Thermo Scientific TSQ 9000 Hardware Manual

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TSQ 9000

Mass Spectrometer

Hardware Manual

1R120618-0003 Revision C December 2018

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Troubleshooting

Summary of Contents for Thermo Scientific TSQ 9000

Page 1 TSQ 9000 Mass Spectrometer Hardware Manual 1R120618-0003 Revision C December 2018...
Page 2 Sale shall govern all conflicting information between the two documents. Release history: Revision A, March 2018; Revision B, April 2018; Revision C, December 2018. Software version: Thermo Scientific TSQ Series 4.0 or later. For Research Use Only. Not for use in diagnostic procedures.
Page 3: Table Of Contents
Powering Off the TSQ 9000 System ....... . . 10...
Page 4: Table Of Contents
Software is not communicating with the TSQ 9000 system... . . 104 Cannot download methods to the TSQ 9000 system....104 GC does not start or is not ready.
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Investigating Power Supply Issues ........116 TSQ 9000 system does not power on......116 TSQ 9000 system powers on temporarily and trips the circuit breaker.
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Anode Feedthrough......... . . 283 Reinstalling the TSQ 9000 System Software ......286 Updating the Firmware on the Instrument .
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Contents Replacing the Boards in the TSQ 9000 Instrument..... 304 Front and Rear RF Boards and Front and Rear Rod Driver Boards ..305 RF Board/Rod Driver Board Kits .
Page 9 081:2015 (ed. 2); IEC 61010-2-010:2014 (ed. 3); IECEE CB SCHEME CERT NO. DE 3-30000 • TSQ 9000, TSQ 9000 and TSQ Duo standards: EMC: EN 61326-1:2013. Safety: IEC 61010-1:2010 (ed. 3); IEC 61010-2-081:2015 (ed. 2); IEC 61010-2-010:2014 (ed. 3); IECEE CB SCHEME CERT NO. DE 3-30034...
Page 10 à l’utilisation sûre de ce produit, avant d’utiliser le dispositif. Notice on Lifting and Handling of Thermo Scientific Instruments For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one person alone to handle safely.
Page 11 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. For manufacturing location, see the label on the instrument. WEEE Compliance This product is required to comply with the European Union’s Waste Electrical &...
Page 12 WEEE Konformität Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC erfüllen. Das Produkt ist durch folgendes Symbol gekennzeichnet: Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Mehr Information über die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific, über die Verwerter, und weitere Hinweise, die nützlich sind, um die Produkte zu identifizieren, die unter diese RoHS Anweisung fallen, finden sie unter www.thermoscientific.com/rohsweee.
Page 13 • Contacting Us About Your System Thermo Scientific systems provide the highest caliber gas chromatography/mass spectrometry (GC/MS) instrumentation available on today’s market. GC/MS represents a combination of two powerful analytical techniques: GC, which acts as a separation technique, and MS, which acts as a detection technique. Complex mixtures of individual compounds can be injected into the GC, either manually or by an autosampler and then separated for presentation to the MS.
Page 14 Related Documentation The TSQ 9000 system includes Help and these manuals as PDF files: • TSQ 9000 Preinstallation Guide, PN 1R120618-0001 • TSQ 9000 User Guide, PN 1R120618-0002 •...
Page 15 Preface System Requirements System Requirements Your TSQ 9000 data system must meet these minimum requirements. System Requirements Hardware • 3.6 GHz dual-core processor enabled • 16 GB RAM with system managed memory enabled • DVD drive • Resolution display 1280 × 1024 (SXGA) •...
Page 16 This damage might not be covered under the standard warranty. LIFTING HAZARD: Indicates that a physical injury could or might occur if two or more people do not lift an object. TSQ 9000 Hardware Manual Thermo Scientific...
Page 17 RISQUE DE BRÛLURE : vous avertit de la présence d’une surface chaude qui peut ou pourrait entraîner des blessures par brûlure. RISQUE D’ÉLECTROCUTION : indique qu’un choc électrique peut ou pourrait survenir. Thermo Scientific TSQ 9000 Hardware Manual xvii...
Page 18 CONSULTER LE MANUEL : vous avertit de lire attentivement la documentation de votre instrument afin de garantir votre sécurité et la capacité opérationnelle de l’instrument. Ne pas lire attentivement la documentation peut ou pourrait vous exposer à un risque de blessure physique. xviii TSQ 9000 Hardware Manual Thermo Scientific...
Page 19 Before you begin using hydrogen, you should conduct a risk assessment based on the quantity of hydrogen to be used and the conditions of your laboratory. You should ask yourself: “What hydrogen hazards associated with this project are most likely to occur?” Thermo Scientific TSQ 9000 Hardware Manual...
Page 20 Using Hydrogen with TSQ 9000 To use hydrogen with the TSQ 9000, you must always shut off the GC carrier gas before venting or turning off the TSQ 9000. There are three hydrogen safety screws on the TSQ 9000 that must be in place.
Page 21 Hydrogen Safety Precautions Before powering on the TSQ 9000 system, ensure that: • All the covers and panels of the TSQ 9000 system are firmly attached. • The vent valve is tightly closed if you vented the system. • All fittings, ferrules, and o-rings are sealed.
Page 22 There is a loss of flow to the ventilation system – A hydrogen detector alarms at 25% of the lower flammable limit of hydrogen in air. The oxygen exhausted by the electrolyzer should be vented to the outside as well. xxii TSQ 9000 Hardware Manual Thermo Scientific...
Page 23 Bulk hydrogen systems represent a level of complexity again which is beyond the scope of this document; however some general guidelines are provided. Thermo Scientific TSQ 9000 Hardware Manual xxiii...
Page 24 • As liquid hydrogen systems also have a cryogenic hazard, additional safety considerations for the use of cryogenic liquids might be necessary. xxiv TSQ 9000 Hardware Manual Thermo Scientific...
Page 25 • NFPA 55, Standard for the Storage, Use, and Handling of Compressed Gases and Cryogenic Fluids in Portable and Stationary Containers, Cylinders, and Tanks, 2005 Edition • NFPA 68, Standard on Explosion Protection by Deflagration Venting • NFPA 70, National Electrical Code Thermo Scientific TSQ 9000 Hardware Manual...
Page 26 • NFPA 497, Recommended Practice for the Classification of Flammable Liquids, Gases, or Vapors and of Hazardous (Classified) Locations for Electrical Installations in Chemical Process Areas • NFPA 13, Standard for the Installation of Sprinkler Systems • NFPA 45, Standard on Fire Protection for Laboratories Using Chemicals •...
Page 27 There are several ways to contact Thermo Fisher Scientific for the information you need. Go to www.thermofisher.com for information about our products.  To get local contact information for sales or service Go to www.unitylabservices.com/en/home.html. Thermo Scientific TSQ 9000 Hardware Manual xxvii...
Page 28 Preface Contacting Us  To suggest changes to documentation or to Help • Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62. • Send an e-mail message to the Technical Publications Editor at techpubs-austin@thermofisher.com. xxviii TSQ 9000 Hardware Manual Thermo Scientific...
Page 29: Chapter 1 Performing Routine Maintenance
Performing Routine Maintenance This chapter describes how to perform routine maintenance on the TSQ 9000 system. Keeping your system in good working condition increases laboratory productivity and helps you get the most out of the instrument. Contents • Maintenance Supplies and Tools •...
Page 30 The foreline pump must be replaced if it seizes There are many more components of the TSQ 9000 system that do not require routine maintenance, but may need to be replaced if there is a problem with the instrument. To replace components not listed in this chapter, refer to Chapter 3: Advanced Troubleshooting.
Page 31: Maintenance Supplies And Tools
Cleanroom Gloves. See the ISQ and TSQ GC-MS Spare Parts Guide for ordering information In addition to the MS Toolkit, you can also purchase a TSQ 9000 Screw Kit, which includes extra screws, nuts, and standoffs. Refer to the ISQ and TSQ GC-MS Spare Parts Guide l for ordering information.
Page 32: Configuring The Tsq 9000 System
Configuring the TSQ 9000 System Configuring the TSQ 9000 System When you receive your TSQ 9000 system, a Field Service Engineer will configure the system for you. However, if you need to reconfigure your system, follow these steps: 1. Place the TSQ 9000 instrument, GC, computer, monitor, and keyboard on a work table and the foreline pump on the floor underneath.
Page 33 2. Connect all the cables to the computer, keyboard, mouse, monitor, and printer (if applicable). 3. Connect the handshaking cable to the GC and to the TSQ 9000 instrument’s GC Start connector. 4. Connect the computer and monitor electrical cables to the wall outlet.
Page 34 Note Condition the column before installing it on the mass spectrometer. 18. Make sure the TSQ 9000 instrument’s power switch is in the Off (down) position. 19. Connect the TSQ 9000 instrument’s electrical cable to the AC Input connector on the mass spectrometer and to the wall outlet.
Page 35: Powering On The Tsq 9000 System
2. Be sure the GC is powered on and there is carrier gas flowing through the column into the TSQ 9000 system. CAUTION INSTRUMENT DAMAGE: If you power-on the TSQ 9000 instrument without column flow, air is drawn through the column, which could damage the instrument. This large air leak may also require that you clean the ion source.
Page 36 Performing Routine Maintenance Powering On the TSQ 9000 System 5. Check the lights on the front of the instrument to make sure it is ready for use. Figure 3. Using the Lights on the TSQ 9000 Instrument Vacuum Busy Power Heaters •...
Page 37 7. Check the status of the vacuum on the TSQ 9000 Dashboard. Within 10 minutes of powering on the instrument, the vacuum should read OK. 8. Check the heater status on the TSQ 9000 Dashboard. If the ion source is not set to the desired temperature, click the Instrument Control button and change the temperature.The temperature set point will change when the send button is pressed.
Page 38: Powering Off The Tsq 9000 System
Once the turbomolecular pump reaches 50% rpm, the foreline pump powers off, and you may vent the system. 4. When the TSQ 9000 system’s temperatures and pumps are ready for shutdown, the vacuum light on the front of the instrument will start blinking rapidly.
Page 39 8. Power-off all the remaining instruments. Refer to their user documentation for specific instructions. CAUTION If you need to work inside the TSQ 9000 instrument, disconnect it from the electrical outlet. Be sure to reconnect it to the AC Input connector on the back of the instrument after finishing your work and closing the instrument.
Page 40: Replacing A Column
Replacing a column in a TSQ 9000 system with no VPI or an AEI ion source If your TSQ 9000 system has no VPI or has an AEI ion source installed on the system, follow the instructions below to replace the column.
Page 41 1. Lower the oven temperature and allow it to cool. 2. If the TSQ 9000 system is running, shut down and vent it. See the instrument’s hardware manual for instructions. CAUTION BURN HAZARD: The injector, detectors, oven, and transfer line may be hot.
Page 42 12. Turn the spring loaded transfer line nut 1 flat (60°) backward so the column is able to move in the ferrule with slight resistance. 13. Line up the outlet of the column with the arrows on the end of the column measuring tool. TSQ 9000 Hardware Manual Thermo Scientific...
Page 43 15. Pull the column back from the spring loaded transfer line nut. Do not move the septum from its position on the column. Figure 11. Pulling the Column Back from the Spring Loaded Transfer Line Nut Spring Loaded Column Transfer Line Nut Septum Thermo Scientific TSQ 9000 Hardware Manual...
Page 44 20. Loosen the nut by turning it exactly 1 flat (60°) backward. 21. Position the column in the transfer line using the cut septum to measure the correct length you should insert the column. TSQ 9000 Hardware Manual Thermo Scientific...
Page 45 26. Close the front door of the GC. 27. Restore working conditions. a. Raise the oven temperature to the initial temperature that you will use. b. Turn on vacuum compensation on the GC. 28. Power on the TSQ 9000 instrument. Thermo Scientific TSQ 9000 Hardware Manual...
Page 46 1. Lower the oven temperature and allow it to cool. 2. If the TSQ 9000 system is running, shut down and vent it. See the instrument’s hardware manual for instructions. CAUTION BURN HAZARD: The injector, detectors, oven, and transfer line may be hot.
Page 47 12. Line up the outlet of the column with the arrows on the end of the column measuring tool. Figure 16. Lining Up the Column in the Column Measuring Tool Column Outlet Thermo Scientific TSQ 9000 Hardware Manual...
Page 48 16. Remove the column, transfer line nut and ferrule from the column measuring tool, making sure not to move the septum from its location on the column. 17. Insert the column into the transfer line. TSQ 9000 Hardware Manual Thermo Scientific...
Page 49 21. Tighten the nut 1 flat (60°) forward—back to where it is secure enough in the transfer line that you cannot move it. 22. Tighten the nut 1 additional quarter turn. 23. Remove the cut septum. Thermo Scientific TSQ 9000 Hardware Manual...
Page 50: Extractabrite Ion Source
Power on the TSQ 9000 instrument. Once the TSQ 9000 instrument is pumped own and able to scan, view air water spectra and look for evidence of leaks with a large m/z 28 signal. If you observe a leak, stop scanning and gently tighten the nut in small increments until no leaks appear when scanning.
Page 51 Performing Routine Maintenance Replacing a Column b. On the TSQ 9000 Dashboard set the MS transfer line temp to 40 °C and the ion source temp to 175 °C (to avoid excessive oxidation of source parts or contamination from the V-lock source plug).
Page 52 IMPORTANT The V-lock source plug should remain attached to the source exchange tool. Do not rotate the source exchange tool handle to attempt to disengage the source plug. Figure 23. V-lock Source Plug Inserted Correctly TSQ 9000 Hardware Manual Thermo Scientific...
Page 53 17. Choose an appropriate ferrule for the outer diameter of your column. 18. Insert the column through the spring loaded transfer line nut and ferrule, entering through the tapered end of the ferrule. 19. Wipe the column again with a tissue soaked in methanol. Thermo Scientific TSQ 9000 Hardware Manual...
Page 54 24. Wipe the column with an alcohol soaked-wipe after inserting through the ferrule. 25. Carefully push the column back into the GC transfer line while keeping the nut and ferrule on the column. TSQ 9000 Hardware Manual Thermo Scientific...
Page 55 Once the TSQ 9000 instrument is pumped down and able to scan, view air water spectra and look for evidence of leaks with a large m/z 28 signal. If you observe a leak, stop scanning and gently tighten the nut in small increments until no leaks appear when scanning.
Page 56: Installing The Column In The Gc Inlet
Adjust the column position so that the septum contacts the bottom of the retaining nut. Use your fingers to tighten the retaining nut until it starts to grip the column. h. Tighten the column nut finger-tight until it starts to grip the column plus a quarter turn. TSQ 9000 Hardware Manual Thermo Scientific...
Page 57 80 °C (176 °F). Dans le cas contraire, il va fondre et endommager l’instrument. c. Repeat the leak check until no leaks are indicated. 5. Calibrate the carrier gas flow (column evaluation): Thermo Scientific TSQ 9000 Hardware Manual...
Page 58 Fix any issues found and rerun column evaluation until an appropriate K-factor is achieved.e a leak in the system, while a K-factor that is too high might indicate a blockage. 6. Disconnect the column flowmeter: TSQ 9000 Hardware Manual Thermo Scientific...
Page 59 Close the GC door. 7. If necessary, condition the column before inserting it into the TSQ 9000 system. Column conditioning consists of passing a carrier gas flow through the column heated to a programmed temperature as described in the column manufacturer’s instructions.
Page 60 Performing Routine Maintenance Replacing a Column ATTENTION DOMMAGES À L’INSTRUMENT : ne dépassez jamais la température de fonctionnement maximum de la colonne indiquée par le fabricant. TSQ 9000 Hardware Manual Thermo Scientific...
Page 61: Maintaining The Foreline Pump
Maintaining the Foreline Pump Maintaining the Foreline Pump The foreline (roughing) pump is usually located on the floor behind the TSQ 9000 instrument and occasionally requires maintenance. It establishes the vacuum needed to run the turbomolecular pump inside the instrument. Typically, the foreline pump oil needs to be replaced every four months.
Page 62 Performing Routine Maintenance Maintaining the Foreline Pump Figure 28. Connecting the TSQ 9000 System to the Foreline Pump Optional Mech Pump Connection System Mech Pump Connection TSQ 9000 Hardware Manual Thermo Scientific...
Page 63: Checking The Oil In The Foreline Pump
à vide. Reportez-vous aux « Précautions de sécurité relatives à l’hydrogène » à la page xix de la préface pour plus d’informations. 1. Click the Shut Down button on the TSQ 9000 Dashboard. 2. Click the Yes button to continue the shutdown process. The heaters and turbomolecular pump power off.
Page 64 Performing Routine Maintenance Maintaining the Foreline Pump powers off, and you may vent the system. At this point, the vacuum light blinks orange rapidly, and the system is ready to shut down. TSQ 9000 Hardware Manual Thermo Scientific...
Page 65 Maintaining the Foreline Pump 3. Reach over to the left side of the instrument and push down on the power switch to power-off the TSQ 9000 system. Figure 29. Powering Off the TSQ 9000 System Vacuum Interlock Shield Power Switch Vent Valve Knob 4.
Page 66: Purging Gas From The Oil In The Foreline Pump
15. Reconnect the foreline pump power cable to the System Mech Pump connector on the back of the instrument. 16. Reconnect the optional mechanical pump to the instrument. 17. Power-on the TSQ 9000 system. 18. Purge the foreline pump for 10 minutes using the gas ballast to remove excess gases from the new oil.
Page 67: Changing The Oil In A Foreline Pump
à vide. Reportez-vous aux « Précautions de sécurité relatives à l’hydrogène » à la page xix de la préface pour plus d’informations. 1. Click the Shut Down button on the TSQ 9000 Dashboard. 2. Click the Yes button to continue the shutdown process.The heaters and turbomolecular pump power off.
Page 68 Performing Routine Maintenance Maintaining the Foreline Pump Figure 30. Powering Off the TSQ 9000 System Vacuum Interlock Shield Power Switch Vent Valve Knob 4. Open the front door of the instrument. 5. Look behind the right side of the vacuum interlock shield and twist the vent valve knob one and a half times in a clockwise direction to open the vent.
Page 69 17. Reconnect the foreline vacuum hose. 18. Reconnect the foreline pump power cable into the System Mech Pump connector on the back of the TSQ 9000 instrument. 19. Reconnect the optional mechanical pump to the instrument. 20. Twist the vent valve one and a half times in a clockwise direction or until the o-ring is fully engaged.
Page 70 Maintaining the Foreline Pump 21. Close the front door of the instrument. 22. Power-on the TSQ 9000 system. 23. Purge the foreline pump for 10 minutes by using the gas ballast to remove excess gases from the new oil. See...
Page 71: Removing The Ion Source Cartridge For Cleaning
Health CP100 Nitrile Cleanroom Gloves. See the ISQ and TSQ GC-MS Spare Parts Guide or ordering information. The following instructions will tell you how to clean the ion source cartridge using abrasives, ultrasonication, and electropolishing. Thermo Scientific TSQ 9000 Hardware Manual...
Page 72: Removing The Ion Source Cartridge
After you reattach the knob, press the Evacuate button to remove any air inside the vacuum interlock. TSQ 9000 Hardware Manual Thermo Scientific...
Page 73 3. Grasp the handle of the source exchange tool in one hand and use your other hand to pull the metal barrel out and away from the handle so that tool is fully extended. 4. Attach the source exchange tool to the front of the instrument. Thermo Scientific TSQ 9000 Hardware Manual...
Page 74 Figure 33. Inserting the Ion Volume Tool b. Twist and push the stainless steel barrel to the right until it clicks into place under the screw at the top of the slot. Figure 34. Twisting the Tool Into Place TSQ 9000 Hardware Manual Thermo Scientific...
Page 75 6. Twist, then loosen the top part of the vacuum interlock handle to allow the entire handle to swing up and down. This handle controls the interior ball valve, which seals the vacuum chamber. Thermo Scientific TSQ 9000 Hardware Manual...
Page 76 Otherwise if you insert the tool with the handle down, you can damage the instrument. ATTENTION DOMMAGES À L’INSTRUMENT : assurez-vous que la poignée de verrouillage du vide est totalement relevée. Dans le cas contraire, si vous insérez l’outil avec la poignée abaissée, vous risquez d’endommager l’instrument. TSQ 9000 Hardware Manual Thermo Scientific...
Page 77 11. Pull the tool toward you and down the left side of the metal track on the barrel. As you keep pulling it toward you, more and more of the barrel will be exposed. You may Thermo Scientific TSQ 9000 Hardware Manual...
Page 78 12. Once you reach the end of the track (when the back line at the end of the barrel is uncovered by the black handle), twist the handle to the left to lock it into place. Figure 39. Locking the Tool in Place Note: Tool Rotated Left TSQ 9000 Hardware Manual Thermo Scientific...
Page 79 ATTENTION DOMMAGES À L’INSTRUMENT : ne relevez pas totalement la poignée ou vous ouvrirez le robinet à tournant sphérique intérieur, ce qui entraînera une perte de vide et de possibles dommages à l’instrument. 16. Remove the tool from the instrument. Thermo Scientific TSQ 9000 Hardware Manual...
Page 80 Performing Routine Maintenance Removing the Ion Source Cartridge for Cleaning Figure 41. Removing the Tool from the Instrument TSQ 9000 Hardware Manual Thermo Scientific...
Page 81 Figure 42. Exposing the Ion Source Cartridge Ion Source Cartridge 19. Invert the source exchange tool so that the barrel is pointed toward the floor. Figure 43. Inverting the Tool Ion Source Cartridge Thermo Scientific TSQ 9000 Hardware Manual...
Page 82 Removing the Ion Source Cartridge for Cleaning 20. Slide the source holder, which is in the TSQ 9000 Toolkit, onto the end of the ion source cartridge. The opening of the source holder is designed to accommodate the handles of the ion volume.
Page 83: Disassembling The Ion Source Cartridge
Figure 46. Ion Source Cartridge Components Lens 2 Ion Volume Ion Cartridge Sleeve Volume-Repeller Insulator Repeller Lens 3/RF Lens Spring Lens 1 Ion Volume Locking Ring Repeller Repeller 2. Set the components on a clean work surface. Thermo Scientific TSQ 9000 Hardware Manual...
Page 84: Reassembling The Ion Source Cartridge
1. Place the ion volume-repeller insulator on the repeller and hold it in place with the repeller nut. Set it aside for now. 2. Insert the ion cartridge sleeve into the source holder. Figure 47. Inserting the Sleeve into the Source Holder TSQ 9000 Hardware Manual Thermo Scientific...
Page 85 4. Place lens 2 on top of lens 3/RF lens with the small hole facing down. It should fit snugly and sit evenly on top of lens 3/RF lens. Figure 49. Inserting Lens 2 into the Source Sleeve Small Hole of Lens 2 Thermo Scientific TSQ 9000 Hardware Manual...
Page 86 1. You may need to rotate lens 1 slightly to make the ion volume fit correctly. Figure 51. Inserting the Ion Volume into the Source Sleeve Handles Fit Ion Volume Here Handles Lens 1 Gap TSQ 9000 Hardware Manual Thermo Scientific...
Page 87 7. Tighten the repeller nut. 8. Insert the large flat end of the repeller so that it rests on top of the ion volume. Figure 52. Inserting the Repeller into the Source Sleeve Large Flat End of Repeller Thermo Scientific TSQ 9000 Hardware Manual...
Page 88 The hooks on the sleeve fit between the larger gaps on the locking ring. Note Do not twist and lock the locking ring on the sleeve at this time. TSQ 9000 Hardware Manual Thermo Scientific...
Page 89: Reinserting The Ion Source Cartridge
IMPORTANT If you try to attach the ion source cartridge to the tool by inverting it, the components will likely fall, so make sure you are working over a table. Otherwise, you may have to stop and clean the components again. Thermo Scientific TSQ 9000 Hardware Manual...
Page 90 Using too much force when inserting the ion source cartridge into the barrel can cause damage. TSQ 9000 Hardware Manual Thermo Scientific...
Page 91 Figure 56. Reattaching the Ion Source Cartridge to the Tool Note The ion volume and lenses have keying features to assure the lens spring contacts will align with the metal parts of the lenses. Thermo Scientific TSQ 9000 Hardware Manual...
Page 92 9. Insert the barrel end of the ion cartridge tool into the vacuum interlock and twist it to the right to lock it into position. Be sure the black handle remains in the locked position. TSQ 9000 Hardware Manual Thermo Scientific...
Page 93 Performing Routine Maintenance Removing the Ion Source Cartridge for Cleaning Figure 58. Evacuating the Instrument Evacuate Button Thermo Scientific TSQ 9000 Hardware Manual...
Page 94 IMPORTANT Make sure you take the correct track on the tool or the ion volume will disassemble inside the instrument. If that happens, the tool will get stuck and you will have to shut down, vent the TSQ 9000 instrument, and manually remove the source cartridge through the top of the instrument.
Page 95 14. Twist the handle of the source exchange tool to the right and pull it back toward you and down the right side of the barrel’s metal track until the line at the end of the track appears. Figure 60. Pulling the Tool Down the Right Track Thermo Scientific TSQ 9000 Hardware Manual...
Page 96 19. For optimal performance, wait at least 30 minutes for the ion source to heat up to the same temperature as the inside of the instrument. Otherwise, the masses or intensities may drift during operation. TSQ 9000 Hardware Manual Thermo Scientific...
Page 97: Maintaining The Calibration Gas Module
Maintaining the Calibration Gas Module Maintaining the Calibration Gas Module The calibration gas module on the TSQ 9000 mass spectrometer is very easy to maintain. It is inside the front door of the instrument, and you only refill the calibration gas reservoir every one to two years.
Page 98: Refilling The Calibrant Reservoir
To refill the calibrant reservoir: Note It is not necessary to vent the instrument to perform this operation 1. Open the front door of the TSQ 9000 instrument. 2. Twist the calibrant reservoir cover counter-clockwise and remove it from the calibration gas controller.
Page 99 à la fois peut endommager le module de gaz d’étalonnage. Assurez-vous qu’aucun liquide n’entre dans le module lorsque vous rattachez le réservoir. 5. Reattach the cover to the calibration gas controller. 6. Close the front door of the instrument. Thermo Scientific TSQ 9000 Hardware Manual...
Page 100: Replacing A Dual Filament
A and B. To replace the dual filament: 7. Open the TSQ 9000 Dashboard and click the Shut Down button. WARNING BURN HAZARD: The injector, oven, and transfer line may be hot. Allow them to cool to room temperature before touching them.
Page 101 Once the turbomolecular pump reaches 50% rpm, the foreline pump powers off, and you may vent the system. 2. When the TSQ 9000 system’s temperatures and pumps are ready for shutdown, the vacuum light on the front of the instrument will start blinking rapidly.
Page 102 9. Use a T20 Torxhead screwdriver to remove the four screws around the manifold door. Figure 65. Opening the Manifold Door Screws 10. Pull the manifold door out to open. Once the alignment pins are clear of the thumbscrews, swing the manifold door open. TSQ 9000 Hardware Manual Thermo Scientific...
Page 103 12. Look through the top of the instrument and use a clean T10 Torxhead screwdriver to loosen the screw holding the filament retaining clip in place. Then rotate the clip away from the filament. Thermo Scientific TSQ 9000 Hardware Manual...
Page 104 Figure 67. Disconnecting the Filament Source Interface Board Filament Filament Screw Retaining Spring 13. Disconnect the filament board and wires from the source interface board. Figure 68. Disconnecting the Filament Board and Wires Filament Board and Wires...
Page 105 16. Bend the filament wires so they do not touch any metal component. You may want the old filament as a model. 17. Attach the connector of the replacement filament to the source interface board. Figure 69. Replacing the Filament Source Interface Board Filament Filament Screw Retaining Spring Thermo Scientific TSQ 9000 Hardware Manual...
Page 106 Do not apply excess force to the thumbscrews or components may be damaged. Note Once the manifold door is closed, ensure the filament wires do not contact the metal surface of the door. TSQ 9000 Hardware Manual Thermo Scientific...
Page 107 22. Twist the vent valve one and a half times in a clockwise direction to close it or until tight. 23. Reach over to the left side of the instrument and pull up on the power switch to power-on the TSQ 9000 system. Thermo Scientific...
Page 108: Replacing The Electron Multiplier
à vide. Reportez-vous aux « Précautions de sécurité relatives à l’hydrogène » à la page xix de la préface pour plus d’informations. 1. Shut down the TSQ 9000 system using the software. See the TSQ 9000 User Guide for more information.
Page 109 6. Look behind the right side of the vacuum interlock shield and twist the vent valve knob one and a half times in a counter-clockwise direction to open the vent. 7. Wait five minutes for the TSQ 9000 instrument to vent. CAUTION - INSTRUMENT DAMAGE Do not proceed until the instrument is vented or pieces of the column or ferrule might blow into the instrument.
Page 110 12. Use a T20 Torxhead screwdriver to remove the four screws at each corner of the electron multiplier plate. WARNING - ELECTRICAL SHOCK HAZARD Avoid dropping screws between chassis and side cover or board. If you drop a screw, find it before powering the instrument on again. TSQ 9000 Hardware Manual Thermo Scientific...
Page 111 Si vous déposez une vis, trouvez-la avant de remettre l'instrument sous tension. Figure 74. Disconnecting the Electron Multiplier Plate Electron Multiplier Plate Screws 13. Lift the electron multiplier plate out of the vacuum manifold. Thermo Scientific TSQ 9000 Hardware Manual...
Page 112 20. Inspect the o-ring between the manifold and detector assembly for debris. If the o-ring is dirty, clean or replace it. 21. Flip the electron multiplier and plate over and insert them into the instrument. TSQ 9000 Hardware Manual Thermo Scientific...
Page 113 23. Reconnect the electrometer board cable and large feedthrough cables. CAUTION INSTRUMENT DAMAGE: Do not mix up the cables or you will damage the power supply. ATTENTION DOMMAGES À L’INSTRUMENT : ne confondez pas les câbles ou vous endommagerez l’alimentation. Thermo Scientific TSQ 9000 Hardware Manual...
Page 114 30. Replace all hydrogen safety screws. 31. Power-on the TSQ 9000 mass spectrometer. 32. If the GC is powered off, power it on and make sure vacuum compensation is on for the carrier gas flowing into the mass spectrometer.
Page 115 Passez-la plutôt par le côté droit ou placez-vous derrière l’instrument et activez l’interrupteur d’alimentation. 33. Open TSQ 9000 Auto Tune on the TSQ 9000 Dashboard. 34. Run any tune that sets the gain of the electron multiplier to 3 x 10...
Page 116: Cleaning Durable Components
Cleaning the other components are not part of the expected maintenance. To clean durable components of the TSQ 9000 instrument, you will need the following cleaning supplies: • Acetone, reagent grade (or other suitable polar solvent) •...
Page 117 If you are cleaning the CI ion volume, use a razor blade to sharpen the wooden end of a wooden cotton swab to a 45° angle. Thermo Scientific TSQ 9000 Hardware Manual...
Page 118 Repeat until the water is clear. 5. Use forceps to immediately transfer the components to a clean beaker of acetone. TSQ 9000 Hardware Manual Thermo Scientific...
Page 119 7. Wearing gloves, blow clean, dry gas on the components to remove the acetone. Note Acetone should not be allowed to dry on the part. It will leave a residue that may affect instrument performance. Thermo Scientific TSQ 9000 Hardware Manual...
Page 120: Cleaning Delicate Components
• Source magnets • Top (glass) manifold cover Note Cleaning these components is not part of the expected maintenance. To clean delicate components of the TSQ 9000 instrument, you will need the following cleaning supplies: • Applicators, cotton-tipped • Deionized water •...
Page 121 3. Rinse the components with methanol. Using forceps, dip the components in a beaker of methanol. Change the methanol if it becomes cloudy. Do not soak or sonicate the components. 4. Wearing gloves, use a clean, dry gas to blow the methanol off the components. Thermo Scientific TSQ 9000 Hardware Manual...
Page 122: Cleaning The Filters
Cleaning the Filters  To clean the filters and fan filter on the TSQ 9000 instrument: Note If your filters wear out or get damaged, refer to the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering new ones.
Page 123 9. Remove the turbo cooling fan filter. 10. Wash the filters in soap and water. 11. Let the filters dry. 12. Reattach the filters. 13. Replace the turbo cooling fan filter cover. 14. Close the front door of the instrument. Thermo Scientific TSQ 9000 Hardware Manual...
Page 124 Performing Routine Maintenance Cleaning the Filters TSQ 9000 Hardware Manual Thermo Scientific...
Page 125: Chapter 2 Troubleshooting
In this section, we describe the symptom and remedy for each known issue with the TSQ 9000 mass spectrometer. All of these issues are related to hardware, but your instrument or software will alert you to them. For issues that you discover while reviewing your data, see the Troubleshooting section of the TSQ 9000 User Guide.
Page 126: Using Diagnostics
Using Diagnostics Using Diagnostics If your TSQ 9000 system is running poorly or suspiciously, you can run software diagnostics to detect the problem and find a solution. Diagnostics tests electronic circuits and reports whether the circuits pass or fail. However, problems in sensitivity due to misalignment, dirty components, or improper tuning are not detected by the software.
Page 127 Troubleshooting Using Diagnostics 2. The TSQ Series AutoTune utility opens. Click Tune Types. Figure 81. Opening TSQ Series AutoTune 3. Select an existing tune type and click Copy. Figure 82. Copying a Tune Type Thermo Scientific TSQ 9000 Hardware Manual...
Page 128 Troubleshooting Using Diagnostics 4. Name your diagnostic tune type. Figure 83. Naming Your Diagnostic Tune Type 5. Select the Diagnostics Only option in the Type field. TSQ 9000 Hardware Manual Thermo Scientific...
Page 129 Troubleshooting Using Diagnostics 6. Click the Diagnostics tab and select the types of diagnostics you would like to perform on your instrument. Figure 84. Selecting Types of Diagnostics 7. Click Save. Thermo Scientific TSQ 9000 Hardware Manual...
Page 130: Running A Diagnostic Tune
Troubleshooting Using Diagnostics Running a Diagnostic Tune To run a diagnostic tune: 1. Select AutoTune Options | Advanced AutoTune on the TSQ 9000 Dashboard to run diagnostics. Figure 85. Running an Automatic Tune TSQ 9000 Hardware Manual Thermo Scientific...
Page 131 2. Select the diagnostics tune type you created and click Start. Figure 86. Running Diagnostics 3. Click View Tune Report on the TSQ 9000 Dashboard to view the diagnostic results. 4. Click the Report Options button in the upper right corner of the window.
Page 132: Investigating Communication Issues
Table 3. Possible Remedies if the GC will not Start Open the Instrument Configuration utility and verify the GC methods and configuration. Make sure the Remote Start cable is properly connected to the Generic/HS port on the GC and to the GC Start port on the TSQ 9000 system.
Page 133 <When Low> or <Do Not Inhibit>. On a FOCUS GC, use the Keypad button in Xcalibur. • Press the Home button. • Scroll down to the <others> option and press <ENTER>. • Scroll down to <Configuration> and press <ENTER>. Thermo Scientific TSQ 9000 Hardware Manual...
Page 134: Sample Data Are Not Acquired
Make sure the Remote Start cable is properly connected to the GC. Make sure the End Run Time is set properly in the TSQ 9000 Instrument Setup file. Add more disk space to the computer by backing up and removing files.
Page 135: Investigating Contamination Issues
WARNING ELECTRICAL SHOCK HAZARD: When troubleshooting any issue that requires removing a cover on the TSQ 9000 mass spectrometer, you should power-off and vent the instrument to avoid harming yourself. AVERTISSEMENT RISQUE D’ÉLECTROCUTION : lorsque vous cherchez à...
Page 136: Chemical Noise Is At M/Z 429, 355, 281
Table 7. Possible Remedies for Chemical Noise at m/z 429, 355, 281 Condition the column. It is best to condition the column outside of the TSQ 9000 mass spectrometer so the contaminants can escape into the air instead of the instrument.
Page 137 Table 11. Possible Remedies for Solvent Contamination You may have a leak that is allowing solvent vapors to get into the TSQ 9000 instrument. Use a spray gas, such as Tetrafluoethane, to check for leaks and then fix them. See Investigating Vacuum Issues for details.
Page 138: Investigating Filament And Lens Control Issues
Investigating Filament and Lens Control Issues Investigating Filament and Lens Control Issues Filament Check diagnostics can test the filament and lenses of the TSQ 9000 mass spectrometer. Handle the lenses with care. Damaged lenses may cause short circuits, which may damage the lens drivers.
Page 139: Investigating Temperature Issues
TSQ 9000 mass spectrometer and the transfer line heater is controlled by the GC. Often, a temperature issue is the result of downloading a method to the TSQ 9000 system that has a different setpoint from the current setting, which causes a delay while the heated zone adjusts the temperature.
Page 140: Lens/Source Heater Does Not Heat
Lens/source heater does not heat. Table 15. Possible Remedies when Lens/source Heater does not Heat Make sure the TSQ 9000 system and computer are properly connected. Check the vacuum status as the heaters will not turn on until vacuum status reads OK.
Page 141: Investigating Vacuum Issues
Investigating Vacuum Issues Investigating Vacuum Issues When you run Vacuum System Check diagnostics on the TSQ 9000 mass spectrometer, the Xcalibur software checks the vacuum system. Vacuum issues may also be found when you run Leak Check diagnostics. Your instrument or software may indicate the following types of issues.
Page 142: An Air Leak Is Detected
• Clean dust or debris from the top cover O-ring. If you do not find a leak, turn on the TSQ 9000 system in full-scan mode. Click Custom Spectrum on the TSQ 9000 Dashboard. Set the Scan Type to Full Scan and Start/End mass to cover the characteristic ions for the compressed gas you are using. Most compressed gases have ions between m/z 35 and 100.
Page 143: Turbomolecular Pump Shuts Off While In Use
Run Leak Check diagnostics to look for leaks and address them. Excessive gas flow may cause the pump to overheat. Ensure the temperature of the lab environment is 15-35 °C. Make sure the flow of carrier gas to the TSQ 9000 is less than 10 mL/min. Thermo Scientific...
Page 144: Investigating Power Supply Issues
TSQ 9000 system does not power on. Table 24. Possible Remedies when TSQ 9000 System does not Power On Make sure the TSQ 9000 instrument’s power cable is properly connected to the instrument and electrical outlet. Verify that the electrical outlet is functioning properly.
Page 145: Investigating Rf/Dc Issues
Table 28. Possible Remedy if RF/DC System Check Diagnostic Fails Use TSQ 9000 Tune to tune the RF system. If the RF system will not tune, contact Technical Support. Make sure the rod driver board is properly installed and undamaged. Replace it, if necessary. See...
Page 146: Investigating Sensitivity Issues
Investigating Sensitivity Issues Investigating Sensitivity Issues When you run Detector Check diagnostics on the TSQ 9000 system, the Xcalibur software checks for noise on the electrometer, multiplier, dynode and RF board. Sensitivity issues are usually the result of an air leak, dirty components, or contamination. Sometimes sensitivity issues can be caused by simple to fix problems such as the carrier gas tank running out or a sample not being injected into the GC.
Page 147: Poor Sensitivity Or Sudden Loss In Sensitivity
If you recently performed maintenance on your ion source, remove the ion source, verify that it is assembled correctly, and reinsert it into the TSQ 9000. Make sure the GC column does not extend into the ion source. Use the column measuring tool to ensure the column is the correct length.
Page 148: Investigating Stability Issues
WARNING ELECTRICAL SHOCK HAZARD: When troubleshooting any issue that requires removing a cover on the TSQ 9000 mass spectrometer, you should power-off and vent the instrument to avoid harming yourself. AVERTISSEMENT RISQUE D’ÉLECTROCUTION : lorsque vous cherchez à...
Page 149: Investigating Tuning Issues
WARNING ELECTRICAL SHOCK HAZARD: When troubleshooting any issue that requires removing a cover on the TSQ 9000 mass spectrometer, you should power-off and vent the instrument to avoid harming yourself. AVERTISSEMENT RISQUE D’ÉLECTROCUTION : lorsque vous cherchez à...
Page 150: Tune Is Interrupted
Tune is interrupted. Table 33. Possible Remedy if Tune is Interrupted Make sure the computer is not set to go into Standby mode while you are acquiring data for your tune. Otherwise, it may interrupt your tune. Cannot find calibration gas peaks. Table 34.
Page 151: Tsq 9000 Tune Reports An Error While Saving A Tune File
Troubleshooting Investigating Tuning Issues TSQ 9000 Tune reports an error while saving a Tune file. Table 39. Possible Remedy if Errors are Reported While Saving a Tune File Check that there is sufficient space on the hard drive to save a new Tune file. If there is not enough space to save a new Tune file, copy old Tune files to another location and delete them from the hard drive.
Page 152: Contacting Technical Support
Support. Be sure to reference the model number and serial number of your instrument when contacting them. Every TSQ 9000 system ships with a label inside the front door that lists the model number and serial number. Figure 87. Identifying Your TSQ 9000 Instrument...
Page 153: Chapter 3 Advanced Troubleshooting
Advanced Troubleshooting This chapter describes the TSQ 9000 system’s components that do not require routine maintenance, but troubleshooting may indicate they need to be replaced. Contents • Replacing Components of the Analyzer • Replacing Components of the Ion Source •...
Page 154: Replacing Components Of The Analyzer
Q1 quad assembly, the Q3 quad assembly, and the collision cell assembly. Figure 88. Replaceable Components of the Analyzer Tray Quadrupole 3 Quadrupole 1 Ion Guide Collision Cell Analyzer Ion Source Assembly Tray TSQ 9000 Hardware Manual Thermo Scientific...
Page 155: Analyzer Tray
This section discusses how to remove and replace the analyzer tray. This part is unlikely to fail, but you must follow these steps any time you remove the analyzer tray from the TSQ 9000 system to service or replace other components.
Page 156 à vide. Reportez-vous aux « Précautions de sécurité relatives à l’hydrogène » à la page xix de la préface pour plus d’informations. 4. Shut down the TSQ 9000 system using the software. See the TSQ 9000 User Guide for more information.
Page 157 Note You might have to move the GC to access the right hydrogen safety screw. Removing the Analyzer Tray from the TSQ 9000 Instrument  To remove the analyzer tray from the TSQ 9000 instrument 1. Slide the top cover panel toward the back of the instrument and lift it off. Thermo Scientific...
Page 158 Large Glass Manifold Cover Small Glass Manifold Cover 5. Disconnect the four wires that go to the ion guide and quadrupole 1. These wires are attached to the front 4-pin feedthrough in the vacuum manifold. TSQ 9000 Hardware Manual Thermo Scientific...
Page 159 Note Pull straight back from the collision cell to prevent damage to the collision gas tube. 8. Use a T20 Torxhead screwdriver to remove the four screws around the manifold door. Note Remove the screws completely so that they do not scratch the manifold when you close the door. Thermo Scientific TSQ 9000 Hardware Manual...
Page 160 Figure 95. Removing the Right Side Panel 13. Identify the set screw on the source heater block. This T10 screw holds the transfer line in alignment with the ion volume heater block. See Figure TSQ 9000 Hardware Manual Thermo Scientific...
Page 161 Place this screw in a clean place until it is needed for reassembly. See Figure Figure 97. Removing the Set Screw Source Interface Board Screw Calibration and Reagent Gas Tubes Right Screw Thermo Scientific TSQ 9000 Hardware Manual...
Page 162 Be careful to not use excessive force so that the transfer line tip and source heater block are not damaged. Be sure not to bend the tubes or scratch the transferline. TSQ 9000 Hardware Manual Thermo Scientific...
Page 163 22. Remove the heat shield and wedge it between the source interface board and the wall of the manifold to disconnect the board from the 20-pin feedthrough. 23. Remove the bottom right screw holding the tray to the manifold. Thermo Scientific TSQ 9000 Hardware Manual...
Page 164 Removing the Analyzer Tray Components  To remove the analyzer tray components from the tray 1. Turn the analyzer tray to access the bottom and disconnect the three lens wires attached to the lenses between the quadrupoles. TSQ 9000 Hardware Manual Thermo Scientific...
Page 165 6. Remove the three screws holding the collision cell to the tray. 7. Remove the screw connecting the tray to the collision cell grounding wire. See Figure 104. 8. Remove the collision cell assembly and Q1 quad assembly from the analyzer tray. Thermo Scientific TSQ 9000 Hardware Manual...
Page 166 10. Remove the Q1 entrance lens wire from the source interface board. 11. Remove the ion guide assembly screws. 12. Remove the ion guide assembly. 13. Use a T10 Torxhead screwdriver to remove the lens heater block grounding strap from the analyzer tray. TSQ 9000 Hardware Manual Thermo Scientific...
Page 167 3. Make sure the ion guide is aligned parallel to the flat on the endcap. 4. Tighten the T10 screws inside the endcap. Note Make sure the Q1 entrance lens sits flush and centered in the Q1 entrance lens endcap. Thermo Scientific TSQ 9000 Hardware Manual...
Page 168 IMPORTANT For optimal performance, the quadrupole ceramics must fit straight and securely in the endcap and be aligned so that the collision cell is level with the tray. Slightly tighten each screw several times going from one to another until all are securely tightened. TSQ 9000 Hardware Manual Thermo Scientific...
Page 169 Tip The endcaps have cutouts that you should use to check to be sure the ceramics are aligned properly before attaching the two screws. Figure 109. Replacing the Collision Cell and Quadrupole 3 in the Analyzer Tray Q3 Exit Lens Assembly Q3 Quad Assembly Collision Cell Assembly Screws Thermo Scientific TSQ 9000 Hardware Manual...
Page 170 Replacing the Analyzer Tray in the TSQ 9000 Instrument  To replace the analyzer tray in the TSQ 9000 instrument 1. Put tray in manifold with transfer line out or pulled away. a. If the gas tubes are attached to the transfer line, it will not pull as far away from the path of the tray as would be best.
Page 171 Note The set screw is made from a special material to resist galling. Do not swap it with other screws. 5. Screw the analyzer tray into the manifold. Push the tray slightly right towards the transfer line, not left or away from the transfer line. Thermo Scientific TSQ 9000 Hardware Manual...
Page 172 Cela peut les désengager du support. 10. Align the manifold door with the ion source and screw it to the manifold. TSQ 9000 Hardware Manual Thermo Scientific...
Page 173 4. If you are using hydrogen, replace the front panel screw. 5. Replace the ion source cartridge. See “Reinserting the Extractabrite Ion Source Cartridge through the Vacuum Interlock” page 215 for more information. 6. Replace all hydrogen safety screws if you are using hydrogen. Thermo Scientific TSQ 9000 Hardware Manual...
Page 174 Advanced Troubleshooting Replacing Components of the Analyzer 7. Power-on the TSQ 9000 mass spectrometer. 8. If the GC is powered off, power it on and make sure vacuum compensation is on for the carrier gas flowing into the mass spectrometer.
Page 175: Ion Guide
127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. Turn the analyzer tray to access the bottom and disconnect the three lens wires attached to the lenses between the quadrupoles.
Page 176 8. Disconnect the Q1 entrance lens wire from the source interface board. 9. Remove the two screws on each side of the Q1 entrance endcap. Figure 115. Removing Screws from the Quadrupole Rod Endcaps Collision Cell Q1 Entrance Lens and Endcap Screws TSQ 9000 Hardware Manual Thermo Scientific...
Page 177 16. Rotate the clamp until the ion guide is locked in place. Make sure the ion guide is aligned parallel to the flat on the endcap. 17. Tighten the two T10 screws inside the endcap. Note Make sure the Q1 entrance lens sits flush and centered in the Q1 entrance lens endcap. Thermo Scientific TSQ 9000 Hardware Manual...
Page 178 IMPORTANT For optimal performance, the quadrupole ceramics must fit straight and securely in the endcap and be aligned so that the collision cell is level with the tray. Slightly tighten each screw several times going from one to another until all are securely tightened. TSQ 9000 Hardware Manual Thermo Scientific...
Page 179 22. Reattach the Q3 exit lens assembly and Q3 to the analyzer tray. Ensure that quadrupole 3 and the collision cell assembly are correctly positioned before tightening screws. 23. Reattach the two screws on each side of the quadrupole rod endcaps. Thermo Scientific TSQ 9000 Hardware Manual...
Page 180 25. Reconnect the Q1 entrance lens wire to the source interface board. 26. Once the components are correctly attached to the analyzer tray, follow the instructions “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142 to replace the tray in the TSQ instrument.
Page 181: Q1 Entrance Lens And Q1 Entrance Lens Endcap
127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. Turn the analyzer tray to access the bottom and disconnect the three lens wires attached to the lenses between the quadrupoles.
Page 182 8. Disconnect the Q1 entrance lens wire from the source interface board. 9. Remove the two screws on each side of the Q1 entrance endcap. Figure 125. Removing Screws from the Quadrupole Rod Endcaps Collision Cell Q1 Entrance Lens and Endcap Screws TSQ 9000 Hardware Manual Thermo Scientific...
Page 183 16. Insert Q1 and the collision cell assembly onto the analyzer tray. 17. Hold the collision cell and Q1 in the tray and make sure the quad and ion guide are correctly positioned before tightening the screws on the Q1 entrance lens endcap. Thermo Scientific TSQ 9000 Hardware Manual...
Page 184 Slightly tighten each screw several times going from one to another until all are securely tightened. Figure 128. Reattaching Quadrupole 1, the Ion Guide, and the Collision Cell Assembly to the Analyzer Tray Q1 Quad Assembly Collision Cell Ion Guide Screws TSQ 9000 Hardware Manual Thermo Scientific...
Page 185 Q3 Exit Lens Assembly Q3 Quad Assembly Collision Cell Assembly Screws 21. Reconnect the three lens wires attached to the lenses between the quadrupoles. 22. Reconnect the Q1 entrance lens wire to the source interface board. Thermo Scientific TSQ 9000 Hardware Manual...
Page 186 Advanced Troubleshooting Replacing Components of the Analyzer 23. Once the components are correctly attached to the analyzer tray, follow the instructions “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142 to replace the tray in the TSQ instrument.
Page 187: Ion Guide Wire Set
127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. Use a T10 Torxhead screwdriver to remove the screw connecting the ion guide wire to the top of the ion guide.
Page 188: Q1 Quad, Q3 Quad, And Collision Cell Assemblies
127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. Turn the analyzer tray to access the bottom and disconnect the three lens wires attached to the lenses between the quadrupoles.
Page 189 13. Slide the collision cell assembly onto the analyzer tray. Hold the collision cell and Q1 in the tray and make sure Q1 and the collision cell are correctly positioned before tightening the screws on the Q1 exit endcap. Thermo Scientific TSQ 9000 Hardware Manual...
Page 190 3 and the collision cell assembly are correctly positioned before tightening screws. 15. Reattach the two screws on each side of the quadrupole rod endcaps. Tip Look through the endcaps to be sure the quadrupole ceramics are aligned properly. TSQ 9000 Hardware Manual Thermo Scientific...
Page 191 Collision Cell Assembly Screws 16. Replace the analyzer tray into the instrument by following the instructions in “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142. 17. Restart your system by following the instructions in “Restarting the System”...
Page 192 127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. For both quad assemblies, use a T10 Torxhead screwdriver to remove the four screws around the rods.
Page 193 The screws are susceptible to falling between the rods. ATTENTION DOMMAGES À L’INSTRUMENT Soyez prudent lorsque vous enlevez et insérez les vis au niveau des bouchons de tige du quadripôle métallique. Ces vis peuvent tomber entre les barres. Thermo Scientific TSQ 9000 Hardware Manual...
Page 194 Quad Assembly Wire 6. Replace the analyzer tray into the instrument by following the instructions in “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142. 7. Restart your system by following the instructions in “Restarting the System” page 145.
Page 195: Q3 Exit Lens Assembly
127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. Turn the tray to access the bottom and remove the wire to the Q3 exit lens.
Page 196 7. Reattach the wire to the Q3 exit lens. 8. Replace the analyzer tray into the instrument by following the instructions in “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142. 9. Restart your system by following the instructions in “Restarting the System”...
Page 197: Replacing Components Of The Ion Source
Grounding Strap Spring Thumbscrew-Repeller Spacers Insulating Spacers NOTE: You can also replace the entire ion source cartridge, which consists of the locking ring, spring, nut, repeller, lenses, and sleeve. Ion Source Cartridge for details. Thermo Scientific TSQ 9000 Hardware Manual...
Page 198: Source Heater Block, Lens Heater Block, And Lens/Source Heater
127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. Disconnect the Q1 entrance lens, Q2 entrance lens, Q3 entrance lens, and Q3 exit lens wires from the source interface board using a flat-tipped screwdriver.
Page 199 8. Using a T10 Torxhead to remove the two screws on the mixing chamber and pull the chamber off. 9. Twist and remove the two source-repeller thumbscrews. Figure 145. Removing the Source-Repeller Thumbscrews Source-Repeller Thumbscrews Thermo Scientific TSQ 9000 Hardware Manual...
Page 200 10. Remove the thumbscrew-repeller spacers and set them aside. Figure 146. Removing the Thumbscrew-Repeller Spacers Thumbscrew-Repeller Spacers 11. Pull away the repeller plate and remove the insulating spacers. Figure 147. Removing the Repeller Plate and Insulating Spacers Repeller Plate TSQ 9000 Hardware Manual Thermo Scientific...
Page 201 à enlever. Pour éviter les dommages, séparez le bloc du plateau avant d’enlever le chauffage de lentille/source. Figure 149. Removing the Ion Source from the Analyzer Tray Ion Source Block Wires Thermo Scientific TSQ 9000 Hardware Manual...
Page 202 Replace the lens/source heater if necessary. Figure 150. Disconnecting the Lens/Source Heater Lens/Source Heater Screws and Cone Washers 15. Remove and replace the source heater block if necessary. Figure 151. Replacing the Source Heater Block Source Heater Block TSQ 9000 Hardware Manual Thermo Scientific...
Page 203 20. Reattach the lens/source heater to the new source heater block and set them next to the rest of the ion source. Figure 153. Reattaching the Lens/Source Heater Lens/Source Heater Screws and Cone Springs Thermo Scientific TSQ 9000 Hardware Manual...
Page 204 22. Reattach the two screws to the back of the ion source. Figure 155. Reconnecting the Source Block to the Analyzer Tray Screws 23. Reattach the repeller plate and insulating spacers. 24. Insert the thumbscrew-repeller spacers into a groove in the thumbscrew. TSQ 9000 Hardware Manual Thermo Scientific...
Page 205 Figure 157. Reconnecting the Lens Heater Block Grounding Strap Lens Heater Block Lens Heater Grounding Strap Screw 27. Reconnect the Q1 entrance lens, Q2 entrance lens, and Q3 exit lens wires to the source interface board using a flat-tipped screwdriver. Thermo Scientific TSQ 9000 Hardware Manual...
Page 206 Figure 158. Locating Wires on the Source Interface Board 28. Replace the analyzer tray into the instrument by following the instructions in “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142. 29. Restart your system by following the instructions in “Restarting the System”...
Page 207: Source-Repeller Thumbscrews
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. 2. Use a T20 Torxhead screwdriver to remove the four screws around the manifold door.
Page 208 Source-Repeller Thumbscrews 6. Attach new source-repeller thumbscrews to the ion source. 7. Reattach the manifold door and the four screws. 8. Restart your system by following the instructions in “Restarting the System” page 145. TSQ 9000 Hardware Manual Thermo Scientific...
Page 209: Thumbscrew-Repeller Spacers
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. 2. Use a T20 Torxhead screwdriver to remove the four screws around the manifold door.
Page 210 Also, do not over-tighten the thumbscrews or it may crack the spacers. 6. Reattach the source-repeller thumbscrews to the spacers. 7. Reattach the manifold door and the four screws. 8. Restart your system by following the instructions in “Restarting the System” page 145. TSQ 9000 Hardware Manual Thermo Scientific...
Page 211: Insulating Spacers
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. 2. Slide the top cover panel toward the back of the instrument and lift it off.
Page 212 Thumbscrew-Repeller Spacers 6. Move the locking ring out of the way. 7. Remove and replace the insulating spacers. Figure 167. Replacing the Insulating Spacers Insulating Spacers 8. Move the locking ring back into place. TSQ 9000 Hardware Manual Thermo Scientific...
Page 213 11. Reattach the manifold door and the four screws. 12. Reattach the top cover and tighten the top cover panel screw. 13. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 214: Repeller Plate
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. 2. Slide the top cover panel toward the back of the instrument and lift it off.
Page 215 5. Twist off each source-repeller thumbscrew. Figure 169. Removing the Source-Repeller Thumbscrews Source-Repeller Thumbscrews 6. Remove the thumbscrew-repeller spacers from the thumbscrews. Figure 170. Removing the Thumbscrew-Repeller Spacers Thumbscrew-Repeller Spacers 7. Move the locking ring out of the way. Thermo Scientific TSQ 9000 Hardware Manual...
Page 216 13. Reattach the source-repeller thumbscrews. 14. Reattach the manifold door and the four screws. 15. Reattach the top cover and tighten the screw. 16. Restart your system by following the instructions in “Restarting the System” page 145. TSQ 9000 Hardware Manual Thermo Scientific...
Page 217: Lens Heater Block Grounding Strap
127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. Use a T10 Torxhead screwdriver to disconnect the lens heater block grounding strap from the lens heater block.
Page 218: Lens Plate And Springs
127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. Use a T10 Torxhead screwdriver to disconnect the lens plate and springs from the lens heater block.
Page 219 6. Reattach the lens 1, lens 2, and lens 3 wires from the source interface board using a flat-tipped screwdriver. 7. Once the components are correctly reattached, follow the instructions in “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142 to replace the tray in the TSQ instrument.
Page 220: Source To Ion Guide Spacer
127. 2. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 3. Disconnect the Q1 entrance lens, Q1 exit lens, Q3 entrance lens, and Q3 exit lens from the source interface board using a flat-tipped screwdriver.
Page 221 5. Use a T20 Torxhead screwdriver to remove the two screws on the back of source block. Figure 177. Disconnecting the Source Block to the Analyzer Tray Screws Note Some of the pieces may detach as you loosen the screws. Do not let them fall. Thermo Scientific TSQ 9000 Hardware Manual...
Page 222 Figure 178. Removing the Ion Source from the Analyzer Tray Source Interface Board Source Block Wires 7. Remove and replace the source to ion guide spacer. Figure 179. Replacing the Source to Ion Guide Spacer Source to Ion Guide Spacer TSQ 9000 Hardware Manual Thermo Scientific...
Page 223 IMPORTANT When assembling the source and optics block, take extra care to ensure the blocks are centered properly and that the ion source cartridge provided with the instrument can easily slide in and out of the assembly. Thermo Scientific TSQ 9000 Hardware Manual...
Page 224 11. Reconnect the Q1 entrance lens, Q1 exit lens, Q3 entrance lens, and Q3 exit lens to the source interface board using a flat-tipped screwdriver. 12. Once the components are correctly reattached, follow the instructions in “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142 to replace the tray in the TSQ instrument.
Page 225: Ion Source Cartridge
Figure 183. Replaceable Components of the Extractabrite Ion Source Cartridge Lens 2 EI Ion Volume AEI Ion Cartridge Sleeve Repeller Lens 3/RF Lens Repeller Spring Lens 1 Ion Volume Locking Ring Ion Volume-Repeller Insulator Repeller Thermo Scientific TSQ 9000 Hardware Manual...
Page 226 Figure 184. Replaceable Components of the Advanced EI Ion Source Cartridge Lens 3/RF AEI Ion Volume Lens Insulator AEI Filament Ion Cartridge Sleeve Insulator Filament Vespel Cap Lens 2 AEI Ion Volume AEI Filament Shield AEI Filament Spacer TSQ 9000 Hardware Manual Thermo Scientific...
Page 227 After you reattach the knob, press the Evacuate button to remove any air inside the vacuum interlock. Thermo Scientific TSQ 9000 Hardware Manual...
Page 228 3. Grasp the handle of the source exchange tool in one hand and use your other hand to pull the metal barrel out and away from the handle so that tool is fully extended. 4. Attach the source exchange tool to the front of the instrument. TSQ 9000 Hardware Manual Thermo Scientific...
Page 229 Figure 187. Inserting the Ion Volume Tool b. Twist and push the stainless steel barrel to the right until it clicks into place under the screw at the top of the slot. Figure 188. Twisting the Tool Into Place Thermo Scientific TSQ 9000 Hardware Manual...
Page 230 6. Twist, then loosen the top part of the vacuum interlock handle to allow the entire handle to swing up and down. This handle controls the interior ball valve, which seals the vacuum chamber. TSQ 9000 Hardware Manual Thermo Scientific...
Page 231 LED will flash on and off. CAUTION INSTRUMENT DAMAGE: Make sure the vacuum interlock handle is all the way up. Otherwise if you insert the tool with the handle down, you can damage the instrument. Thermo Scientific TSQ 9000 Hardware Manual...
Page 232 11. Pull the tool toward you and down the left side of the metal track on the barrel. As you keep pulling it toward you, more and more of the barrel will be exposed. You may TSQ 9000 Hardware Manual Thermo Scientific...
Page 233 12. Once you reach the end of the track (when the back line at the end of the barrel is uncovered by the black handle), twist the handle to the left to lock it into place. Figure 193. Locking the Tool in Place Note: Tool Rotated Left Thermo Scientific TSQ 9000 Hardware Manual...
Page 234 16. Remove the tool from the instrument. TSQ 9000 Hardware Manual Thermo Scientific...
Page 235 Advanced Troubleshooting Replacing Components of the Ion Source Figure 195. Removing the Tool from the Instrument Thermo Scientific TSQ 9000 Hardware Manual...
Page 236 Figure 196. Exposing the Ion Source Cartridge Ion Source Cartridge 19. Invert the source exchange tool so that the barrel is pointed toward the floor. Figure 197. Inverting the Tool Ion Source Cartridge TSQ 9000 Hardware Manual Thermo Scientific...
Page 237 Advanced Troubleshooting Replacing Components of the Ion Source 20. Slide the source holder, which is in the TSQ 9000 Toolkit, onto the end of the ion source cartridge. The opening of the source holder is designed to accommodate the handles of the ion volume.
Page 238: Reassembling The Extractabrite Ion Source Cartridge
26. Replace the ion source cartridge or any individual component. Reassembling the Extractabrite Ion Source Cartridge 1. Place the ion volume-repeller insulator on the repeller and hold it in place with the repeller nut. Set it aside for now. TSQ 9000 Hardware Manual Thermo Scientific...
Page 239 3. Align the long tooth of lens 3/RF lens with the notch on the bottom of the sleeve and drop the lens into the sleeve. Figure 202. Inserting Lens 3/RF Lens into the Source Sleeve Long Tooth on Lens 3/RF Lens Tooth Fits Here Thermo Scientific TSQ 9000 Hardware Manual...
Page 240 5. With the longer teeth of lens 1 facing down toward lens 2, align the larger metal section of lens 1 with the sleeve window and let it fall into place. Figure 204. Inserting Lens 1 into the Source Sleeve Larger Metal Longer Teeth Section of Lens 1 Sleeve Window TSQ 9000 Hardware Manual Thermo Scientific...
Page 241 Lens 1 Gap Note The ion volume handles are different sizes and will only fit into the sleeve one way. 7. Insert the ion volume repeller insulator onto the repeller. 8. Tighten the repeller nut. Thermo Scientific TSQ 9000 Hardware Manual...
Page 242 9. Insert the large flat end of the repeller so that it rests on top of the ion volume. Figure 206. Inserting the Repeller into the Source Sleeve Large Flat End of Repeller 10. Slide the repeller spring onto the repeller. Figure 207. Inserting the Repeller Spring into the Sleeve Repeller Spring TSQ 9000 Hardware Manual Thermo Scientific...
Page 243: Interlock
IMPORTANT If you try to attach the ion source cartridge to the tool by inverting it, the components will likely fall, so make sure you are working over a table. Otherwise, you may have to stop and clean the components again. Thermo Scientific TSQ 9000 Hardware Manual...
Page 244 Using too much force when inserting the ion source cartridge into the barrel can cause damage. TSQ 9000 Hardware Manual Thermo Scientific...
Page 245 5. Gently pull the source holder away from the ion source cartridge. Figure 211. Removing the Source Holder Tip When the source exchange tool is inverted, the source should stay attached. If this does not happen, the source will not insert correctly into the instrument. Thermo Scientific TSQ 9000 Hardware Manual...
Page 246 9. Insert the barrel end of the ion cartridge tool into the vacuum interlock and twist it to the right to lock it into position. Be sure the black handle remains in the locked position. Figure 212. Evacuating the Instrument Evacuate Button TSQ 9000 Hardware Manual Thermo Scientific...
Page 247 IMPORTANT Make sure you take the correct track on the tool or the ion volume will disassemble inside the instrument. If that happens, the tool will get stuck and you will have to shut down, vent the TSQ 9000 instrument, and manually remove the source cartridge through the top of the instrument.
Page 248 14. Twist the handle of the source exchange tool to the right and pull it back toward you and down the right side of the barrel’s metal track until the line at the end of the track appears. Figure 214. Pulling the Tool Down the Right Track TSQ 9000 Hardware Manual Thermo Scientific...
Page 249: Removing The Extractabrite Ion Source Cartridge On A Tsq
Otherwise, the masses or intensities may drift during operation. Removing the Extractabrite Ion Source Cartridge on a TSQ 9000 System without a Vacuum Interlock 1. Click Shut Down on the TSQ Series Dashboard.
Page 250 3. Reach around the left side to the back of the instrument and push down on the power switch to power-off the instrument. 4. Open the front door of the TSQ 9000 mass spectrometer. 5. Open the front door of the instrument.
Page 251 9. Open the manifold door. You can now see the ion source block. Figure 218. Locating the Ion Source Block Ion Source Block 10. Insert the small source removal tool into the ion source block as shown in Figure 219. Thermo Scientific TSQ 9000 Hardware Manual...
Page 252 11. Twist the tool to the left. The ion source cartridge should now be connected to the small source removal tool. See Figure 220. Figure 220. Twisting the Small Source Removal Tool 12. Slowly remove the ion source cartridge from the instrument. TSQ 9000 Hardware Manual Thermo Scientific...
Page 253: Reinserting The Extractabrite Ion Source Cartridge Into A Tsq
16. Follow the steps in Reassembling the Extractabrite Ion Source Cartridge. Reinserting the Extractabrite Ion Source Cartridge into a TSQ 9000 System without a Vacuum Interlock IMPORTANT When inserting a cold ion source cartridge such as after cleaning, the ion...
Page 254 4. Remove the small source tool from the instrument. 5. Be sure that the source interface board wires do not touch anything metal in the manifold before closing the door. TSQ 9000 Hardware Manual Thermo Scientific...
Page 255 6. Close the manifold door and slightly tighten the vent valve knob by turning it one half turn clockwise. 7. Flip the power switch on the back of the TSQ 9000 instrument upwards to power on the instrument. This will help you achieve good vacuum.
Page 256: Removing The Advanced Ion Source Cartridge On A Tsq 9000 System
RF Lens spring contacts. Inserting the source with the gap shown in the tip above can help prevent contact issues. Removing the Advanced Ion Source Cartridge on a TSQ 9000 System 1. Click Shut Down on the TSQ Series Dashboard.
Page 257 Replacing Components of the Ion Source 5. Twist the vent valve knob one and a half times in a counter-clockwise direction to open the vent. Figure 225. Venting the TSQ 9000 Mass Spectrometer Vent Valve Knob 6. Wait five minutes for venting to complete.
Page 258 10. Disconnect the filament wires from the source interface board. Figure 227. Disconnect the Filament Wires Filament Wires 11. Grasp the Vespel cap and gently remove the Advanced EI ion source from the ion source block. See Figure 219. TSQ 9000 Hardware Manual Thermo Scientific...
Page 259: Reassembling The Advanced Ei Ion Source Cartridge
Source Cartridge” page 210 up until the filament although you may use gloved hands instead of the source holder. 1. Add the filament to the correctly assembled Advanced EI ion source cartridge. See Figure 230. Thermo Scientific TSQ 9000 Hardware Manual...
Page 260 Figure 230. Adding the Filament to the Advanced EI Ion Source Cartridge 2. Slide the ion source cartridge onto the Vespel cap. See Figure 231. Figure 231. Removing the Ion Source Cartridge 3. Insert the ion source cartridge into the source block. See Figure 232. TSQ 9000 Hardware Manual Thermo Scientific...
Page 261 7. Tighten the vent valve knob completely by turning it approximately one turn clockwise. 8. Close the front door of the instrument. 9. Restart the system as in “Powering On the TSQ 9000 System” page Thermo Scientific TSQ 9000 Hardware Manual...
Page 262: Replacing Components Of The Source Exchange Tool
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. Figure 234. Replaceable Components of the Source Exchange Tool Seal Clip Bushing TSQ 9000 Hardware Manual Thermo Scientific...
Page 263 Figure 236. Removing the Endcap Set Screw Endcap 6. Slide the handle off the rest of the tool. Set it aside. 7. Remove the interior shaft from the barrel. Figure 237. Removing the Interior Shaft Interior Shaft Barrel Thermo Scientific TSQ 9000 Hardware Manual...
Page 264 Replace the seal, if necessary. 11. Insert the flared end of the seal into the end of the barrel. Figure 239. Inserting the Seal Flared End of Seal Bushing Barrel TSQ 9000 Hardware Manual Thermo Scientific...
Page 265 20. Tighten the set screw. Note The purpose of the set screw is to keep the components together. Don’t overtighten it or the handle will be hard to slide up and down the barrel. Thermo Scientific TSQ 9000 Hardware Manual...
Page 266: Replacing Components Of The Vacuum Interlock
Inner Ball Seal Sealing Ball Outer Ball Seal  To replace the components of the vacuum interlock 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. TSQ 9000 Hardware Manual Thermo Scientific...
Page 267 Be sure to catch them and set them aside. Replace the spring and safety interlock, if necessary. Figure 244. Removing the Vacuum Interlock Knob Screws Spring and safety interlock are behind this screw Thermo Scientific TSQ 9000 Hardware Manual...
Page 268 5. Unscrew and then lower the vacuum interlock handle. 6. Pinch together the two springs on the left side the vacuum interlock shield and remove it. Figure 246. Removing the Vacuum Interlock Shield Vacuum Springs Interlock Handle Lower the Vacuum Interlock Handle TSQ 9000 Hardware Manual Thermo Scientific...
Page 269 8. Use a T20 Torxhead screwdriver to remove the four screws found in the four corners of the manifold door. 9. Use a flathead screwdriver to disconnect the foreline hose at the 90° hose connector. Thermo Scientific TSQ 9000 Hardware Manual...
Page 270 Figure 248. Removing the Clamp Foreline Hose Black Pillow Block Screws 11. Remove the three screws holding the metal valve body to the front manifold plate. Figure 249. Removing the Vacuum Interlock Handle Front Screws TSQ 9000 Hardware Manual Thermo Scientific...
Page 271 16. Remove the inner ball seal from the metal valve body. Replace the inner ball seal, if necessary. Tip It may be easier to remove the sealing ball if you push on it from the front, but be careful not to scratch the ball. Thermo Scientific TSQ 9000 Hardware Manual...
Page 272 Sealing Ball Outer Ball Seal 19. Pry the thin metal clip out of the groove. It holds all of the other components inside the metal valve body. Figure 253. Replacing the Metal Clip Clip TSQ 9000 Hardware Manual Thermo Scientific...
Page 273 21. Pull the valve axle out of the side of the metal valve body. Replace the valve axle, if necessary. 22. Remove the axle seal from the metal valve body. Replace the axle seal on the valve axle if necessary. Figure 255. Replacing the Axle Seal Axle Seal Thermo Scientific TSQ 9000 Hardware Manual...
Page 274 Figure 256. Reinserting the Valve Axle and Inner Ball Seal Inner Ball Seal Valve Axle 24. Reinsert the axle bearing into the metal valve body. 25. Press and twist the thin metal clip into the top groove. Figure 257. Reinserting the Clip Clip TSQ 9000 Hardware Manual Thermo Scientific...
Page 275 28. Insert the inner ball seal into the metal valve body. 29. Reattach the small spring and safety interlock to the metal valve body. Figure 259. Reattaching the Spring and Safety Interlock to the Metal Valve Body Safety Interlock Spring Thermo Scientific TSQ 9000 Hardware Manual...
Page 276 Figure 260. Reattaching the Metal Valve Body from the Front Manifold Plate Vacuum Interlock Handle Shaft Valve Axle Screws Pillow Block 31. Slide the black pillow block over and onto the end of the valve axle. TSQ 9000 Hardware Manual Thermo Scientific...
Page 277 Confirm the ball is fully opened and closed as the handle is moved up and down. Thermo Scientific TSQ 9000 Hardware Manual...
Page 278 34. Reattach the manifold door and the four screws. Figure 263. Reattaching the Manifold Door Screws 35. Hold the spring and safety interlock in place as you attach the vacuum interlock shield and screws. 36. Reattach the vacuum interlock knob. TSQ 9000 Hardware Manual Thermo Scientific...
Page 279 37. Reconnect the vacuum interlock cable from the connector. Figure 264. Reconnecting the Vacuum Interlock Cable Vacuum Interlock Cable Connector 38. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 280: Replacing Components Of The Manifold
Figure 265. Replaceable Components of the Manifold Back Source Magnet Plate Retainer Manifold O-Ring Manifold Door Hinge Vent Valve Knob and O-Ring Back Tray Alignment Pin Source Magnets Manifold O-Ring Bracket Front Plate TSQ 9000 Hardware Manual Thermo Scientific...
Page 281: Manifold Door Hinge
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge or the column.
Page 282 Replacing Components of the Manifold 4. The lens driver board is the first board standing on end in the center of the instrument. Figure 267. Locating the Lens Driver Board Lens Driver Board Bracket TSQ 9000 Hardware Manual Thermo Scientific...
Page 283 7. Pinch together the two springs on the left side the vacuum interlock shield to free the hinge from the vacuum interlock shield. Figure 269. Freeing the Hinge from the Vacuum Interlock Shield Springs Thermo Scientific TSQ 9000 Hardware Manual...
Page 284 8. Look through the left side of the instrument and use a T20 Torxhead screwdriver to remove the three screws connecting the hinge to the chassis. Figure 270. Replacing the Manifold Door Hinge Screws TSQ 9000 Hardware Manual Thermo Scientific...
Page 285 11. Align the connector on the bottom of the lens driver board with the connectors on the distribution board beneath it. It will click into place when its in the right position. Figure 271. Reinstalling the Lens Driver Board Connector Thermo Scientific TSQ 9000 Hardware Manual...
Page 286 Figure 272. Replacing the Lens Driver Board Lens Driver Board Screw 13. Replace the left hand front panel and tighten the two screws. 14. Restart your system by following the instructions in “Restarting the System” page 145. TSQ 9000 Hardware Manual Thermo Scientific...
Page 287: Front Manifold Plate
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge or the column.
Page 288 5. Lift the vacuum interlock shield off the instrument. The notch at the bottom of the track will go around the handle. Be sure to straighten the ball valve handle prior to removing the VPI shield. TSQ 9000 Hardware Manual Thermo Scientific...
Page 289 6. Use a T20 Torxhead screwdriver to remove the four screws found in the four corners of the manifold door. 7. Use a flat head screwdriver to remove the VPI pump tube. Figure 276. Detaching the Manifold Door VPI Pump Tube Screws Thermo Scientific TSQ 9000 Hardware Manual...
Page 290 9. Remove the three screws holding the metal block to the front manifold plate. Figure 278. Removing the Vacuum Interlock Handle Front Note: Tube attached Screws 10. Set the vacuum interlock and all of its components aside. TSQ 9000 Hardware Manual Thermo Scientific...
Page 291 13. Twist and remove the source magnet retainers that hold the magnet yoke to the back of the manifold door. The magnet yoke will pull free of the door, releasing the alignment collar. Figure 281. Removing the Magnet Yoke and Source Magnet Retainers Magnet Yoke Source Magnet Retainers Thermo Scientific TSQ 9000 Hardware Manual...
Page 292 Figure 283. Reattaching the Front Plate O-Ring Manifold O-ring 16. Reattach the magnet yoke, alignment collar, and source magnet retainers. Figure 284. Reattaching the Magnet Yoke and Source Magnet Retainers Magnet Yoke Source Magnet Retainers TSQ 9000 Hardware Manual Thermo Scientific...
Page 293 Figure 285. Reattaching the Vent Valve Knob and O-Ring Vent Valve O-ring Vent Valve Knob 18. Reattach the three screws and metal block to the front manifold plate. Figure 286. Reattaching the Metal Block Note: Tube attached Screws Thermo Scientific TSQ 9000 Hardware Manual...
Page 294 19. Reattach the two screws and black clamp to the front manifold plate Figure 287. Reattaching the Clamp Clamp Screws 20. Pinch the springs together and reattach the vacuum interlock shield to the hinge. Figure 288. Removing the Vacuum Interlock Shield Ball Valve Springs Handle TSQ 9000 Hardware Manual Thermo Scientific...
Page 295 Figure 289. Reattaching the Vacuum Interlock Shield Screws Vacuum Interlock Shield 22. Reconnect the vacuum interlock cable and tubing Figure 290. Reattaching the Vacuum Interlock Cable and Vacuum Interlock Knob Vacuum Interlock Knob Vacuum Interlock Cable Connector Thermo Scientific TSQ 9000 Hardware Manual...
Page 296 Advanced Troubleshooting Replacing Components of the Manifold 23. Reattach the vacuum interlock knob. 24. Restart your system by following the instructions in “Restarting the System” page 145. TSQ 9000 Hardware Manual Thermo Scientific...
Page 297: Back Manifold Plate
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge.
Page 298 6. Remove the analyzer tray from the instrument by following the instructions in “Removing the Analyzer Tray from the TSQ 9000 Instrument” page 129. 7. Disconnect the power cable from the left side of the TSQ 9000 instrument. Figure 292. Disconnecting the Power Cables Power Cable 8.
Page 299 14. Reattach the two screws holding the power supply to the instrument. 15. Reconnect the power cables on the left hand sub panel of the TSQ 9000 instrument. 16. Replace the analyzer tray into the instrument by following the instructions in “Replacing...
Page 300: Magnet Yoke, Manifold O-Ring, And Source Retainer Magnets
Back Manifold Plate. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. You do not have to remove the ion source cartridge or the column. If you are using hydrogen as a carrier gas, power off the GC.
Page 301 Figure 295. Replacing the Magnet Yoke, Manifold O-ring, and Source Magnets Manifold O-ring Magnet Yoke Source Retainer Magnets 4. Close the manifold door and reattach the four screws. 5. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 302: Vent Valve Knob And O-Ring
127. You do not have to remove the ion source cartridge or column. If you are using hydrogen as a carrier gas, power off the GC. Figure 296. Powering Off the TSQ 9000 Instrument Top Cover Panel Vacuum Interlock Shield...
Page 303: Replacing Components Of The Electron Multiplier
Electron Multiplier For information about replacing the electron multiplier, see Replacing the Electron Multiplier. The electron multiplier is replaced more frequently than the other components, so it is described in Chapter 2: Performing Routine Maintenance. Thermo Scientific TSQ 9000 Hardware Manual...
Page 304: Electron Multiplier Plate
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge or the column. However, you must vent the instrument.
Page 305 CAUTION - ELECTRICAL HAZARD Avoid dropping screws between chassis and side cover or board. If you drop a screw, find it before powering the instrument on again. Figure 300. Removing the Electrometer Board Screws Electron Multiplier Plate Thermo Scientific TSQ 9000 Hardware Manual...
Page 306 Feedthrough and O-ring Screws 7. Use a T20 Torxhead screwdriver to remove the four screws at each corner of the electron multiplier plate. Figure 302. Disconnecting the Electron Multiplier Plate Electron Multiplier Plate Screws TSQ 9000 Hardware Manual Thermo Scientific...
Page 307 13. Put the electron multiplier plate back into place on the manifold and reattach the four screws. Reattach the electrometer board and the four screws. 14. Reattach the electrometer shield and the two screws Thermo Scientific TSQ 9000 Hardware Manual...
Page 308 CAUTION INSTRUMENT DAMAGE: Do not mix up the cables or you will damage the power supply. 16. Reattach the top cover panel and tighten the screw. 17. Restart your system by following the instructions in “Restarting the System” page 145. TSQ 9000 Hardware Manual Thermo Scientific...
Page 309: Large Feedthroughs
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering these components. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge or the column. However, you must vent the instrument.
Page 310 8. Use a T20 Torxhead screwdriver to reattach the four screws at each corner of the electron multiplier plate 9. Reconnect the large feedthrough cables. 10. Reattach the top cover panel and tighten the screw. 11. Restart your system by following the instructions in “Restarting the System” page 145. TSQ 9000 Hardware Manual Thermo Scientific...
Page 311: Anode Feedthrough
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge or the column. However, you must vent the instrument.
Page 312 Figure 308. Removing the Electrometer Board Screws 6. Remove the electrometer board to reveal the anode feedthrough. Figure 309. Removing the Anode Feedthrough, O-ring, Standoff and Screws Anode Feedthrough and O-ring Standoff Screws TSQ 9000 Hardware Manual Thermo Scientific...
Page 313 10. Reattach the electrometer board and the four screws that hold it in place. 11. Reattach the electrometer shield and the four screws. 12. Reconnect the electrometer board cable and large feedthrough cables. 13. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 314: Reinstalling The Tsq 9000 System Software
Reinstalling the TSQ 9000 System Software Reinstalling the TSQ 9000 System Software Your TSQ 9000 system has software on the instrument, as well as on the computer that was shipped with it. This section describes how to upgrade both of them.
Page 315: Upgrading Software On The Computer
Foundation and Xcalibur. If the CD contains later versions, follow the steps in the installation help document on the CD to update your software. To use Thermo Foundation 3.1 SP4 and Xcalibur 4.0 on Thermo Scientific GC-MS systems, you must have Xcalibur 4.0 Core Components for GC-MS installed on your computer.
Page 316: System Requirements
The following system requirements apply to the Xcalibur 4.0and Foundation 3.1 SP4 core components. Layered applications may have different, higher requirements. Please refer to the applicable documentation and ensure that your PC meets the requirements before proceeding. Your TSQ 9000 data system must meet these minimum requirements. System Requirements Hardware •...
Page 317: Installing The Software Set
Note Check the latest Xcalibur Core Components for GC-MS CD for the most recent version of these installation instructions. To view the installation help document, select Browse CD and open the TSQ 9000 Installation Help pdf. 1. Insert the Xcalibur 4.0 Core Components for GC-MS CD into the CD/DVD-ROM drive of your computer.
Page 318 Advanced Troubleshooting Reinstalling the TSQ 9000 System Software 6. Click on the NIST Browser button to install the NIST MS Browser. This functionality is required to allow automatic searching of libraries from Xcalibur or layered applications. Install the NIST Browser according to the installation instructions. The NIST installer will automatically create the required folders for the browser and demo libraries.
Page 319: Replacing The Covers Of The Tsq 9000 Instrument
If the covers of your instrument get damaged, you can use the illustration below to visually locate a component and then follow the process to replace it. Figure 312. Replaceable Covers of the TSQ 9000 Instrument Top Cover Panel and Screws...
Page 320: Top Cover Panel
Replacing the Covers of the TSQ 9000 Instrument Top Cover Panel  To replace the top cover panel of the TSQ 9000 instrument Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System”...
Page 321: Left Hand Front Panel And Left Hand Sub Panel
Left Hand Front Panel and Left Hand Sub Panel  To replace the left hand front panel and the left hand sub panel of the TSQ 9000 instrument Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component.
Page 322 Advanced Troubleshooting Replacing the Covers of the TSQ 9000 Instrument Figure 315. Finding the Inputs and Screws on the Left Hand Sub Panel Screw System Mech Pump Reagent Gas Connectors Optional Mech Pump AC Input Connector Collision Gas Intake Accessory...
Page 323: Right Side Panel
Replacing the Covers of the TSQ 9000 Instrument Right Side Panel  To replace the right side panel of the TSQ 9000 instrument Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System”...
Page 324: Top Manifold Cover
Advanced Troubleshooting Replacing the Covers of the TSQ 9000 Instrument Top Manifold Cover  To replace the top manifold cover Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System”...
Page 325: Replacing The Chassis Feet
4. Remove the small and large glass covers in the manifold. 5. Carefully tip the TSQ 9000 instrument and rest it on its left side. 6. Use a T20 Torxhead screwdriver to remove the screws holding any damaged feet to the bottom of the instrument.
Page 326 Advanced Troubleshooting Replacing the Covers of the TSQ 9000 Instrument 11. Replace the analyzer tray into the instrument by following the instructions in “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142. 12. Restart your system by following the instructions in “Restarting the System”...
Page 327: Replacing Components Of The Front Door
Replacing Components of the Front Door Replacing Components of the Front Door If the front door of your TSQ 9000 instrument gets damaged, you can use the illustration below to visually locate a replaceable component and then follow the process to replace it.
Page 328: Front Door Hinges And Supports
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. You do not have to remove the ion source cartridge or column or vent the instrument.
Page 329 Note Replace one hinge at a time to prevent the door from falling. 7. Reattach the left hand front and top cover panels and tighten the screws. 8. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 330: Front Door Latch
4. Slide the top cover panel off the instrument. 5. Open the front door of the GC and disconnect the column and transfer line nut. 6. Move the TSQ 9000 instrument away from the GC so you can access the transfer line on the right side.
Page 331 11. Reattach the right side and top cover panels and tighten the screws. 12. Reattach the GC to the transfer line. 13. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 332: Replacing The Boards In The Tsq 9000 Instrument
Replacing the Boards in the TSQ 9000 Instrument Replacing the Boards in the TSQ 9000 Instrument If the boards in your TSQ 9000 instrument get damaged, you can use the illustration below to visually locate a board and then follow the process to replace it.
Page 333: Front And Rear Rf Boards And Front And Rear Rod Driver Boards
3. The front RF board is the second board standing on end toward the center of the instrument. The rear RF board is the third board standing on end toward the center of the TSQ 9000 instrument. Use a T20 Torxhead screwdriver to remove the screw holding the board and bracket to the chassis.
Page 334 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Rear RF Front RF Board Board Brackets 5. To remove the front RF board, use your fingers to pry the brackets of the board away from the chassis and toward the left side of the instrument.
Page 335 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 327. Removing the RF Board from the Instrument 7. Use a T10 Torxhead screwdriver to remove the three screws at each corner of the rod driver board. Be careful not to drop the parts under the metal cover.
Page 336 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 8. Use a 2.5 mm nut driver to remove the standoffs on the rod driver board. Figure 328. Disconnecting the Rod Driver Board from the RF Board Screws Standoffs Rod Driver Board 9.
Page 337 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 330. Disconnecting the Rod Driver Board 7-Pin Connector 7-Pin Connector Note Be careful not to bend the connector on the rod driver board on the pins on the RF board.
Page 338 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 14. Insert a new RF board by aligning the connectors on the bottom of the board with the connectors on the distribution board beneath it. It will drop into the slot when it is in the right position.
Page 339: Rf Board/Rod Driver Board Kits
2. Slide the top cover panel toward the back of the instrument and lift it off. Note The TSQ 9000 system contains a front and a rear RF board/rod driver kit. The steps are the same to replace each kit, except for the location.
Page 340 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Rear RF Front RF Board Board Brackets 5. Use your fingers to pry the bracket of the board away from the chassis and toward the left side of the instrument.
Page 341 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 7. Insert a new RF board/rod driver board kit by aligning the connectors on the bottom of the board with the connectors on the distribution board beneath it. It will drop into the slot when it is in the right position.
Page 342: Pin Feedthrough
Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 4- Pin Feedthrough  To replace the 4-pin feedthrough: Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering these components. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System”...
Page 343 6. Remove the RF board attached to the feedthrough you wish to change. The front RF board is the second board standing on end toward the center of the TSQ 9000 instrument. The rear RF board is the second board standing on end toward the center of the instrument.
Page 344 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 7. Locating the RF Boards and Brackets Rear RF Front RF Board Board Brackets 8. Use your fingers to pry the bracket of the board away from the chassis and toward the left side of the instrument.
Page 345 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 338. Removing the Large Glass Manifold Covers Large Glass Manifold Cover CAUTION - ELECTRICAL HAZARD Avoid dropping screws between chassis and side cover or board. If you drop a screw, find it before powering the instrument on again.
Page 346 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 13. Remove and replace the 4-pin feedthrough. You can also remove and replace the o-ring, if necessary. 14. Reattach the 4-pin feedthrough to the chassis. 15. Replace the large glass manifold cover.
Page 347: Lens Driver Board
Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Lens Driver Board  To replace the lens driver board Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System”...
Page 348 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 5. The lens driver board is the first board standing on end in the center of the instrument. Figure 341. Locating the Lens Driver Board Lens Driver Bracket Board CAUTION - INSTRUMENT DAMAGE Limit handling of the boards as much as possible.
Page 349 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 6. Look through the left side of the instrument and use a T20 Torxhead screwdriver to loosen the screw holding the board to the chassis. Tip The bracket has a white diagram describing the location of this screw. It is approximately two inches from the top of the board directly under the white label.
Page 350 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 9. Insert a new lens driver board by aligning the connector on the bottom of the board with the connectors on the distribution board beneath it. It will drop into the slot when it is in the right position.
Page 351 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 20-Pin Feedthrough To replace the 20-pin feedthrough: Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System”...
Page 352 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument ATTENTION DOMMAGES À L’INSTRUMENT Limitez au maximum la manipulation des cartes. Ne touchez aucun composant de carte. Gardez la carte uniquement près du support en tôle. Figure 345. Locating the Lens Driver Board...
Page 353 8. Remove the top manifold cover (glass) out of the top of the instrument and set it aside. 9. Open the front door of the TSQ 9000 instrument. 10. Use a T20 Torxhead screwdriver to remove the four screws around the manifold door.
Page 354 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 347. Opening the Manifold Door Screws 11. Open the manifold door and slide the filament board and wires off the pins on the source interface board. Figure 348. Disconnecting the Filament Wires...
Page 355 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 349. Removing the Heat Shield Filament Board Source Interface Left and Wires Board Screw Heat Shield Note Keep all manifold parts you remove covered on a clean work surface so they will not accumulate dust.
Page 356 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 14. From the left side of the instrument, use a T20 Torxhead screwdriver to remove the three screws around the 20-pin feedthrough. Figure 351. Removing the 20-Pin Feedthrough 20-Pin Feedthrough Screws 15.
Page 357 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 16. From the left side of the instrument, reattach the three screws around the 20-pin feedthrough. Tighten the screws uniformly. Figure 353. Reattaching the 20-Pin Feedthrough 20-Pin Feedthrough Screws 17. Look through the top of the instrument and align the pins on the 20-pin feedthrough with the holes in the source interface board to connect them together.
Page 358 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 21. Reinsert the lens driver board by aligning the connector on the bottom of the board with the connectors on the distribution board beneath it. It will drop into the slot when it is in the right position.
Page 359: Bracket
Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument PC Communication Board, Controller Interface Board, and Support Bracket  To replace the PC communication board, controller interface board, or support bracket Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering these components.
Page 360 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument ATTENTION DOMMAGES À L’INSTRUMENT Limitez au maximum la manipulation des cartes. Ne touchez aucun composant de carte. Gardez la carte uniquement près du support en tôle. 5. Locate the PC communication board, which is attached to the controller interface board.
Page 361 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 8. Remove the controller interface board and PC communication board from the instrument. Figure 357. Removing the Controller Interface Board Support Bracket Controller Interface Board Support Bracket PC Communication Board 9.
Page 362 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 358. Removing the Support Bracket Screws Screws TSQ 9000 Hardware Manual Thermo Scientific...
Page 363 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 11. Incrementally, and very carefully, disconnect the PC communication board from the controller interface board by separating the two connectors. Inspect the pins to be certain they are not bent.
Page 364 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 15. Insert the new controller interface board by aligning the two connectors on the bottom of the board to the connectors on the distribution board beneath it. It will drop into the slot when it is in the right position.
Page 365: Distribution Board
Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Distribution Board The distribution board lies on the bottom of the TSQ 9000 instrument chassis.  To replace the distribution board Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component.
Page 366 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument ATTENTION DOMMAGES À L’INSTRUMENT Limitez au maximum la manipulation des cartes. Ne touchez aucun composant de carte. Gardez la carte uniquement près du support en tôle. 5. Locate the PC communication board, which is attached to the controller interface board.
Page 367 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 8. Remove the controller interface board and PC communication board from the instrument. Figure 363. Removing the Controller Interface Board Support Bracket Controller Interface Board Support Bracket PC Communication Board 9.
Page 368 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 364. Removing the Chassis Cooling Fan and Pan Plenum Fan Plenum Front Screws 12. Disconnect the fan from the distribution board on the bottom of the instrument. TSQ 9000 Hardware Manual...
Page 369 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 13. The lens driver board is the first board standing on end in the center of the instrument. Figure 365. Locating the Lens Driver Board Lens Driver Bracket Board Thermo Scientific...
Page 370 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 14. Look through the left side of the instrument and use a T20 Torxhead screwdriver to loosen the screw holding the board to the chassis. Tip The bracket has a white diagram describing the location of this screw. It is approximately two inches from the top of the board directly under the white label.
Page 371 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument the TSQ 9000 instrument. Use a T20 Torxhead screwdriver to remove the screws holding the board and brackets to the chassis. Figure 367. Locating the RF Boards and Brackets Front RF...
Page 372 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 368. Removing the Front RF Board from the TSQ 9000 Instrument 20. To remove the rear RF board, use your fingers to pry the brackets of the board away from the chassis and toward the left side of the instrument.
Page 373 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 24. Use a T20 Torxhead screwdriver to remove the two screws holding the power module to the instrument. Figure 370. Removing the Power Module Screws Screws 25. Pull the power supply out of the top of the instrument.
Page 374 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 371. Removing the Dynode/Multiplier Power Supply Dynode/Multiplier Power Supply Bottom Screw 27. Disconnect the 1/16 in. collision gas tubing from the bulkhead compression fitting located on the left hand sub panel.
Page 375 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 372. Disconnecting the Cable to the Bulkhead Fitting Collision Gas Module Bulkhead Tubing Fitting 28. Disconnect the collision gas module cable from the distribution board. 29. If you are using CI, follow the instructions in the...
Page 376 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Figure 373. Disconnecting the Distribution Board Distribution Board Cables 31. Disconnect all the cables from the distribution board. Also remove the cable that enters the chassis from the back panel.
Page 377 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 43. Reconnect the large feedthrough cables on the electron multiplier plate. 44. Reattach the RF boards by aligning the connectors on the bottom of the board with the connectors on the distribution board beneath it. The boards will drop into their slots when they are in the right position.
Page 378 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument connectors on the distribution board beneath it. It will click into place when its in the right position. Figure 375. Reinstalling the Controller Interface Board Connectors Figure 376. Reinstalling the Controller Interface Board...
Page 379: Source Interface Board And Heat Shield
Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Source Interface Board and Heat Shield  To replace the source interface board and heat shield Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering these components.
Page 380 Figure 378. Reconnecting the Source Interface Board Wires 8. Once the components are correctly attached to the analyzer tray, follow the instructions “Replacing the Analyzer Tray in the TSQ 9000 Instrument” page 142 to replace the tray in the TSQ instrument.
Page 381: Electrometer Board Cable
2. Slide the top cover panel toward the back of the instrument and lift it off. 3. Disconnect the electrometer board cable Figure 379. Disconnecting the Electrometer Board Cable Electrometer Board Cable 4. Remove all power connections from the TSQ 9000 instrument. Thermo Scientific TSQ 9000 Hardware Manual...
Page 382 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 5. Use a T20 Torxhead screwdriver to remove the two screws holding the power module to the instrument. Figure 380. Removing the Power Module Screws Screws 6. Pull the power supply out of the top of the instrument.
Page 383: Electrometer Board And Shield
Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument Electrometer Board and Shield  To replace the electrometer board and shield Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering these components. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System”...
Page 384 Advanced Troubleshooting Replacing the Boards in the TSQ 9000 Instrument 6. Remove the four screws holding the electrometer board in place Figure 382. Replacing the Electrometer Board Screws 7. Remove and replace the electrometer board if necessary. 8. Reattach the screws that hold the electrometer board in place.
Page 385: Replacing The Power Supplies
Replacing the Power Supplies Replacing the Power Supplies If the power supplies in your TSQ 9000 instrument get damaged, you can use the illustration below to visually locate a power supply and then follow the process to replace it. Figure 383. Replaceable Power Supply Components...
Page 386: Power Module
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge or the column or vent the instrument.
Page 387 Advanced Troubleshooting Replacing the Power Supplies Figure 384. Locating the TSQ 9000 System Power Cables System Mech Pump Optional Mech Pump AC Input Connector Thermo Scientific TSQ 9000 Hardware Manual...
Page 388 It will drop into the connector when it is in the right position. 8. Make sure the new module is flush against the top of the chassis and the screw holes line 9. Reattach the two screws holding the power module to the instrument. TSQ 9000 Hardware Manual Thermo Scientific...
Page 389 11. Reattach the top cover panel and tighten the screw holding it in place. Reattach the hydrogen safety screws if you are using hydrogen. 12. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 390: Dynode And Multiplier Power Supply
If you are using hydrogen as a carrier gas, power off the GC. 2. Slide the top cover panel toward the back of the instrument and lift it off. 3. Remove all power connections from the TSQ 9000 instrument. TSQ 9000 Hardware Manual...
Page 391 5. Make sure the electrometer board cable is not in the way when you remove the power module. 6. Grasp the power supply system and lift it out of the instrument. It fits snugly, so you may have to gently shake it as you lift it out. Thermo Scientific TSQ 9000 Hardware Manual...
Page 392 7. Disconnect the large feedthrough cables labeled Dynode and Electron Multiplier. Figure 387. Disconnecting the Electron Multiplier Cables Electrometer Board Cable Dynode Electron Multiplier Electron Multiplier Plate 8. Disconnect the cables from the clips attached to the chassis. TSQ 9000 Hardware Manual Thermo Scientific...
Page 393 It will drop into place when it is in the right position. Note A new dynode/multiplier power supply may have a right angle bracket attached to the top of the supply. Remove this bracket before placing the supply into the TSQ 9000 instrument. Thermo Scientific...
Page 394 14. Connect the large feedthrough cables. 15. Replace the main power supply. 16. Reattach the top cover panel and tighten the screw. 17. Restart your system by following the instructions in “Restarting the System” page 145. TSQ 9000 Hardware Manual Thermo Scientific...
Page 395: Replacing The Calibration Gas Components
Replacing the Calibration Gas Components Replacing the Calibration Gas Components If the calibration gas components of your TSQ 9000 instrument get damaged, you can use the illustration below to visually locate a component and then follow the process to replace it.
Page 396: Calibration Gas Module
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge or column.
Page 397 Interface Board Support Bracket 6. Disconnect the Ethernet cable from the PC communication board. Figure 393. Disconnecting the Ethernet Cable from the PC Communication Board Controller Interface Board PC Communication Ethernet Board Cable Connector Connectors Thermo Scientific TSQ 9000 Hardware Manual...
Page 398 The rear RF board is the third board standing on end toward the center of the TSQ 9000 instrument. Use a T20 Torxhead screwdriver to remove the screw holding the board and bracket to the chassis.
Page 399 12. Lift the lens driver board out of the instrument. Be careful as space is limited. CAUTION - INSTRUMENT DAMAGE Limit handling of the boards as much as possible. Do not touch any board components. Hold the board by the sheet metal bracket only. Thermo Scientific TSQ 9000 Hardware Manual...
Page 400 Note If you are using CI, you will have P1 and P2 electrical wires. 15. Disconnect the P1 and P2 electrical wires from the front of the calibration gas controller. Note If you have a single-level calibration gas controller, your instrument only has a P1 connector. TSQ 9000 Hardware Manual Thermo Scientific...
Page 401 23. Push the board down into the connectors. 24. Gently push the RF board toward the instrument, carefully aligning the board over the feedthrough pins, until it stops. 25. Reattach the screw holding the RF board to the bracket. Thermo Scientific TSQ 9000 Hardware Manual...
Page 402 27. Push the board down into the connectors. 28. Look through the left side of the instrument and use a T20 Torxhead screwdriver to reattach the screw holding the lens driver board in place on the chassis. TSQ 9000 Hardware Manual Thermo Scientific...
Page 403 33. Reattach the top cover and left hand front panels and tighten the screws. If you are using hydrogen, reattach the hydrogen safety screws. 34. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 404: Calibrant Reservoir Kit
If you are using hydrogen as a carrier gas, power off the GC. 2. Unscrew the hydrogen safety screw. 3. Open the front door of the TSQ 9000 instrument. 4. Twist the calibrant reservoir cover counter-clockwise and remove it from the calibration gas module.
Page 405 8. Close the front door of the instrument. 9. If you are using hydrogen as a carrier gas, attach the hydrogen safety screws and restart your GC by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 406: Transfer Line
127. 2. Open the front door of the GC and disconnect the column and transfer line nut. 3. Move the TSQ 9000 instrument away from the GC so you can access the transfer line on the right side. WARNING BURN HAZARD: The transfer line may be hot, so be careful.
Page 407 9. Remove the screw on the lower right side that is holding the analyzer tray to the manifold. Figure 404. Disconnecting the Analyzer Tray from the Instrument Calibration and Reagent Gas Tubes Right Screw Hole Thermo Scientific TSQ 9000 Hardware Manual...
Page 408 15. Attach a new transfer line. Note The reagent gas and calibration gas tubes in the manifold conduct gas to the mixing chamber. Make sure these two tubes are attached to the transfer line and mixing chamber before proceeding. TSQ 9000 Hardware Manual Thermo Scientific...
Page 409 20. Close the front door of the manifold and reattach the four screws. 21. Slide the right side panel back onto the instrument and reattach the screws. 22. Reposition the TSQ 9000 instrument closer to the GC. 23. Reinsert the column to the proper length and tighten the transfer line nut. See “Replacing...
Page 410: Replacing The Collision Gas Components
Replacing the Collision Gas Components Replacing the Collision Gas Components The collision gas components you can order and replace in the TSQ 9000 system are the collision gas module, the collision gas tubing, the tee that connects the collision gas tubing to the foreline adapter, and the foreline adapter itself.
Page 411 Advanced Troubleshooting Replacing the Collision Gas Components 7. Move the TSQ 9000 instrument away from the GC so you can access the transfer line on the right side. WARNING BURN HAZARD: The transfer line may be hot, so be careful.
Page 412 12. To remove the rear RF board, use your fingers to pry the brackets of the board away from the chassis and toward the left side of the instrument. 13. Lift the board out of the TSQ 9000 instrument. TSQ 9000 Hardware Manual...
Page 413 Figure 409. Removing the Controller Interface Board Support Bracket Controller Interface Board Support Bracket 15. Remove the controller interface board and PC communication board from the instrument. The boards are attached together. 16. Disconnect the Ethernet cable from the PC communication board. Thermo Scientific TSQ 9000 Hardware Manual...
Page 414 18. If you need to replace the tee, unscrew it from the foreline adapter and replace it. You may also replace the foreline adapter if necessary. 19. Disconnect the collision gas tubing from the module. The tubing is secured to the module using a compression fitting. TSQ 9000 Hardware Manual Thermo Scientific...
Page 415 If you are replacing the tubing to the collision cell, disconnect the collision gas tubing from the collision cell and from the compression fitting on the manifold. Figure 413. Disconnecting the Tubing from the Collision Cell Collision Gas Tubing Thermo Scientific TSQ 9000 Hardware Manual...
Page 416 Figure 415. Disconnecting the Cable to the Bulkhead Fitting Collision Gas Module Bulkhead Tubing Fitting 25. Use a T20 Torxhead screwdriver to remove the two screws on the collision gas module. 26. Remove the collision gas module and replace if necessary. TSQ 9000 Hardware Manual Thermo Scientific...
Page 417 36. Replace the rear RF board. 37. Replace the top, left hand front, and right side panels and secure with screws. 38. Move the TSQ 9000 next to the GC. 39. Restart your system by following the instructions in “Restarting the System”...
Page 418: Replacing Fans And Filters
Replacing Fans and Filters Replacing Fans and Filters To efficiently cool the TSQ 9000 instrument while it is being used, air must be allowed to flow in through the front of the instrument and out the back. The instrument is equipped with a fan that keeps the air flowing and filters that minimize the amount of dust that enters the system.
Page 419 Advanced Troubleshooting Replacing Fans and Filters Fan Plenum Air Deflector Left Rear Wire Turbo Cooling Fan Thermo Scientific TSQ 9000 Hardware Manual...
Page 420: Front Wire Mesh Filter
Note If needed, you can order an additional dust filter. See the ISQ and TSQ GC-MS Spare Parts Guide for ordering information. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127.
Page 421: Left Rear Wire Mesh Filter
To replace the left rear wire mesh filter Note See the ISQ and TSQ GC-MS Spare Parts Guide for ordering information. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge or column or vent the instrument.
Page 422: Chassis Cooling Fan And Fan Plenum
Note See the ISQ and TSQ GC-MS Spare Parts Guide for information about ordering this component. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. Note You do not have to remove the ion source cartridge or column or vent the instrument.
Page 423 Tip The bracket has a white diagram describing the location of this screw. It is approximately two inches from the top of the board directly under the white label. Thermo Scientific TSQ 9000 Hardware Manual...
Page 424 Figure 421. Removing the Lens Driver Board Lens Driver Board Screw 7. Loosening the screw will separate the board from the instrument. The screw is captured, so do not attempt to completely remove it from the board and bracket. 8. Lift the lens driver board out of the instrument. Be careful as space is limited. CAUTION - INSTRUMENT DAMAGE Limit handling of the boards as much as possible.
Page 425 Fan Plenum Front Screws 9. Remove the six screws holding the fan plenum to the chassis. Two are on the left side of the instrument, and four are attached to the interior front panel. Thermo Scientific TSQ 9000 Hardware Manual...
Page 426 19. Replace the lens driver board by aligning the connector on the bottom of the board with the connectors on the distribution board beneath it. It will drop into the slot when it is in the right position. 20. Push the lens driver board down into the connector. TSQ 9000 Hardware Manual Thermo Scientific...
Page 427 22. Reattach the left hand front panel and tighten the four screws holding it in place. 23. Reattach the top cover panel and tighten the screw holding it in place. 24. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 428: Air Deflector
Note See the ISQ and TSQ GC-MS Spare Parts Guide for ordering information. 1. Shut down your system by following the steps in “Shutting Down the TSQ 9000 System” page 127. You do not need to remove the ion source cartridge or column or vent the instrument.
Page 429 8. Reattach the two rivets holding the air deflector to the chassis cooling fan. 9. Reattach the four screws securing the left hand front panel to the chassis. 10. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 430: Turbo Cooling Fan And Turbo Cooling Fan Filter
2. Slide the top cover panel toward the back of the instrument and lift it off. 3. Move the GC away from the TSQ 9000 instrument. 4. Use a T20 Torxhead screwdriver to remove the five screws on the right side panel.
Page 431 7. Lift the left hand front panel off the instrument. 8. The lens driver board is the first board standing on end in the center of the instrument. Figure 429. Locating the Lens Driver Board Lens Driver Bracket Board Thermo Scientific TSQ 9000 Hardware Manual...
Page 432 11. Lift the lens driver board out of the instrument. Be careful as space is limited. CAUTION - INSTRUMENT DAMAGE Limit handling of the boards as much as possible. Do not touch any board components. Hold the board by the sheet metal bracket only. TSQ 9000 Hardware Manual Thermo Scientific...
Page 433 Advanced Troubleshooting Replacing Fans and Filters ATTENTION DOMMAGES À L’INSTRUMENT Limitez au maximum la manipulation des cartes. Ne touchez aucun composant de carte. Gardez la carte uniquement près du support en tôle. Thermo Scientific TSQ 9000 Hardware Manual...
Page 434 Fan Plenum Front Screws 12. Remove the six screws holding the fan plenum to the chassis. Two are on the left side of the instrument, and four are attached to the interior front panel. TSQ 9000 Hardware Manual Thermo Scientific...
Page 435 17. If you need to replace the turbo cooling fan filter, use a T10 Torxhead screwdriver to remove the four screws holding the turbo cooling fan filter to the interior front panel. 18. Remove and replace the turbo cooling fan filter. Thermo Scientific TSQ 9000 Hardware Manual...
Page 436 Figure 433. Replacing the Turbo Cooling Fan Filter Screws 19. Reattach the two screws holding the turbo cooling fan filter to the interior front panel. Figure 434. Replacing the Turbo Cooling Fan Turbo Cooling TSQ 9000 Hardware Manual Thermo Scientific...
Page 437 28. Replace the left hand front panel and reattach the four screws. 29. Replace the top cover panel and reattach the top cover panel screw. 30. Reattach the GC. 31. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 438: Replacing The Turbomolecular Pump
Right Side Panel Screws 4. Make sure the electrometer board cable is not in the way when you remove the power module. 5. Disconnect the power cables from the side of the TSQ 9000 instrument. TSQ 9000 Hardware Manual Thermo Scientific...
Page 439 Advanced Troubleshooting Replacing the Turbomolecular Pump Figure 437. Locating the TSQ 9000 System Power Cables System Mech Pump Optional Mech Pump AC Input Connector Thermo Scientific TSQ 9000 Hardware Manual...
Page 440 Figure 438. Removing the Power Module Screws Screws 7. Grasp the power supply system and lift it out of the instrument. It fits snugly, so you may have to gently shake it as you lift it out. TSQ 9000 Hardware Manual Thermo Scientific...
Page 441 11. Use a 13 mm wrench to loosen the four clamps at the top of the turbomolecular pump. 12. Remove the two clamps that hold the turbomolecular pump to the manifold on the transfer line side. Thermo Scientific TSQ 9000 Hardware Manual...
Page 442 15. Insert a new turbomolecular pump into the chassis. Note There is a centering ring with an o-ring seal that must be correctly placed between the pump and the vacuum manifold. Figure 441. Installing the Turbomolecular Pump TSQ 9000 Hardware Manual Thermo Scientific...
Page 443 24. Replace the right side panel and tighten the five screws. 25. Replace the top cover panel and tighten the screw. 26. Reattach the GC. 27. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 444: Convectron Gauge And Foreline Adapter With Hose
Figure 442. Locating the Left Hand Front Panel Screws Screws Left Hand Front Panel Screw on Front of Instrument 4. Lift the left hand front panel off the instrument. 5. Move the GC away from the TSQ 9000 instrument. TSQ 9000 Hardware Manual Thermo Scientific...
Page 445 Figure 443. Removing the Right Side Panel Screws Right Side Panel Screws 7. Disconnect the vacuum hose from the adapter on the foreline pump. 8. Remove the rough pump clamp on the turbomolecular pump and the adapter. Thermo Scientific TSQ 9000 Hardware Manual...
Page 446 13. Reattach the right side panel and the screws holding it in place. 14. Replace the top cover panel and tighten the screw. 15. Reattach the GC. 16. Restart your system by following the instructions in “Restarting the System” page 145. TSQ 9000 Hardware Manual Thermo Scientific...
Page 447: Chapter 4 Upgrade Equipment
Upgrade Equipment This chapter describes how to install the upgrade equipment that is available for the TSQ 9000 mass spectrometer. See the TSQ 9000 Spare Parts Manual for information about ordering the equipment in this chapter. Contents • Advanced EI Ion Source •...
Page 448: Advanced Ei Ion Source
Advanced EI Ion Source Advanced EI Ion Source If you did not order a TSQ 9000 system with an Advanced EI ion source, you can order a system later. You must change the source magnets on the manifold door to use an Advanced EI source.
Page 449 Figure 447. Assembling the Advanced EI Source Magnets and Yoke Advanced EI Magnet Yoke Source Magnets 8. Attach the source magnets and yoke to the manifold door using the new tray alignment pins in the Advanced EI source kit. See Figure 448. Thermo Scientific TSQ 9000 Hardware Manual...
Page 450 Figure 448. Attaching the Magnets and Yoke to the Manifold Door 9. Use a T20 Torx key to align the magnets correctly. See Figure 449. Figure 449. Aligning the Magnets 10. Use the same T20 Torx key to tighten the magnets. See Figure 450. TSQ 9000 Hardware Manual Thermo Scientific...
Page 451 Figure 451. Removing the ExtractaBrite Ion Source 12. Remove the AEI Source from the case. See Figure 452. Figure 452. Removing the AEI Source from the Storage 13. Install the AEI Source manually. See Figure 453. Thermo Scientific TSQ 9000 Hardware Manual...
Page 452 16. Restart your system by following the instructions in “Restarting the System” page 145. 17. Store the ExtractaBrite source and the magnet parts in the AEI Case and screw the case insert top down. See Figure 455. TSQ 9000 Hardware Manual Thermo Scientific...
Page 453 Upgrade Equipment Advanced EI Ion Source Figure 455. Storing Extra Source Parts in the AEI Source Case Thermo Scientific TSQ 9000 Hardware Manual...
Page 454: Dust Filter
Dust Filter Dust Filter An optional dust filter is available for the TSQ 9000 system. It helps prevent dust from accumulating on the electrical components and damaging your system. If you have a particularly dusty environment, the dust filter will help your instrument operate at a cooler temperature for a longer period of time.
Page 455: Ci Reagent Gas Flow Module
The CI reagent gas flow module controls the flow of CI reagent gas into the ion source and is located at the back left of the TSQ 9000 instrument. The module uses electronic pressure control to precisely set the flow of reagent gas. The flow is programmed using the instrument control software, which allows you to accurately reproduce flows.
Page 456 Figure 458. Locating Components on the Left Hand Sub Panel Left Hand System Mech Pump Reagent Gas (A & B) Connectors Screw Sub Panel Power Switch Optional Mech Pump Connection AC Input Connector Screw Screw TSQ 9000 Hardware Manual Thermo Scientific...
Page 457 8. Remove the three screws holding the left hand sub panel to the chassis and pull the panel away to expose the screws that hold the CI reagent gas flow module to the chassis. Thermo Scientific TSQ 9000 Hardware Manual...
Page 458 Bracket Screws 10. Disconnect the Ethernet cable from the PC communication board. 11. Remove the controller interface board and PC communication board from the instrument. The two boards are connected. Do not separate them. TSQ 9000 Hardware Manual Thermo Scientific...
Page 459 14. Use a T20 Torxhead screwdriver to detach the two screws holding the CI reagent gas flow module to the chassis Figure 462. Installing the CI Reagent Gas Flow Module Screws CI Reagent Gas Flow Module CI Output Foreline Gas Connector Tube Thermo Scientific TSQ 9000 Hardware Manual...
Page 460 20. Look through the top of the instrument and confirm that the CI tube is attached to the mixing chamber and manifold wall. Figure 464. Attaching a CI Tube to the Mixing Chamber and Manifold Wall Small Glass Manifold Cover CI Tube Manifold Wall TSQ 9000 Hardware Manual Thermo Scientific...
Page 461 Make sure these gases are properly exhausted and all gas fittings on the system are leak-free. Consult your local Environmental and Safety Regulations for information about how to properly exhaust fumes from your laboratory. Thermo Scientific TSQ 9000 Hardware Manual...
Page 462 33. Restart your system by following the instructions in “Restarting the System” page 145. Note Purge air fro the CI reagent gas supply tubing overnight before using your TSQ 9000 instrument to acquire data. TSQ 9000 Hardware Manual Thermo Scientific...
Page 463: Ci Ion Volume
Locking Ring Repeller Spring Ion Cartridge Sleeve Lens 1 Lens 3/RF Lens Repeller Repeller Figure 467. Ion Volumes Available for the TSQ 9000 Mass Spectrometer EI Ion Volume CI Ion Volume EI/CI Ion Volume Thermo Scientific TSQ 9000 Hardware Manual...
Page 464: Ei/Ci Ion Volume
Locking Ring Repeller Spring Ion Cartridge Sleeve Lens 1 Lens 3/RF Lens Repeller Repeller Figure 469. Ion Volumes Available for the TSQ 9000 Mass Spectrometer CI Ion Volume EI Ion Volume EI/CI Ion Volume TSQ 9000 Hardware Manual Thermo Scientific...
Page 465: Ion Gauge And Tube Shield
2. Slide the top cover panel toward the back of the instrument and lift it off. 3. Move the GC away from the TSQ 9000 instrument. 4. Use a T20 Torxhead screwdriver to remove the five screws on the right side panel.
Page 466 9. Attach the 14-pin cable to the distribution board and ion gauge board. Figure 472. Connecting the Ion Gauge Cable to the Distribution Board Ion Gauge Cable Connector 10. Remove the plug on the bottom of the manifold. TSQ 9000 Hardware Manual Thermo Scientific...
Page 467 13. Replace the right side panel and attach the screws holding it in place. 14. Reattach the top cover panel and tighten the screw holding the top cover panel in place. 15. Restart your system by following the instructions in “Restarting the System” page 145. Thermo Scientific TSQ 9000 Hardware Manual...
Page 468: Probe Controller
 To install a DIP or DEP 1. Place the direct probe controller on top of or near the TSQ 9000 instrument. 2. Connect the 9-pin cable to the direct probe controller and to the Accessory Start connector on the left hand sub panel of the instrument.
Page 469 CI ion volume installing, back manifold plate CI reagent gas flow module installing, installing, boards cleaning replacing delicate components, drying delicate components, 20-pin feedthrough kit, drying durable components, 4-pin feedthrough, Thermo Scientific TSQ 9000 Hardware Manual...
Page 470 TSQ 9000 Hardware Manual Thermo Scientific...
Page 471 Thermo Scientific TSQ 9000 Hardware Manual...
Page 472 TSQ 9000 Hardware Manual Thermo Scientific...
Page 473 (complete), probe controllers electron multiplier components installing, pumps anode feedthrough, foreline (roughing), electron multiplier plate, large feedthroughs, front door components quadrupole rod endcap (metal), replacing, hinges and supports, quadrupole wires, replacing, latch, Thermo Scientific TSQ 9000 Hardware Manual...
Page 474 TSQ 9000 Hardware Manual Thermo Scientific...
Page 475 TSQ 9000 vent valve knob and o-ring, replacing, configuring, 4, 294, 359, 411, venting the TSQ 9000, filters, V-lock source plug foreline pump, lights on front panel, model and serial number, power supplies,...

Thermo Scientific TSQ 9000 Hardware Manual

Preface

Chapter 1 Performing Routine Maintenance

Chapter 2 Troubleshooting

Chapter 3 Advanced Troubleshooting

Quick Links

Troubleshooting

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Summary of Contents for Thermo Scientific TSQ 9000

Table of Contents