highly Selective Reaction Monitoring H SRM 000 13 Intelligent Selected Reaction Monitoring iSRM 0 00004 13 Quantitation Enhanced Data Dependent MS QED MS 14 AutoSIM isi ees rate he ease tht Sea eb Pd NUR Saw Gace 14 Data TYPES P P 14 Profile Dati Type cs esaaaua edt des tisa sare otai r E EEE 8d 14 Cepiroid Data Type 224b eb ach ROC ey a E HOw ces 15 Mass Charge Rangers sesso quic dor CR aU d FAXO E C EC Ee e dee 15 Chapter2 Functio
125. ive or semi quantitative analysis of materials that don t require a GC column separation or are difficult if not impossible to elute chromatographically such as solids The direct sample probes introduce samples directly into the ion source via a vacuum interlock A single controller box Figure 7 with interchangeable probe tools makes it easy to select the best method of sample introduction The direct sample probe system includes two probe tools Direct exposure probe Direct insertion probe TSO Quantum XLS and TSO Quantum GC User Guide 19 2 Functional Description Transfer Line The direct exposure probe DEP has a heated filament that rapidly vaporizes liquids or solutions The DEP is ideal for rapid molecular weight confirmation of liquids or solids dissolved in a suitable solvent The DEP can vaporize compounds with a high boiling point The direct insertion 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 it passes from the GC into the ion source in the mass spectrometer This prevents the sample from condensing The transfer line includes an inlet for calibration gas an
126. l parts When your mass spectrometer is clean and in good working order perform benchmark tests and record the results When the tested performance of your 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 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 have all the tools needed before starting each procedure Figure 46 shows an exploded view of the ion source assembly Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 85 Figure 46 lon source assembly of the TSQ Quantum XLS exploded and assembled views 86 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Figure 47 lon source assembly of the TSQ Quantum GC exploded and assembled views 87 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Cleaning lon Source Components Cleaning lon Volumes You do not need to vent the mass spectrometer to atmosphere to clean the ion volume Toclean t
127. l 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 Note Now is a good time to clean the ion source block and lenses Use the procedure described in Cleaning Stainless Steel Parts on page 113 to clean the ion source block and lenses 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 104 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Replacing the Filament of the TSQ Quantum GC lon Source c Align the filament leads with the EI CI Source PCB connectors and gently press the leads into the connectors Normally there is a small gap about 0 016 in between the filament and the connectors The gap allows the ceramic centering ring to properly position and align the electron lens hole with the ion volume d Secure the filament and centering ring with the retainer clip 10 Press the heater ring and lens assemblies onto the cartridge heaters on the ion source block 11 Use the retainer clip and threaded standoff to secure the lens assemblies to the ion source IMPORTANT For accurate tempera
128. lds and if all these scans are within a specified retention time window then the mass spectrometer performs secondary SRM scans to confirm the identity of the analyte The maximum number of secondary SRM reactions is 12400 TSO Quantum XLS and TSO Quantum GC User Guide 13 1 Introduction Data Types The mass spectrometer uses reference SRM scans to adjust the acquisition time window of subsequent SRM scans It uses the time difference between the expected and observed retention times of reference SRM reactions to correct the retention times that it uses to make procedural decisions The mass spectrometer still records data with the true retention times You should specify two to four reference reactions spaced throughout the LC run The mass spectrometer uses the preceeding two retention time corrections to calculate a piecewise linear retention time correction for the primary SRM scans that follow As with primary SRM scans reference SRM scans may trigger secondary SRM scans The maximum number of primary plus reference SRM transitions is 3600 Quantitation Enhanced Data Dependent MS QED MS AutoSIM Data Types Profile Data Type Quantitation enhanced data dependent MS QED MS scan type provides simultaneous quantitation SRM and structural confirmation full scan MS MS product ion spectra If the intensity of an SRM reaction that you specify for a parent ion is above its trigger threshold the mass spectrometer performs a full
129. leaning 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 TSO Quantum XLS and TSO Quantum GC User Guide 115 6 Maintenance Maintaining the Forepump Rinse the parts with clean water Use a clean applicator or toothbrush to remove the aluminum oxide slurry Do not let the slurry dry on the metal dried aluminum oxide is difficult to remove Scrub all of the parts with a warm detergent solution a Scrub the parts with a toothbrush or clean applicator Do not soak or sonicate the parts in detergent b Using forceps rinse the parts thoroughly with tap water to remove the detergent CAUTION Do not leave aluminum parts such as the heater ring in the detergent Basic solutions like detergent discolor aluminum Rinse the parts in deionized water Using forceps dip the parts in a beaker of deionized water Change the water if it becomes cloudy Do not soak or sonicate the parts Rinse the parts with acetone Using forceps dip the parts in a beaker of acetone Change the acetone if it becomes cloudy Do not soak or sonicate the parts Blow dry the parts immediately Use 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
130. led by the data system You can set the collision gas pressure 0 to 5 milli Torr 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 36 Argon enters the mass spectrometer through a 1 8 in port on the left side of the mass spectrometer TSO Quantum XLS and TSO Quantum GC User Guide 45 2 Functional Description Mass Spectrometer A second proportional valve allows the forepump to evacuate the Q2 collision cell of argon and waste gasses when CID is turned off The mass spectrometer automatically opens and closes the collision gas evacuation valve depending on whether Q2 is acting as an ion transmission device or a collision cell Calibration Compound and CI Reagent Gas Flow Control The calibration compound gas flow control valve controls the flow of calibration compound gas into the ion source via the transfer line The calibration gas flow can be either high or low Normally low flow is used but high flow might be necessary for negative ion CI calibration The CI gas flow control valve controls the flow of chemical ionization reagent gas into the ion source via the transfer line The maximum CI gas flow rate is about 4 mL min depending on the gas Electronic Assemblies The electronic assemblies that control the operation of the mass spe
131. ll the heater ring off the ion source 7 Unscrew and remove the three base studs CAUTION Shock Hazard Do not pull the EI CI Source PCB out of the ion source block This might damage the EI CI Source PCB 8 Remove the EI CI Source PCB a Place the ion source on a clean surface with 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 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 111 6 Maintenance Disassembling and Reassembling the TSQ Quantum GC lon Source Completely 11 Clean the ion source block and lenses See Cleaning Stainless Steel Parts on page 113 Clean non stainless steel parts as described in Cleaning Non Stainless Steel or Hybrid Part on page 115 To reassemble the ion source Reinstall the EI CI Source PCB and filament 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 IMPORTANT Ensure that the temperature sensor is seated snugly 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 b
132. ltage The offset voltage applied to the two rod pairs of the assemblies is equal in magnitude and equal in sign The quadrupole offset voltage accelerates or decelerates ions and therefore sets the TKE of the ions as they enter the quadrupole rod assembly TSO Quantum XLS and TSO Quantum GC User Guide 37 2 Functional Description Mass Spectrometer In general for a given experiment the mass spectrometer has fixed offset voltages for O1 and Q2 However in MS MS experiments the quadrupole offset voltage applied to Q3 usually varies as a scan proceeds The mass spectrometer automatically computes the Q3 quadrupole offset voltage necessary and then varies the voltage as appropriate as each scan proceeds The offset voltage applied to Q2 which contains the collision cell is responsible for the collision energy The collision energy is the difference in potential between the ion source where parent ions are formed and Q2 where they collide with collision gas As the offset voltage on Q2 increases the TKE of the parent ions also increases As a result increases in the Q2 offset voltage increase the energy of ion Ar collisions The collision energy is usually ramped downward with m z to promote the fragmentation of low mass ions Before obtaining any mass spectra the mass spectrometer tunes Q1 in the Q1MS scan mode Q2 and Q3 rf voltage only and tunes Q3 in the Q3MS scan mode Q1 and Q2 rf voltage only During tuning the mass spectromet
133. lume The ion volume is not inserted properly While running the instrument you can push on the ion volume with the I R tool Be sure to monitor the pressure to ensure that you get a good seal around the I R tool Otherwise you may damage the filament An increase in signal calibration gas as you push on the ion volume usually indicates that the filament is not aligned properly Stability helps provide consistent instrument precision and the reproducibility of accurate results Good operating conditions for the mass spectrometer gas chromatograph and autosampler contribute to instrument stability 142 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Issue The signal response is unstable or drops out unexpectedly Tuning Issues Issue Cannot find Calibration Gas error message received Issue The electron multiplier gain calibration fails Thermo Scientific 7 Diagnostics and Troubleshooting Troubleshooting 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 lenses or checking for air leaks Usually a hardware fault that affects stability shows different issues than those which might be attributed to stability Possible causes solutions There is a problem with the filament or lens control
134. ly the electron multiplier is set to a gain of about 3 x 10 that is for each ion or electron that enters 3 x 10 electrons exit in MS mode and 2 x 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 detection system of the mass spectrometer increases signal and decreases noise The high voltage applied to the conversion dynode results in a high conversion efficiency and increased signal That is for each ion striking the conversion dynode many secondary particles are produced The increase in conversion efficiency is more pronounced for more massive ions than it is for less massive ions Because of the off axis orientation of the ion detection system relative to the mass analyzer neutral molecules from the mass analyzer tend not to strike the conversion dynode or electron multiplier As a result noise from neutral molecules is reduced 40 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer Vacuum System and Inlet Gasses Hardware The vacuum system evacuates the region around the ion source ion optics mass analyzer and ion detection system The principal components of the vacuum system include the following Vacuum Manifold e Turbomolecular Pump Forepump Convectron Gauges Ion Gauges The inlet gasses hardware controls the flow of collision
135. m 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 38 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer The voltage applied to each of the lenses can vary from about 300 to 300 V Typically however the voltage applied to the first and third elements of the L2x lens set is somewhat greater than the quadrupole offset voltage applied to Q1 Because the Q1 quadrupole offset voltage is generally set to about 5 V depending on the charge of the ions of interest the voltage applied to lenses L21 and L23 is typically about 10 V for positive ions and 10 V for negative ions The voltage applied to the central lens of the L2x lens set is typically about 225 V In the Q3MS scan mode the voltage applied to the lenses of the L3x lens set is about the same as that applied to the corresponding lens in the L2x lens set Note however that in the MS MS scan modes the voltage applied to the L3x lens set automatically varies with the quadrupole offset voltage applied to Q3 As the Q3 quadrupole offset voltage ramps the voltages applied to the lenses ramp correspondingly Lens L is located between Q3 and the ion detection system L4 is held at ground potential Its p
136. m a full tune and calibration of the instrument in the negative ion mode 8 Save the calibration file as follows a Click Save Calib As to open the Save Calibration File dialog box b Inthe File Name box enter a name for your calibration file 68 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 4 Tuning and Calibrating Saving the Tune and Calibration Report c Click Save to save the calibration file The Save As dialog box appears 9 Save the tune method file as follows a Inthe 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 from the tune and calibration report follow Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 69 4 Tuning and Calibrating Saving the Tune and Calibration Report Figure 35 Tune and calibration report status page 91 O O S ds uds us ce 0n oOo550 1U UU CO OOOOOOOOOOOOOOOOOOOOOOOOOOOooOooooocoooocoocooocoooococococococo May 09 2007 11 17 28 155429 5573 93 Quantum Tune Master Tune and Calibration Results from System Tune and Calibration using FC43 Pos Ions Q1 and Q3 Tuning amp Calibrating
137. mbly 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 and the spacers See Cleaning Stainless Steel Parts on page 113 and Cleaning Non Stainless Steel or Hybrid Part on page 115 respectively 5 Reassemble the ion source lens assembly and install it onto the ion source See Reassembling the L1 L2 L3 Lens Assembly on page 93 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 95 6 Maintenance Cleaning lon Source Components 6 Reinstall the ion source into the mass spectrometer See Reinstalling the TSQ Quantum XLS Ion Source on page 94 7 Restart the system See Starting Up the System after a Complete Shutdown on page 51 Removing the TSQ Quantum GC lon Source Remove the ion source to clean the lenses or replace the filament Tools Needed e Gloves cleanroom grade P N 23827 0008 and 23827 0009 e int free cloth Jar Frequency As needed to perform ion source maintenance To remove the ion source CAUTION Do not remove the ion source without first pulling back the capillary column or else the capillary column might break 1 Shut down and vent the TSQ Quantum GC mass spectrometer See Shutting Down the System Completely on page 49 CAUTION Shock Hazard Unplug the TSQ Quantum GC mass spectrometer before proceeding 2 Pull back the capillary column a Lower the oven injector an
138. n by completing the following steps a To restore the prior tuning and calibration settings click Undo b To reload the prior tuning and calibration settings to the mass spectrometer click Accept c Troubleshoot and correct the problem that caused the tuning and calibration procedure to fail See Tuning Issues on page 143 d Go to step 5 and restart the tuning and calibration procedure Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 67 4 Tuning and Calibrating Running Auto Tune and Calibration Figure 34 Typical parameter optimization plot Peak Width vs Resolution for Q3 Mass 69 00 m z OK 1 0_ Mass 218 99 m z OK Mass 501 97 m z OK 0 8 z E E L S 0 6 Qa 0 4 26 22 18 14 10 Resolution Settings 7 Click Accept to accept the results of the tuning and calibration procedure After you accept the results of the tuning and calibration procedure a message box asks whether you want to copy the positive ion tuning and calibration settings to the negative ion mode Ifyou 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 Ifyou 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 spectrum analysis Thermo Fisher Scientific recommends that you also perfor
139. nal Description 00c cece cece e eee eee eee eens 17 PULP pian steal cece etachasetdcbecddd chen aea bbe ee aE 18 Gas Chromatograph xd cen ene pba the du ide eke baw 19 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide i Contents Chapter 3 Chapter 4 Chapter 5 Direct Sample Probes cae eee eee dct voca ides aec RO Pesto cath 19 Transfer AS aed scares eso cet led Raters d ee iO bs e eti odeur b e b Sd oy 20 Mass Specttometer z wiri V del ee eer ele ie bel ip bra eed pP RE 21 Controls and Indicators 2 ain As OE xad E PR P AC eae 22 EL CE Ton Source o eios v rReEPU P HS EUER d PPP Ages 25 Inlet Wal VE sius vaerdos p ATE SR SAL Sora ode She buc Era ial Ele bi ul 29 lon Optics vede ee mee ende ete e que Mats be ree rete eie AR 30 Mass Analyzer siruina t oto RUNS dde nM ende os tbe fiios 32 Ion Detection System secr eissecar i e ee 39 Vacuum System and Inlet Gasses Hardware 00 ce eee eee e eee 4 Electronic Assemblies iis 2003 913233 eL tee Ns aera sas es dede 46 Data System 12st eset Roe Heed died He doe coe Pe sda 48 Computer Mardwate i nse Ca Ds Re t te ee eee ear ees 48 Data System Mass Spectrometer GC Interface 00 00 0000 ee 48 Data System Local Area Network Interface 0 00 cee eee eee 49 System Shutdown Startup and Reset 0 ec cece cence eee eee 51 Shutting Down the System in an Emergency 0 0 0 eee eee eee eee 51 Placing the System in Stan
140. nation Issues Thermo Scientific 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 appear high level TSO Quantum XLS and TSO Quantum GC User Guide 133 7 Diagnostics and Troubleshooting Troubleshooting Issue Excessive chemical background due to a column bleed m z 429 355 281 Issue Fxcessive injection port septum bleed Typical m z 207 429 355 281 Issue Phthalate background m z 149 167 279 Issue Fxcessive hydrocarbon contamination Typical ions are m z 43 57 71 85 99 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 Possible causes solutions
141. nded period of time Thermo Fisher Scientific recommends that you turn off the GC data system and autosampler as described in steps 7 through 12 below 7 Turn off the GC Follow the procedure described in the manual that came with the GC 8 Turn off the autosampler by using the main power on off switch 9 Press the System Power Off button Figure 27 to remove all power from the TSQ Quantum XLS or TSQ Quantum GC system 10 If the system is not to be used for an extended period turn off the argon collision gas supply at the tank 11 Turn off the data system a Choose Start gt Shut Down from the Windows task bar The Shut Down Windows dialog box appears b To start the Windows shutdown procedure select Shut down and click OK 12 Turn off the optional printer by using the on off switch CAUTION Burn Hazard The ion source GC oven injector and transfer line are hot Allow them to cool to room temperature before touching them Starting Up the System after a Complete Shutdown Starting the TSQ Quantum XLS or TSQ Quantum GC system after it has been shut down completely requires the following 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 for Operation Thermo Scientific TSQ Quantum XLS and TSQ Quantum GC User Guide 55 3 System
142. neutralized and are pumped away or they are ejected from the rod assembly Then at a later time both rf and dc voltages change and ions of the next mass to charge ratio for example m z 181 are allowed to pass while all other ions including m z 180 become unstable and undergo unbounded oscillations This process continues with ions of one mass to charge ratio after another being transmitted as the rf and dc voltages change in value At the end of the scan the rf and dc voltages are discharged to zero 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 the MS MS scan modes the mass spectrometer applies a large voltage of opposite polarity to the Q2 rod pairs between scans which empties the collision cell This process ensures that no ions remain in the collision cell from scan to scan The collision cell quadrupole rod assembly Q2 which always acts as an ion transmission device is a quadrupole array of square profile 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 rati
143. nterst tzungsorganisation f r Thermo Fisher Scientific San Jose Produkte in Verbindung ATTENTION Choc lectrique l instrument utilise des tensions capables d infliger des blessures corprelles l instrument doit tre arr t et d branch de la source de courant avant tout intervention Ne pas utiliser l instrument sans son couvercle Ne pas elensver les tuis protecteurs des cartes de circuits imprim s Chimique Des produits chemiques dangereux peuven se trouver dans l instrument Proted dos gants pour manipuler tous produits chemiques toxiques canc rig nes mutag nes ou corrosifs irritants Utiliser des r cipients et des proc dures homologu es pour se d barrasser des d chets d huile Haute Temperature Permettre aux composants chauff s de refroidir avant tout intervention Incendie Agir avec pr caution lors de l utilisation du syst me en pr sence de gaz inflammables Danger pour les yeux Dex projections chimiques liquides ou solides peuvent tre dangereuses pour les yeux Porter des lunettes de protection lors de toute manipulationde produit chimique ou pour toute intervention sur l instrument Danger g n ral Indique la pr sence d un risque n appartenant pas aux cat gories cit es plus haut Ce symbole figure galement sur l instrument pour renvoyer l utilisateur aux instructions du pr sent manuel Si la s ret d un proc dure est incertaine avant de continuer contacter le plus p
144. ntitative analysis of the compound Selected lon Monitoring SIM Selected ion monitoring SIM monitors a particular ion or set of ions SIM experiments are useful in detecting small quantities of a target compound in a complex mixture when you know the mass spectrum of the target compound Thus SIM is useful in trace analysis and in the rapid screening of a large number of samples for a target compound 12 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 1 Introduction Scan Types Because SIM monitors only a few ions it can provide lower detection limits and greater speed than the full scan modes SIM achieves lower detection limits because more time is spent monitoring significant ions that are known to occur in the mass spectrum of the target analyte SIM can achieve greater speed because it monitors only a few ions of interest SIM does not monitor regions of the spectrum that are empty or have no ions of interest SIM can improve the detection limit and decrease analysis time but it can also reduce specificity Because SIM monitors only specific ions any compound that fragments to produce those ions will appear to be the target compound The result could be a false positive Selected Reaction Monitoring SRM Selected reaction monitoring SRM monitors a particular reaction or set of reactions such as the fragmentation of an ion or the loss of a neutral moiety SRM monitors a limited number of parent product ion p
145. ntrol fault Contamination causes lens performance to deteriorate over time the amount of time depends on what type of sample and ionization mode you use Be careful to handle the lenses with care and do not use harsh cleaning techniques Damaged lenses cause short circuits which in turn can cause damage to the lens drivers TSO Quantum XLS and TSO Quantum GC User Guide 135 7 Diagnostics and Troubleshooting Troubleshooting Issue Diagnostics Possible cause solution indicate that the filament is open The filament is open Vent the system and remove the filament Normal resistance is 1 0 Q Replace if open Issue Unstable Possible cause solution emission current f The filament is near the end of its life span Replace the filament Issue Short Possible causes solutions filament lifetime There is an air leak contributing to short filament lifetime Check for leaks repair if any are found See High Vacuum Issues on page 138 for more information The filament is on during the solvent peak Increase acquisition delay time until the solvent peak has passed High emission current is being used Use lower emission current to extend lifetime Issue Diagnostics Possible causes solutions indicate a flat lens response 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 Suppo
146. ocal Technical Support organization for Thermo Fisher Scientific San Jose Products VORSICHT Elektroschock In diesem Ger t werden Hochspannungen verwendet die Verletzungen verursachen k nnen Vor Wartungsarbeiten mu das Ger t abgeschaltet und vom Netz getrennt werden Betreiben Sie Wartungsarbeiten nicht mit abgenommenem Deckel Nehmen Sie die Schutzabdeckung von Leiterplatten nicht ab Chemikalien Dieses Ger t kann gef hrliche Chemikalien enthalten Tragen Sie Schutzhandschuhe beim Umgang mit toxischen karzinogenen mutagenen oder tzenden reizenden Chemikalien Entsorgen Sie verbrauchtes Ol entsprechend den Vorschriften in den vorgeschriebenen Beh ltern Hitze Warten Sie erhitzte Komponenten erst nachdem diese sich abgek hlt haben Feuer Beachten Sie die einschl gigen VorsichtsmaBnahmen wenn Sie das System in Gegenwart von entz ndbaren Gasen betreiben Verletzungsgefahr der Augen Verspritzte Chemikalien oder kleine Partikel k nnen Augenverletzungen verursachen Tragen Sie beim Umgang mit Chemikalien oder bei der Wartung des Ger tes eine Schutzbrille Allgemeine Gefahr Es besteht eine weitere Gefahr die nicht in den vorstehenden Kategorien beschrieben ist Dieses Symbol wird im Handbuch auBerdem dazu verwendet um den Benutzer auf Anweisungen hinzuweisen Wenn Sie sich ber die Sicherheit eines Verfahrens im unklaren sind setzen Sie sich bevor Sie fortfahren mit Ihrer lokalen technischen U
147. olume on page 73 iii Insert the column into the transfer line and tighten the transfer line nut by hand iv Push the column in until you can see it through the inlet valve v Pullthe 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 lon 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 maximum temperature at which you will operate the column normally 300 C Wait 10 minutes Lower the oven temperature to 30 C and allow it to cool before continuing CAUTION The oven might be hot Allow it to cool to room temperature before opening it Do not touch the injector which will still be hot Re tighten the transfer line nut and the transfer line union 126 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Thermo Scientific 6 Maintenance Removing and Installing a GC Capillary Column 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 Raise the oven temperature to the initial temperature that you will use normally 40 C Turn on the vacuum compensation under the Right or Left Carrier menu TSQ Quantum XLS
148. ometer is operated as a conventional mass spectrometer with one stage of mass analysis The ion source ionizes the sample and the ion products are subjected to mass analysis in the first rod assembly The second and third rod assemblies transmit the resulting mass selected ions to the ion detection system 2 TSQ Quantum XLS and TSQ Quantum GC User Guide Thermo Scientific 1 Introduction lonization Modes The mass spectrometer is operated as a tandem mass spectrometer with two stages of mass analysis The ion source ionizes the sample and the ion products are mass analyzed by the first rod assembly In this case however mass selected ions exiting the first rod assembly collide with an inert gas in the second rod assembly and fragment to produce a set of ions known as product ions A chamber called the collision cell surrounds the second rod assembly The collision cell can be pressurized with an inert gas The product ions undergo further mass analysis in the third rod assembly to detect selected ions Two stages of mass analysis yield far greater chemical specificity than a single stage can achieve because of the systems ability to select and determine two discrete but directly related sets of masses In a first stage of mass analysis the mass spectrometer can be used 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 spectrome
149. on of the mass spectrum Tuning and calibrating the TSQ Quantum XLS or TSQ Quantum GC mass spectrometer automatically with TSQ EZ Tune uses perfluorotributylamine FC 43 as the tuning and calibration compound FC 43 resides in a vial inside the mass spectrometer Contents Displaying the FC 43 Mass Spectrum Running Auto Tune and Calibration Saving the Tune and Calibration Report 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 5096 of the tuned value Also re tune and calibrate after switching between EI and CI modes or between positive and negative polarity modes Note You may need to calibrate more often if you operate in H SRM mode as opposed to SRM mode only Table 5 lists typical peaks that are observed in the FC 43 mass spectrum in EI positive polarity mode Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 63 4 Tuning and Calibrating Displaying the FC 43 Mass Spectrum Table 5 Typically observed FC 43 peaks in El positive polarity mode m z 69 m z 100 m z114 m z 119 m z 131 m z 169 m z 219 m z 264 m z314 m z 352 m z 402 m z 414 m z 464 m z 502 m z 614 Displaying the FC 43 Mass Spectrum The first step in tuning and calibrating the mass spectrometer is to display t
150. on electronic assemblies produce the QO Q1 Q2 and Q3 rf voltages that enable ion transmission and mass analysis All rf voltages are controlled by the Analyzer Control PCB and the System Control PCB The Q1 and Q3 rf voltage amplifier circuits are identical and the circuits for QO and Q2 are similar The rf voltage generation electronic assemblies include the following components rf oscillator rf Voltage Amplifier PCB Low Pass Filter PCB rf voltage coil rf voltage detector Mass DAC Integrating amplifier The ion detection 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 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 detection system These circuits are in turn monitored by the PowerPC processor of the System Control PCB via the SPI bus The Analyzer Control PCB controls and monitors the rf voltages for QO Q1 Q2 and Q3 quadrupoles It also has lens voltage drivers that convert 330 V dc power from the DC Rod Driver PC
151. on 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 The head of the arrow on the I R tool Figure 44 when viewed through the window of the ion source manifold should not be visible Figure 43 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 Tock position and is holding the ion volume c Withdraw the I R tool with the ion volume attached until the guide ball reaches the first stop see Figure 42 d Pull the lever down to close the inlet valve 78 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 5 Changing lonization Modes Removing the lon Volume CAUTION Do not withdraw the I R tool 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 atmosphere 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 CAUTION Because the ion volume might be too hot to touch let it cool to room temperature before handling it 9 Remove the ion volume from the I R tool See Figure 44 a Wearing clean gloves press the ion volume for
152. oni descritte nel presente manuale Quando e in dubbio la misura di sicurezza per una procedura prima di continuare si prega di mettersi in contatto con il Servizio di Assistenza Tecnica locale per i prodotti di Thermo Fisher Scientific San Jose CAUTION Symbol gt OPP f CAUTION Electric Shock This instrument uses high voltages that can cause personal injury Before servicing shut down the instrument and disconnect the instrument from line power Keep the top cover on while operating the instrument Do not remove protective covers from PCBs Chemical This instrument might contain hazardous chemicals Wear gloves when handling toxic carcinogenic mutagenic or corrosive or irritant chemicals Use approved containers 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 in the above categories Also this symbol appears on the instrument to refer the user to instructions in this manual When the safety of a procedure is questionable contact your local Technical Support organization for Thermo Fisher Scientific San Jose Products CREE US OHWS
153. ons 14 regulatory compliance iii removed 98 Replaceable 161 replaceable parts 161 Replacing 120 RF dc voltages applied to mass analyzer discussion 33 RF voltage generation discussion 47 right side power panel figure 25 right side power panel description 54 figure 54 rod assemblies description 34 ion transmission 6 mass analysis 6 mass analyzer s quadrupole 33 Q1 Q2 and Q3 note 7 roughing pump 44 S Safe to Open Valve message direct sample probe 154 safety precautions vii safety standards iii Save 68 scan data types centroid scan 15 profile scan 14 Scan LED description 23 figure 22 scan modes data dependent 11 discussed 5 mass spectrometer 5 Neutral Loss 9 Neutral Loss example figure 11 Neutral Loss illustrated figure 10 Parent 8 Parent illustrated figure 9 Product 7 Thermo Scientific Product illustrated figure 8 Q1MS and Q3MS 7 summary table 6 scan types AutoSIM 14 discussed 12 full scan 12 intelligent selected reaction monitoring iSRM 13 quantitation enhanced data dependent MS QED MS 14 selected ion monitoring SIM 12 selected reaction monitoring SRM 13 sectional 31 32 selected ion monitoring SIM scan type 12 selected reaction monitoring SRM scan type 13 sensitivity problems troubleshooting 140 septum bleedcontamination 133 sequence 150 creating 150 direct sample probe running 153 Sequence Setup view 150 shutdown data system 55 emergency procedure 51 emergency front
154. ons are transmitted to the mass analyzer for mass analysis by changing the polarity of the potentials applied 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 both positive ion and negative ion mass spectra aids you in the qualitative analysis of your sample You can choose the ion polarity mode and ionization mode to obtain maximum sensitivity for the particular analyte of interest You can operate the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers in a variety of scan modes The most commonly used scan modes can be divided into two categories single mass spectrometry MS scan modes and MS MS scan modes The scan modes in each category are as follows MS scan modes Q1MS and Q3MS scan modes MS MS scan modes Product scan mode Parent scan mode Neutral Loss scan mode e Data dependent scan mode The scan modes that can be employed depend on the number and type of rod assemblies and the voltages applied to the rod assemblies TSQ Quantum XLS and TSQ Quantum GC User Guide 5 1 Introduction Scan Modes The mass analyzer or the mass spectrometer has three rod assemblies The first and
155. or the proper operation of the turbomolecular pump A Granville Phillips 342 mini ion gauge measures the pressures in the analyzer region of the vacuum manifold and the Q0 ion source region The ion gauge produces energetic electrons that cause the ionization of molecules in the ion gauge Positive ions formed in the ion gauge are attracted to a collector The collector current is related to the pressure in the vacuum manifold The ion gauge is also involved in vacuum protection 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 the power fails or the main power circuit breaker is placed in the Off O position a 4 farad capacitor located in the Power Entry Module keeps the solenoid in the closed position for several minutes If power is not restored in this time then the solenoid opens and the system is vented with filtered air The vent valve closes after power is restored to the mass spectrometer Collision Gas Flow Control Valves Thermo Scientific The collision gas flow control valves control the flow of argon collision gas into and out of the Q2 collision cell A solenoid valve acts to shut off argon gas flow to the cell The collision gas pressure is regulated by a proportional valve that is control
156. orized representatives FCC Compliance Statement THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES OPERATION IS SUBJECT TO THE FOLLOWING TWO CONDITIONS 1 THIS DEVICE MAY NOT CAUSE HARMFUL INTErfERENCE AND 2 THIS DEVICE MUST ACCEPT ANY INTErfERENCE RECEIVED INCLUDING INTErfERENCE THAT MAY CAUSE UNDESIRED OPERATION CAUTION Read and understand the various precautionary notes signs and symbols contained inside this manual pertaining to the safe use and operation of this product before using the device Notice on Lifting and Handling of Thermo Fisher Scientific San Jose Instruments For your safety and in compliance with international regulations the physical handling of this Thermo Fisher Scientific San Jose instrument requires a team effort to lift and or move the instrument This instrument is too heavy and or bulky for one person alone to handle safely 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 controlled electromagnetic environment Do not use radio frequency transmitters such as mobile phones in close proximity to the instrument WEEE Compliance This product is required to comply with
157. os The collision cell surrounds Q2 and is usually pressurized from about 1 x 10 to 4 x 10 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 with a neutral atom or molecule and then because of the collision dissociates into smaller fragments The mechanism of dissociation involves converting some of the translational kinetic energy TKE of the ion into internal energy This collision places the ion in an excited state If the internal energy is sufficient the ion fragments 36 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer Three expression convey the efficiency of the CID process Collection efficiency Fragmentation efficiency Overall CID efficiency Collection efficiency The ion flux ratio measured at the exit of the collision cell and at its entrance With no collision gas present the mass spectrometer obtains virtually 100 percent collection efficiency Collection efficiency is a mass dependent parameter For example with mid range collision gas pressure the collection efficiency might vary from about 50 percent for comparatively less massive ions which are more prone to scatter up to 75 percent for comparatively more massive ions which are less prone to scatter Fragmentation efficiency The fraction of the ion flux at the exit of the collision cell that
158. p Conditions for Operation Starting Up the Autosampler To start the autosampler Place the main power switch on the autosampler in the On position If necessary configure the autosampler For procedures for placing sample vials preparing solvent and waste bottles installing syringes and so on refer to the manual that came with the autosampler Setting Up Conditions for Operation To set up your TSO Quantum XLS or TSO Quantum GC mass spectrometer for operation 1 Before you begin data acquisition with your TSQ Quantum XLS system allow the system to pump down for at least one hour Operation of the system with excessive air and water in the vacuum manifold can cause reduced sensitivity tuning problems and reduced lifetime of the electron multiplier 2 Ensure that the argon pressure is within the operational limits argon 135 70 kPa 20 10 psig Note Air in the argon line must be purged or given sufficient time to be purged for normal TSQ Quantum XLS mass spectrometer performance 3 In the TSQ EZ Tune window choose View gt Instrument Status Look at the Status view Check that the pressure measured by the ion gauge is below about 3 x 10 Torr 2 x 10 Torr with H carrier gas with the collision gas turned off Note You do not need to calibrate and tune the mass spectrometer each time you restart the TSQ Quantum XLS or TSQ Quantum GC system To tune and calibrate the mass spectrometer see Chapter 4 Tuning and C
159. perature sensor RTD is defective Replace the EI CI Source PCB if necessary 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 Possible causes solutions e Auxl zone of the GC is not configured for MS Transfer Line Configure Aux 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 TSO Quantum XLS and TSO Quantum GC User Guide 137 7 Diagnostics and Troubleshooting Troubleshooting Issue Transfer Possible cause solution line overheats The transfer line temperature sensor is defective Replace the transfer line High Vacuum Issues High vacuum problems can manifest themselves in two ways An intermittent vacuum condition the vacuum pressure in the vacuum manifold fluctuates intermittently can cause chromatographic signals to drop out or if the pressures exceed the maximum allowed pressures set in Xcalibur See Table 3 on page 57 then the TSQ Quantum XLS or TSQ Quantum GC turns off Ifthe vacuum is consistent enough that it does not exceed the maximum allowed pressure and avoids the Xcalibur automatic shutdown non reproducible false chromatographic peaks can be gener
160. r 12 hours or more you can leave the system in standby mode To place the TSQ Quantum XLS or TSQ Quantum GC system in standby mode 1 Wait until data acquisition if any is complete A ol aj 2 From the TSQ EZ Tune window choose Control Standby or click the On Standby On 0 ff Standby button to put the mass spectrometer in standby 52 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 3 System Shutdown Startup and Reset Shutting Down the System Completely When you choose Control gt Standby the TSQ Quantum XLS or TSQ Quantum GC system turns off the electron multiplier the conversion dynode the ion source filament and lenses but not the heater and the mass analyzer and ion optics rf voltages See Table 4 on page 60 for the On Off status of mass spectrometer components 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 Leave the mass spectrometer power on A Oo Leave the GC power on with column flow MA Leave the autosampler power on 6 Leave 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
161. reaker switch located on the right side power panel Figure 29 is in the Off O position and the electronics service switch and the vacuum service switch are both in the Service Mode position 56 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 3 System Shutdown Startup and Reset Starting Up the System after a Complete Shutdown 3 Plug in the power cord for the mass spectrometer 4 Place the mass spectrometer main power circuit breaker switch in the On position When you place the main power circuit breaker switch in the On position power is supplied to those mass spectrometer components that are not affected by the vacuum service switch and the electronics service switch 5 Place the vacuum service switch in the Operational position 6 Place the electronics service switch in the Operational position When you place the electronics service switch in the Operational position the following occurs Thermo Scientific The Power LED on the mass spectrometer front panel illuminates green to indicate that power is provided to the mass spectrometer electronics The electron multiplier conversion dynode ion source and mass analyzer and ion optics rf voltages remain off The embedded computer reboots After several seconds 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 se
162. ring C Seat the filament on the EI CI Source PCB d Secure the filament with the retainer clip 10 Press the heater ring and lens assembly onto the ion source block 11 Use the retainer clip and threaded standoff to secure the lens assembly to the ion source See Figure 56 IMPORTANT For accurate temperature readings of the heater block fully screw the threaded standoff into the ion source to ensure contact between the temperature sensor with the heater block 12 Reinstall the ion source onto the magnet yoke 13 Reinstall the ion source 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 lon 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 components Tools Needed J r Gloves cleanroom grade P N 23827 0008 and 23827 0009 f Lint free cloth A Frequency As needed To disassemble the ion source completely 1 Prepare a clean work area by covering the area with lint free cloth Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 107 6 Maintenance Disassembling and Reassembling the TSQ Quantum XLS lon Source Completely 2 Shut down and vent the TSQ Quantum XLS See Shutting Down the System
163. rmo Scientific 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 water Detergent Alconox Micro or equivalent Dremel rotary tool or equivalent recommended Forceps P N 76360 0400 Gloves cleanroom grade P N 23827 0008 and 23827 0009 Glycerol reagent grade Lint free cloth Protective eyewear Tap water Toothbrush soft Frequency As needed to clean non stainless steel parts such as aluminum ceramic or gold plated or to clean hybrid parts that are partially made of stainless steel Lens holder and spacers Filament spacer Heater ring CAUTION Material and Eye Hazard Wear impermeable laboratory gloves and eye protection when performing cleaning procedures To clean non stainless steel or hybrid parts 1 Remove contamination from stainless steel surfaces It is only necessary to clean a surface that comes in contact with the ion beam a Use a slurry of number 600 aluminum oxide in glycerol and a cleaning brush or cotton tipped applicator Contamination appears as dark or discolored areas but often is not visible Clean each part thoroughly even if no contamination is visible To clean the inside corners use the wooden end of an applicator cut at an angle Use a Dremel tool with the polishing swab at its lowest speed to increase c
164. roche Service Client le pour les produits de Thermo Fisher Scientific San Jose PRECAUCION Descarga el ctrica Este instrumento utiliza altas tensiones capaces de producir lesiones personales Antes de dar servicio de mantenimiento al instrumento ste debera apagarse y desconectarse de la linea de alimentacion el ctrica No opere el instrumento sin sus cubiertas exteriores quitadas No remueva las cubiertas protectoras de las tarjetas de circuito impreso Quimica El instrumento puede contener productos quimicos peligrosos Utilice guantes al manejar productos quimicos t xicos carcinogenos mutagenos o corrosivos irritantes Utilice recipientes y procedimientos aprobados para deshacerse del aceite usado Altas temperaturas Permita que lop componentes se enfr en ante de efectuar servicio de mantenimiento Fuego Tenga cuidado al operar el sistema en presencia de gases inflamables Peligro par los ojos Las salicaduras de productos qu micos o particulas que salten bruscamente pueden causar lesiones en los ojos Utilice anteojos protectores al mnipular productos qu micos o al darle servicio de mantenimiento al instrumento Peligro general Significa que existe un peligro no incluido en las categorias anteriores Este simbolo tambi n se utiliza en el instrumento par referir al usuario a las instrucciones contenidas en este manual Cuando la certidumbre acerca de un procedimiento sea dudosa antes de prosegu
165. rometer 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 CAUTION The oven injector and transfer line are hot Allow them to cool to room temperature before touching them 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 122 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Removing and Installing a GC Capillary Column Figure 64 GC injector and transfer line unions 000 PH 0000 goonono FARO DODD p000 oooood0 DD DD o 00 3 Remove the column from the injector Refer to the Column chapter of the TRACE GC Ultra Operating Manual for instructions Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 123 6 Maintenance Removing and Installing a GC Capillary Column Installing a GC Capillary Column L JAKA 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 other suitable solvent Scoring wafer or sapphire scribe to cut capillary column Tr
166. rs Figure 39 Figure 39 Insert Probe message Instrument Messages Insert probe and tighten seal Click OK to proceed or Cancel to abort ES operation DK Cancel Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 75 5 Changing lonization Modes Removing the lon Volume 5 Inset 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 40 c Tighten the inlet valve knob clockwise to ensure a leak tight seal Figure 40 R tool at the first stop on guide bar and the inlet valve knob tightened I R tool First stop of Inlet valve knob guide bar 76 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 5 Changing lonization Modes Removing the lon Volume 6 Click OK The forepump 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 Instrument Messages lt is safe to insert the probe Click OK to proceed Em 7 Once evacuation is complete pull the inlet valve lever up to open the inlet valve Figure 42 R tool at first stop and inlet valve lever up I R tool First stop of Inlet valve lever guide bar Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 77 5 Changing lonization Modes Removing the lon Volume 8 Remove the i
167. rt 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 GC A heated zone problem is often the result of downloading an instrument method to the instrument that has a different setpoint than the current setting causing a delay while the heated zone heats or cools Component failures are less common but can occur These are usually related to open circuits in heater cartridges or faulty temperature sensors This manual does not discuss heated zones in the gas chromatograph Issue Excessive Possible causes solutions chromatographic peak f tailing The ion source transfer line or both are not hot enough Increase the transfer line temperature It should be at least as hot as the highest GC oven temperature Then try increasing the ion source temperature 136 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Issue Source heater will not heat Issue Source heater overheats Issue Transfer line will not heat Thermo Scientific 7 Diagnostics and Troubleshooting Troubleshooting The sample analyte is adsorbing in the GC injector Clean and deactivate the injection liner You can also try liners made of different materials The GC oven is not ramped to a high enough temperature Extend upper oven temperature The GC column must be replaced
168. s are due to defective electronic hardware components How do detect communication issues Issue Data system is unable to initiate communication with the mass spectrometer Thermo Scientific You might detect communication issues from an error message delivered by the data system or you might notice the failure of the data system to perform some expected task Possible causes solutions The software is not configured correctly Select and configure the mass spectrometer from the Instrument Configuration window TSO Quantum XLS and TSO Quantum GC User Guide 131 7 Diagnostics and Troubleshooting Troubleshooting Issue Computer intermittently loses communication with the mass spectrometer Issue Unable to download methods to the mass spectrometer Issue Acquisition does not begin as expected The Ethernet cable is unplugged Verify that the Ethernet cable is connected to the Ethernet port on the mass spectrometer See Figure 12 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 mass spectrometer is in Service Mode Return the electronics service switch to operating position An incorrect Ethernet cable is used for the mass spectrometer Use the supplied 10 Base T Category 5 crossover cable P N 76396 0052 in TSQ Quantum XLS Accessory Kit Note You can extend the length of the Ethernet cable by plugging a s
169. selected by this first stage of mass analysis are called parent ions As a result Q1 is referred to as the parent mass analyzer and the mass to charge ratio of ions transmitted by 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 Note When referring to the first second and third rod assemblies as pieces of hardware it is convenient to call them Q1 Q2 and Q3 respectively However when discussing their function in MS MS scan modes it often adds clarity to refer to them as the parent mass analyzer collision cell ion transmission device surrounded by the collision cell and product mass analyzer respectively 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 This latter step is known as collision induced dissociation CID Ions formed in the collision cell enter Q3 the product mass analyzer for the second stage of mass analysis Q3 is scanned to obtain a mass spectrum that shows the product ions produced from the fragmentation of the selected parent ion A mass spectrum obtained in the Product scan mode product mass spectrum is the mass spectrum of a selected parent ion The Product scan mode is illustrated in Figure 2 T
170. semblies The ion source block is also heated to assist in the rapid temperature equilibration of the ion source block and ion volume after the filament is turned on In EI mode the ion source is typically maintained at 150 C to 220 C However lower or higher temperatures are sometimes used for certain applications In the CI mode the ion source is typically maintained at 180 C to 200 C The ion source heater is feedback controlled The filament assembly positioned in a recess at the top of the ions source block contains the filament reflector and electron 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 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 magnet yoke in the proper position above and below the ion source block The permanent magnets collimate the electron beam and cause the beam to spiral through the ion volume This ensures optimum ionization of the sample Two ion source len assemblies called the L1 L2 and
171. sest to the L3 lead pin and the side with the rounded corners is closest to the L1 lead pin 94 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Cleaning lon Source Components 6 Reconnect the 3 pin connector to the lead pins on the L1 L2 and L3 lenses See Figure 48 7 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 73 b Push the capillary column in until you can see it in the ion source 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 Installing the Ion Volume on page 80 8 Close and secure the cover to the ion source vacuum manifold Cleaning the Lenses of the TSQ Quantum GC lon Source If cleaning the ion volume does not restore system performance clean the ion source lenses Note Lens L requires cleaning less often than lens L1 L2 and L3 To clean the ion source lenses 1 Shut down and vent the system See Shutting Down the System Completely on page 49 CAUTION Shock Hazard Unplug the TSQ Quantum GC before proceeding CAUTION Burn Hazard The ion source might be hot Allow the ion source to cool to room temperature before touching it 2 Remove the ion source See Removing the TSQ Quantum XLS Ion Source on page 89 3 Remove the ion source lens asse
172. smission devices In the ion transmission mode the quadrupole rod assemblies allow ions in a wide window of mass to charge ratios to pass The square quadrupole rod assembly Q2 operates in the ion transmission mode only Surrounding Q2 is a collision cell where collision induced dissociation CID can take place if the argon collision gas is present in the cell Figure 23 Magnitude of the rf and dc voltages applied to the rods of the Q1 and 03 mass analyzers 6000 4500 3000 PEPPER bd RF VOLTAGE 10 000 V P P 1500 840 V DC VOLTAGE 750 A ditt ul VOLTAGE Y Foe 750 1500 3000 u 4500 6000 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 35 2 Functional Description Mass Spectrometer Mass Analysis The Q1 and Q3 rods are charged with a variable ratio of rf voltage and dc voltage Figure 23 These potentials give rise to an electrostatic field that gives stable oscillations to ions 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 other ions undergo unbounded oscillations These ions strike one of the rod surfaces become
173. sues on page 138 for more information Solvent Spectra Acetone m z 43 58 59 Hexane m z 41 43 56 57 58 85 86 Methanol m z 31 Methylene chloride m z 84 83 Toluene m z 91 92 Trichloroethane m z 151 153 Xylene m z 105 106 Possible causes solutions There is residual solvent from a cleaning procedure or laboratory background contamination When you finish performing a cleaning procedure allow cleaned components to dry thoroughly Warm parts in the GC oven to drive off residual solvent The observed compounds have been introduced through sample injection The ultimate source is either a sample solvent or the autosampler rinsing solvent Optimize GC method to separate solvent peak from the area of interest in the chromatogram Filament and Lens Control Issues Thermo Scientific 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 that an open filament condition will stop an autosampler sequence and generate an error message Diagnostics test the lenses of the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers A flat line which represents voltage readback versus the predicted voltage ramp indicates a lens or other co
174. t common scan types are as follows Full Scan Selected Ion Monitoring SIM Selected Reaction Monitoring SRM Intelligent Selected Reaction Monitoring iSRM e Quantitation Enhanced Data Dependent MS QED MS e AutoSIM The full scan scan type provides a full mass spectrum of each analyte With full scan the scanning mass analyzer is scanned from the first mass to the last mass without interruption in a given scan time Full scan experiments are used to determine or confirm the identity of unknown compounds or the identity of each component in a mixture of unknown compounds Generally a full mass spectrum is needed to determine the identity of an unknown compound The full scan scan type gives you more information 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 you can perform an experiment with these scan types Thus you might use a full scan for SIM to determine the identity of an analyte and to obtain its mass spectrum and a full scan for SRM to determine the mass spectrum and product mass spectra for parent ions of interest Then you might use SIM or SRM to do routine qua
175. t valve housing 4 Engage the ball valve seal by pushing the plunger 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 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 valve seal into the ball valve manifold with your finger 4 Install the inlet valve knob and insert 5 Install the inlet valve plug and tighten the inlet valve knob clockwise Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 121 6 Maintenance Removing and Installing a GC Capillary Column Removing and Installing a GC Capillary Column You replace the GC capillary column if the chromatographic separation is bad or if it does not have the appropriate stationary phase for your application Tools Needed J 4 Gloves cleanroom grade P N 23827 0008 and 23827 0009 Wrench open ended 5 16 in Wrench open ended 7 16 in Wrench open ended 6 mm A Frequency As needed for maintenance or column replacement JARS Removing a GC Capillary Column To remove a GC capillary column 1 Shut down the TSQ Quantum XLS or TSQ Quantum GC and the gas chromatograph a Shut down and vent the mass spect
176. tandard Category 5 cable in series with the supplied crossover cable Possible cause solution The Ethernet cable is loose or damaged Inspect the cable and replace it if necessary Possible cause solution The software is not properly configured Verify the correct settings in Instrument Configuration 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 incorrect settings Check the start time in the Instrument Setup file The forepressure is too high due to solvent peak Reduce injection volume or extend filament multiplier delay time until after solvent peak The remote start cable to the GC is disconnected Connect the remote start cable The GC did not start Verify GC instrument method and configuration Verify the connection between the autosampler and GC The autosampler did not start Verify autosampler instrument method and configuration Verify that the sample is present The heated zone stipend is not attained See Heated Zone Issues on page 136 132 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Issue Acquisition terminates unexpectedly Issue Unable to initialize the gas chromatograph Issue Unable to download methods to the gas chromatograph Issue Unable to ini
177. tect an ion between the time the ion leaves Q1 and enters Q3 it must lose a neutral moiety whose mass the neutral loss mass is equal to the difference in the mass ranges being scanned by the two mass analyzers Thus a neutral loss mass spectrum is a spectrum that shows all the parent ions that lose a neutral species of a selected mass Note that a neutral gain or association experiment can also be performed in which the mass range scanned 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 useful when a large number of compounds are being surveyed for common functionality Neutral moieties are frequently lost from substituent functional groups for example CO from carboxylic acids CO from aldehydes HX from halides and H O from alcohols Figure 4 Illustration of the Neutral Loss scan mode Q2 RF Only Ar Q1 Scanning Q3 O1 a M eu SIV 8585 WSS e E BH 10 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 1 Introduction Scan Modes Figure 5 Examples of compounds with a common neutral loss fragment D
178. ted into the ion source block Listen for a click which indicates that the ion volume has connected with the ion source block b Turn the I R tool handle to the unlock position DE to release the ion volume from the I R tool Figure 45 lon volume seated in the ion source block lon source block lon volume 11 Verify that the ion volume is fully seated in the ion source block e Withdraw the I R tool away from the ion volume about 2 5 cm 1 in and turn the I 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 42 b Close the inlet valve by pulling the inlet valve lever down see Figure 40 CAUTION Do not withdraw the I R tool 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 atmosphere c Loosen the inlet valve knob by turning it counter clockwise d Continue withdrawing the I R tool completely from the inlet valve by sliding the I R tool through the guide ball track in the guide bar 13 Remove the guide bar by rotating it 90 counter clockwise and sliding it out of the entry housing Thermo Scient
179. tem See Starting Up the System after a Complete Shutdown on page 55 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 119 6 Maintenance Replacing the Ball Valve Seal Replacing the Ball Valve Seal Tools Needed L Ball valve seal kit P N 119265 0003 Frequency If the ball valve seal leaks air after you insert the direct insertion probe or I R tool into the inlet valve and tighten the inlet valve knob The ball valve seal in the inlet valve can become worn over time Replace the ball valve seal if it leaks air after you insert the direct insertion probe or I R tool and tighten the inlet valve knob The ball valve seal kit P N 119265 0003 is included 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 Inlet valve housing Ball valve seal components Inlet valve insert Inlet valve knob You use the ball valve seal extraction tool part of the ball valve seal kit P N 119265 0003 to remove the ball valve seal See Figure 63 120 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Replacing the Ball Valve Seal To remove the ball valve seal 1 Loosen the inlet valve knob counter clockwise until you can remove it 2 Remove the inlet valve knob plug and insert 3 Insert the not engaged ball valve seal extraction tool into the inle
180. tenance program 140 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific Issue The chromatogram has a low total ion current signal Issue Poor compound sensitivity Thermo Scientific 7 Diagnostics and Troubleshooting Troubleshooting 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 upper temperature or the time at upper temperature in the GC oven ramp The instrument is out of tune or the tune file is incorrect Select correct tune file for the method or run automatic tune as described in Tuning and Calibrating on page 63 The ion volume is contaminated Clean the ion volume The ion volume is incorrectly positioned Position the ion volume properly The magnets above and below the ion source are installed incorrectly Position both magnets so 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 the emission current Choose Tune gt Manual and select the Controls tab The ground connection between the electrometer PCB and anode feedthrough is faulty Contact Thermo Fisher Scientifi
181. ter 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 T Q 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 the final mass spectrum allow for very selective and sensitive analysis Each sequence of single or triple stage mass analysis of the ions is called a scan The mass spectrometer uses several different scan modes and different scan types to filter fragment or transmit ions in the mass analyzer Along with the ionization and ion polarity modes the ability to vary the scan mode and scan type affords the user great flexibility in the instrumentation for solving complex analytical problems lonization Modes Thermo Scientific The specific process used to ionize the analyte is referred to as the ionization mode You can operate the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers in either of two ionization modes Flectron ionization mode Chemical ionization mode 1 The instrument can also be used as a single stage mass spectrometer by transmitting the ions through the first and second rod assemblies followed by mass analysis in the third rod assembly TSQ Quantum XLS and TSQ Quantum GC User Guide 3 1 Introduction lonization Modes Elec
182. tered according to their mass to charge ratios An ion detection system then produces a signal proportional to the number of ions detected The system electronics receive and amplify the ion current signal from the ion detection system That signal is then passed on to the data system for further processing storage and display The data system provides the primary mass spectrometer user interface Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 17 2 Functional Description Autosampler Figure 6 Functional block diagram of the TSO Quantum XLS or TSO Quantum GC system Sample flow lt Electrical connection Mass spectrometer l Data system Autosampler l l l Optional Printer optional Instrument lon lon Mass lon detection control l Personal chromatograph J source optics analyzer system electronic computer l Transfer assemblies line EN Vacuum Video system monitor Ij E gn ae a CORRER J Gnn Autosampler The optional Thermo Scientific TriPlus autosampler is used to inject samples automatically into the GC inlet With an autosampler you can automate your GC MS MS analyses The TriPlus autosampler is shown in Figure 1 on page 2 Autosampler Start Stop signals with the mass spectrometer are provided by contact closure You configure the Tr
183. tialize the autosampler Issue Unable to download methods to the autosampler 7 Diagnostics and Troubleshooting Troubleshooting Possible causes solutions The end run time in the TSQ Quantum XLS or TSQ Quantum GC 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 up and remove files Possible causes solutions The GC is not turned on Turn on the GC The GC is not configured properly in Xcalibur Check Instrument Configuration The cable between COMI and GC is disconnected Verify connection COMI is not configured properly Verify COM port configuration Possible causes solutions There is a discrepancy between the instrument method and configuration Verify consistency between method and instrument configuration COMI is not configured properly Verify COM port configuration 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 connection The autosampler instrument configuration is not set to the correct port Verify connection and configuration Possible cause solution There is a discrepancy between instrument method and configuration Verify consistency between instrument method and instrument configuration Contami
184. ting 138 turbomolecular pump 44 Vacuum LED 22 vacuum service switch 24 vent valve 45 vent valve description 45 LED 24 Vent Valve Closed LED 24 voltages conversion dynode 39 QO offset 30 quadrupole RF and DC 34 W WEEE compliance vii Thermo Scientific
185. ting that the intensity of calibration gas ions is too low This message indicates that calibration compound must 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 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 continuing CAUTION The transfer line is hot Allow it to cool to room temperature before moving the GC 3 Move the GC far enough from the mass spectrometer to access the calibration compound vial compartment See the location of the calibration compound vial compartment in Figure 60 TSO Quantum XLS and TSO Quantum GC User Guide 117 6 Maintenance Adding Calibration Compound Figure 60 location of the calibration compound vial compartment Calibration compound vial compartment 4 Remove the cover to the calibration compound vial compartment 5 Remove the calibration compound vial from the calibration gas flow module See Figure 61 a Usea9 16 in wrench to remove the nut from the calibration compound vial b Slide the vial away from the calibration valve fitting with the ferrule and nut attached c Remove the ferrule and nut CAUTION Having more than 0 1 mL of the calibration compound can damage t
186. tor 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 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 89 6 Maintenance Cleaning lon Source Components 4 Undo the two latches that secure the lid of the ion source vacuum manifold and open the lid 5 Disconnect the connectors from the lead pins at the EI CI Source PCB and L1 L2 L3 lens assembly Figure 48 TSQ Quantum XLS ion source installed Q0 quadrupole mount Lens L1 L2 L3 connector EI CI Source PCB connector Thumbscrew Transfer line Thumbscrew CAUTION Burn Hazard The ion source might be hot Allow the ion source to cool to room temperature before touching it Note Wear clean lint and powder free gloves when you handle the ion source 6 While holding the 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 90 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Cleaning lon Source Components 9 Place the ion source and
187. 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 decontaminate dissolved solvents If the pump oil is still discolored change it You should change the pump oil every 3000 hours about four months of operation Refer to the manufacturers documentation for procedures for purging adding and changing the forepump oil CAUTION If you use ammonia as a chemical ionization reagent gas change the oil every month Ammonia is highly basic and quickly damages seals in the forepump Purging the oil with the Gas Ballast Control helps remove dissolved ammonia from the oil 116 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Adding Calibration Compound Adding Calibration Compound Thermo Scientific Tools Needed Calibration compound P N 50010 02500 e Syringe P N 36502019 9 16 in open ended wrench Frequency Yearly or as needed NIS The calibration compound is a liquid whose mass spectrum of ions is used to tune and calibrate the TSQ Quantum XLS and TSQ Quantum GC mass spectrometers The mass spectrometer uses FC 43 as its calibration compound Although you cannot visually determine when a calibration compound needs to be added Xcalibur Automatic Tune produces an error message indica
188. tron lonization Mode In electron ionization EI mode electrons are emitted by a heated wire filament that has electric current running through it by thermionic emission The filament and its reflector are typically maintained at a 70 V potential relative to the ion source block This potential accelerates the electrons through the ionization space called the ion volume These energetic electrons interact with neutral gas phase analyte molecules present in the ion volume and cause the analyte to lose an electron and produce a radical cation M e gt M 2e7 Frequently numerous cleavage reactions give rise to fragment ions which provide structural information about the analyte EI positive ion mode is the only commonly used EI mode Chemical lonization Mode In chemical ionization 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 This reaction also produces thermal electrons 3 Reagent gas ions react with reagent gas molecules to form a variety of secondary ions that are stable with respect to further reaction with reagent gas For example for methane CH e
189. tum XLS and TSO Quantum GC User Guide 109 6 Maintenance Disassembling and Reassembling the TSQ Quantum GC lon Source Completely Disassembling and Reassembling the TSQ Quantum GC lon Source Completely Disassemble the ion source completely to clean the ion source block or replace the EI CI Source PCB See Figure 58 for the location of the ion source components b Tools Needed e Gloves cleanroom grade P N 23827 0008 and 23827 0009 e int free cloth Jn Frequency As needed 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 CAUTION Shock Hazard Unplug the TSQ Quantum XLS before proceeding 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 110 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Disassembling and Reassembling the TSQ Quantum GC lon Source Completely ba Filament retainer clip Figure 59 Disassembling the ion source Filament Heater ring Centering ring O lon source block 9 Lens assembly LE e Heater ring and lens assembly Threaded standoff retainer clip EI Cl Source PCB Base studs 5 Pull the lens assembly off the ion source 6 Pu
190. ture readings of the heater block fully screw the threaded standoff into the ion source to ensure contact between the temperature sensor with the heater block 12 Reinstall the ion source onto the magnet yoke 13 Reinstall the ion source into the vacuum manifold See Reinstalling the TSQ Quantum XLS Ion Source on page 94 Restart the system See Starting Up the System after a Complete Shutdown on page 55 Replacing the Filament of the TSQ Quantum GC lon Source Thermo Scientific 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 current is set to or if the measured emission current decreases over time then the filament has failed or is failing and requires replacement See Figure 46 on page 86 and Figure 56 on page page 104 for the location of the ion source components To replace the ion source filament Tools Needed e Filament P N 120320 0030 e Gloves cleanroom grade P N 23827 0008 and 23827 0009 e int free cloth Jar Frequency If filament fails 1 Prepare a clean work area by covering the area with lint free cloth TSO Quantum XLS and TSO Quantum GC User Guide 105 6 Maintenance Replacing the Filament of the TSQ Quantum GC lon Source 2 Shut down and vent the TSQ Quantum GC See Sh
191. uency component location Ion source Cleaning the ion As needed Page 87 volume Ion source Cleaning the lenses As needed Page 88 TSQ Quantum XLS page 95 TSQ Quantum GC Ion source Cleaning the entireion As needed Page 107 TSQ source Quantum XLS page 110 TSQ Quantum GC Ion source Replacing the filament Ifthe filament fails Page 102 TSQ Quantum XLS page 105 TSQ Quantum GC Inlet valve Replacing the ball valve If there is an air Page 120 seal leak in the inlet valve Calibration compound Adding calibration If EZ Tune error Page 117 compound message indicates low intensity of calibration gas ions Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 83 6 Maintenance Table 6 Maintenance procedures Sheet 2 of 2 Mass spectrometer Procedure Procedure Frequency component location Gas chromatograph Replacing the capillary Ifchromatographic Page 122 column separation is bad or if a different stationary phase is needed for the application QO ion optics Cleaning the QO As needed quadrupole and L11 and L12 lenses Mass analyzer Cleaning the Q1 Q2 As needed and Q3 quadrupoles and lenses Forepump Purging the forepump If pump oil is Manufacturer s pump oil cloudy documentation Forepump Adding pump oil If pump oil level is Manufacturer s low documentation Forepump Changing the pump oil Every 4 months or Manufacturer s if pump oil is documentation cloudy and discolored Ion
192. urpose is to shield Q3 from the high voltage applied to the ion detection system and to shield the ion detection system from the high rf voltages applied to Q3 lon Detection System Thermo Scientific The TSQ Quantum XLS and TSQ Quantum GC mass spectrometers are equipped with a high sensitivity off axis ion detection system 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 surface located at a right angle to the ion beam The mass spectrometer applies to the conversion dynode a potential of 15 kV for negative ion detection or 15 kV for positive ion detection When an ion strikes the surface 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 positive ions The curved surface of the conversion dynode focuses these secondary particles and a voltage gradient acc
193. utting Down the System Completely on page 49 CAUTION Shock Hazard Unplug the TSQ Quantum GC before proceeding 3 Remove the ion source See Removing the TSQ Quantum GC Ion Source on page 96 4 Wearing clean lint and powder free gloves remove the ion source from the magnet yoke Figure 57 Disassembling the ion source to replace the filament Filament retainer clip Filament Heater ring and lens assembly Heater ring and lens assembly retainer clip lon source block and EI CI Source PCB Threaded standoff 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 106 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Disassembling and Reassembling the TSQ Quantum XLS lon Source Completely 8 Remove the filament and centering ring from the ion source block Note Now is a good time to clean the ion source block Use the procedure described in Cleaning Stainless Steel Parts on page 113 to clean the ion source block 9 Inspect and install a new filament P N 120320 0030 in the TSQ Quantum GC Accessory Kit a Verify that the filament wire is centered in the electron lens hole b Insert the filament into the centering
194. utton 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 computer on the System Control PCB to reboot The mass spectrometer software is then reloaded from the data system See Resetting the Mass Spectrometer on page 59 for information on how to reset the mass spectrometer Three LEDs are located on the power panel The Pump On LED is green when the rough pump current sensor detects current to the forepump The LED is off when the rough pump current sensor does not detect current to the forepump If the current sensor detects a loss of current when the mass spectrometer is on the vacuum system vents The Vent Valve Closed LED is green whenever the vent valve current sensor detects current through the vent valve and the vent valve is closed The LED is off when the vent valve is open 24 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer The Ethernet Link OK LED is green when the System Control PCB is communicating with the data system PC The LED is off when there is no communication between the System Control PCB and the data system PC Figure 12 Right side power panel of the mass spectrometer LO Main Power Power In Operating Mode Operating Mode Service Mode Service Mode Electronics
195. valve lever Inlet valve I R tool Doo oz Ball valve lever Guide bar TSO Quantum XLS and TSO Quantum GC User Guide 29 2 Functional Description Mass Spectrometer lon Optics The ion optics focus the ions produced in the ion source and transmit them to the mass analyzer The ion optics includes the Q0 quadrupole and lenses L11 and L12 The QO 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 QO offset voltage increases the translational kinetic energy of ions emerging from the ion source Figure 17 00 quadrupole Figure 18 gives a cross sectional view of the transfer line ion source and Q0 quadrupole 30 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 2 Functional Description Mass Spectrometer Figure 18 Cross sectional view of the transfer line ion source and Q0 quadrupole of the TSO Quantum XLS Lens L1 000 quadrupole Lens L2 lon source Q0 quadrupole Lens L3 ion volume ry i I C Transfer line Capillary column Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 31 2 Functional Description Mass Spectrometer Figure 19 Cross sectional view of the transfer line ion source and Q0 quadrupole of the TSO Quantum GC Lens L2 Lens L3 Lens L4 Lens L1
196. veral 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 to indicate that the software transfer from the data system to the mass spectrometer is complete and that the instrument is in standby The Vacuum LED on the front panel of the mass spectrometer remains off until the turbomolecular pump reaches 80 percent of its operational speed of 750 Hz At this time the ion gauge is turned on and the Vacuum LED illuminates yellow The Vacuum LED illuminates green and the high voltage can be turned on only if the pressure in the mass analyzer region of the vacuum manifold is less than the appropriate value listed in Table 3 Table 3 Maximum allowed pressure to turn on high voltage Carrier gas Ar collision gas Maximum pressure Torr He Off 6 x 10 He On 5 x 10 H2 Off 5 x 10 H2 On 1 x 104 TSQ Quantum XLS and TSQ Quantum GC User Guide 57 3 System Shutdown Startup and Reset Starting Up the System after a Complete Shutdown Figure 30 Front panel LEDs of the mass spectrometer c MAL LS Power Vacuum Communication EE System Scan If you have an autosampler go to Starting Up the Autosampler If you do not have an autosampler go to Setting U
197. ward into the tip of the I R tool and rotate it to disconnect the bayonet pins from the pin guides b Pull the ion volume out of the I R tool Figure 44 lon volume ion volume holder and I R tool Bayonet Arrow Bayonet pin lock Arrow l R tool ze S ws pin guide lon volume holder Spring washer a ER E lon volume 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 Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 79 5 Changing lonization Modes Installing the lon Volume Installing the lon Volume You install an ion volume after cleaning or to change ionization modes To install the ion volume Note Wear clean lint and powder free gloves when you handle a clean ion volume 1 Place the clean ion volume on the I R tool with the arrows aligned See Figure 44 CAUTION Make sure the arrows on the I R tool and ion volume are aligned to avoid damage to the ion source 2 Turn the I R tool handle to the lock position sic 3 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 w
198. y away from the QO quadrupole and 2 mm to the right to clear the transfer line bellows 8 Slide the ion source off the magnet yoke 9 Place the ion source and magnet yoke on a clean lint free cloth Thermo Scientific TSO Quantum XLS and TSO Quantum GC User Guide 97 6 Maintenance Cleaning lon Source Components 10 Close the lid of the ion source vacuum manifold Removing the lon Source Lens Assembly The ion source lens assembly includes lens L1 L2 L3 and L4 You must remove and disassemble the ion source lens assembly to clean the lenses A retainer clip fastens the lens assembly to the 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 Lens assembly lon source Retainer clip Threaded standoff Disassembling the lon Source Lens Assembly To disassemble the lens assembly 1 Pull the L1 L2 L3 lens assembly from the L4 lens assembly 98 TSO Quantum XLS and TSO Quantum GC User Guide Thermo Scientific 6 Maintenance Cleaning lon Source Components Figure 53 lon source lens assembly separated into L1 L2 L3 lens assembly left and L4 lens assembly
199. ytical chemistry though the high temperatures used in GC make it unsuitable for high molecular weight biopolymers frequently encountered in biochemistry It is well suited for use in the petrochemical environmental monitoring and industrial chemical fields It is also used extensively in chemistry research You configure the TRACE GC Ultra gas chromatograph from the data system computer Select the TRACE GC Ultra instrument button in the Instrument Configuration window which is available 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 TRACE GC Ultra page Refer to the Help for instructions for operating the TRACE GC Ultra Front panel keypad operation of the GC and maintenance procedures for the GC are described in the documentation provided with the GC To replace the GC capillary column see Removing and Installing a GC Capillary Column on page 122 Direct Sample Probes Thermo Scientific With the optional direct sample probes you can introduce compounds directly into the ion source without GC column separation See Figure 7 The direct sample probes are ideal for qualitat

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