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Thermo Scientific Ion Trap Series Hardware Manual

Thermo Scientific Ion Trap Series Hardware Manual

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Xcalibur
Ion Trap Series
Hardware Manual
120425-00HW Revision B
November 30, 2009

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Summary of Contents for Thermo Scientific Ion Trap Series

  • Page 1 Xcalibur Ion Trap Series Hardware Manual 120425-00HW Revision B November 30, 2009...
  • Page 2 SGE product. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries. Ion Trap series refers to ITQ and PolarisQ instruments. DSQ series refers to all DSQ and DSQ II instruments. Information about the TRACE GC and FOCUS GC instruments is included in this document.

  • Page 3: Reader's Survey

    Reader’s Survey Ion Trap Series Hardware Manual, 120425-00HW, Revision B Free gift for your returned Reader’s Survey. Please help us improve the quality of our documentation by completing and returning this survey. Circle one number for each statement: Strongly Strongly...
  • Page 5 EMC Directive 89/336/EEC EMC compliance has been evaluated by Professional Testing. • PolarisQ, ITQ, and Ion Trap Series standards: EMC EN 55011:1998 + EN 50082-1:1998, Safety EN 61010-1:1990 + A1:1992 + A2:1995 • DSQ standards: EMC EN 61326-1:1998 + A1:1998. Safety EN 61010-1:1990 + A1:1992 + A2:1995 •...
  • Page 6 WARNING Read and understand the various precautionary notes, signs, and symbols contained inside this manual pertaining to the safe use and operation of this product before using the device. Notice on Lifting and Handling of Thermo 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.
  • Page 7 WEEERoHS for further information on Thermo Fisher Scientific’s compliance with these Directives and the recyclers in your country. WEEE Konformität Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC erfüllen. Das Produkt ist durch folgendes Symbol gekennzeichnet: Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann.

  • Page 9: Table Of Contents

    Replacing the Calibration Gas Flow Module ......83 Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 10 Vacuum Manifold ..........161 Ion Trap Series Hardware Manual...
  • Page 11 Cable Connections ..........225 Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 12 Index ............. . .231 Ion Trap Series Hardware Manual...

  • Page 13: Preface

    The repair of instrument failures caused by operation in a manner not specified by the manufacturer is specifically excluded from the Standard Warranty and service contract coverage. Thermo Scientific Ion Trap Series Hardware Manual xiii...

  • Page 14: Power Ratings

    Note Emphaizes important information about a task. Tip Helpful information that can make a task easier. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 15: Safety Symbols And Signal Words

    We use this symbol and another appropriate safety symbol to alert to an imminent or potential hazard that could cause personal injury. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 16: Contacting Us

    Series. These documents are also available on a “Print-By-Request” basis. Ion Trap Series Document Set, PN 120425-0ALL • ITQ Preinstallation Guide, PN 120425-00PI • Ion Trap Series Hardware Manual, PN 120425-00HW • Ion Trap Series User’s Guide, PN 120425-USER Instrument Help is available from within the software.

  • Page 17: Chapter 1 Routine Operations

    Routine Operations This chapter describes how to use the Ion Trap Series mass spectrometer. This mass spectrometer uses ion trap technology that gives analysts, technicians, and technical directors a powerful tool for mass spectrometry and complete control when using the Xcalibur software.

  • Page 18: Installing A Gc Column

    1. Connect the column to the injector, as shown in Figure Figure 1. GC Injector (Front) Distance Injector Column Injector Ferrule Column Outlet Injector Nut Transfer Line Note Wear clean, lint- and powder-free gloves when you handle the column and injector ferrule. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 19 Raise the oven and injector temperatures to 50 °C and allow them to stabilize. Then confirm that the carrier gas is on. CAUTION - INSTRUMENT DAMAGE. Do not allow the clear plastic component to exceed 80 °C. Otherwise, it will melt and damage the instrument. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 20 LEFT COLUMN INFO Length (m) 15.00 ID (mm) 0.25 Film th. (um) 0.25 1. These settings could also apply to a right column. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 21 4.90 Use <STOP> to abort Note To abort column evaluation, you can press STOP. The following message will display if the operation was successful. L. COL. EVALUATION COMPLETED Calc’d ID 0.242 K. 0.9020 Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 22 1. This item appears if the relevant channel is present and configured. c. Scroll to a channel to open the left or right column’s leak check menu. L. COL. LEAK CHECK Start Leak Check Leak Check Settings Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 23 Tip Leaks can be caused by not tightening the fitting on the clear plastic component. We recommend that you check that fitting before looking elsewhere. Repeat the column evaluation and leak check until no leaks are indicated. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 24 Column Measuring Tool Column Measuring Tool* Column Transfer Line Ferrule Septum Transfer Line Nut * The Column Measuring Tool is sold separately and can be purchased through Thermo Fisher Scientific using part number 119640-0550. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 25 5. Remove the column, transfer line nut and ferrule from the column measuring tool, as shown in Figure Figure 5. Transfer Line (Front) Purchase the Column Measuring Tool PN 119640-0550 from Thermo Fisher Scientific. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 26 4. Push the column in until you can see it through the inlet valve. 5. Pull the column back just far enough that you cannot see it. 6. Tighten the transfer line nut and transfer line union. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 27 Raise the oven temperature to the maximum temperature you will operate the column (normally 300 °C). b. Wait 10 minutes. c. Lower the oven temperature to 40 °C and allow it to cool before continuing. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 28 Raise the oven temperature to the initial temperature you will use (normally 40 °C). Note Turn on vacuum compensation (under the Right or Left Carrier menu). Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 29: Removing A Gc Column

    2. Remove the column from the transfer line, as shown in Figure Figure 6. Transfer Line (Front) Septum Transfer Line Union Transfer Line Nut Transfer Line a. Unscrew the transfer line nut. b. Remove the column from the transfer line. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 30: Starting Up

    This forces air to be drawn through the column. This large air leak into the mass spectrometer may cause the ion source to require cleaning as well as potentially damaging the column. c. Plug in the mass spectrometer power cord. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 31 Within 10 minutes of powering on the detector, vacuum should read OK. If it does not read OK, refer to “Troubleshooting” page 123. c. Allow the mass spectrometer to stabilize for at least 30 minutes before running samples. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 32: Shutting Down

    • Tune waits for the ion source to cool to < 175 C to prevent oxidizing the hot parts when they are exposed to air 4. Wait for the transfer line to cool below < 175 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 33 Turn off the gas chromatograph using the GC main circuit breaker. b. Turn off the GC helium supply at the tank. c. Turn off the optional autosampler by using the main power On/Off switch. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 34 Routine Operations Shutting Down Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 35: Maintenance

    “Cleaning the Ion Trap” page 61 • “Maintaining the Ion Detector System” page 65 • “Maintaining a High-Vacuum Pump” page 70 • “Maintaining a Rotary-Vane Pump” page 71 • “Finding Components and Assemblies” page 75 Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 36: Main Components

    Maintenance Main Components Main Components Figure 10. Maintenance Components (Top View) Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 37: Recommended Maintenance Schedule

    • Screwdriver, flat blade • Wrench, adjustable • Wrench, Allen, 2 mm, 2.5 mm, 3 mm, 4 mm, 5/32-in., 5/64-in., 1/16-in. • Wrench, open-ended, 1/4-in., 5/16-in., 7/16-in. (2), 1/2-in., 9/16-in. • Wrench, socket, 1/2-in. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 38 * As needed depends on how close the component is to the sample introduction point. For example, the Ion Volume is closer to the sample introduction point than any other component and requires the most frequent cleaning. ** Perform every month if you use ammonia as a chemical ionization reagent gas. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 39 Maintenance Recommended Maintenance Schedule Figure 11 illustrates the sequence to follow when performing routine maintenance on the mass spectrometer. Figure 11. Sequence of Routine Maintenance (no inlet valve) Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 40: Removing The Covers

    Figure 12. Removing the Front Cover Left-Hand Slot Right-Hand Slot 4. Reverse these steps to reinstall the cover. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 41 4. Slide the top cover forward about 2.5 cm (1-inch). 5. Lift the top cover up and away from the mass spectrometer. 6. Reverse these steps to reinstall the mass spectrometer top cover. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 42 Figure 14. Removing the Right Cover Screws holding the right cover 5. Slide the cover towards the back and pull it away from the instrument. 6. Reverse these steps to reinstall the mass spectrometer right cover. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 43 Figure 15. Removing the Left Cover Screw holding left cover in place WAR NING H IG H VO LTA G E A ND H O T SU R FA C E S C AU TIO N Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 44 )Remove the front and top covers, as described in “Removing the Covers” page Note Completely vent the instrument to atmospheric pressure for approximately four minutes, or the cover will be difficult to remove. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 45 CAUTION INSTRUMENT DAMAGE. Even the smallest amount of dust or lint on the electron multiplier, or ion trap can cause spectral noise or instrument damage. 3. Replace the vacuum manifold cover. 4. Replace the covers. 5. Restart your system. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 46: Assembling The Ion Source And Ion Trap

    With your right hand, grasp the exit lens mounting bracket and move it left and right as you slide the magnet yoke to the left. 2. Replace the ion source and ion trap. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 47 CAUTION INSTRUMENT DAMAGE. Overtightening the thumbscrews can cause the ion trap spacers or the ceramic lens holders to crack when the ion source is heated. The thumbscrews should only be tight enough to prevent the endcap electrodes from rotating. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 48: Cleaning Parts

    These procedures can be used to clean other stainless steel, ceramic, aluminum, and gold-plated parts within the mass spectrometer. However, use caution when doing so, as some components can be damaged when exposed to liquids. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 49 Clean each part thoroughly, even if no contamination is visible. c. Use the wooden end of an applicator cut at an angle to clean the inside corners. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 50 GC oven. 8. Dry the parts in an oven set at 100 C for 30 minutes. 9. Allow the parts to cool before putting them back together. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 51 WARNING - BURN HAZARD. The Dremel tool uses an electric motor that may generate sparks. These sparks can set solvents on fire. Do not use flammable solvents with the Dremel tool. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 52 5. Rinse the parts with acetone. Using forceps, dip the parts in a beaker of acetone. Change the acetone if it becomes cloudy. Do not soak or sonicate the parts. 6. Blow-dry the parts immediately. Use clean, dry gas to blow the acetone off the parts. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 53: Cleaning The Ion Source Components

    59 Figure 18 illustrates the ion source. Figure 18. Ion Source Components (Left View) Ion Source Lenses Magnet Support Filament Assembly Magnets Ion Source Block Ion Volume (inside the Ion Source Block) Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 54 Click Insert/Remove Probe in the mass spectrometer Status tab. Figure 19. I/R Tool and Guide Bar Alignment Line Guide Bar Track Lock Position First Stop Unlock Position Guide Bar I/R Tool Guide Ball Hole Bayonet Lock Guide Ball Second Stop Handle Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 55 Figure 19. Push the guide bar in as far as it will go, then rotate it 90-degrees counter-clockwise to lock the guide bar in position. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 56 Tighten the inlet valve knob to ensure a leak-tight seal. e. In Xcalibur’s Insert/Remove Probe window, click the Evacuate Inlet Valve button. Figure 22. Insert/Remove Probe Window Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 57 . Listen for a click indicating the handle is fully engaged in the lock position and is holding the ion volume. c. Withdraw the I/R tool (the ion volume is attached) until the guide ball reaches the first stop (see Figure 21). Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 58 If you are cleaning a CI ion volume, be sure to clean out the small electron entrance hole. Aluminum oxide can get trapped in this hole, which can adversely affect sensitivity. Use a dental pick or old syringe needle to clean the hole. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 59 Turn the I/R tool so the guide ball is in the groove at the first stop. This prevents the probe from being pulled forward when the inlet valve is evacuated. c. Tighten the inlet valve knob to ensure a leak-tight seal. d. In Xcalibur’s Insert/Remove Probe window, select Evacuate Inlet Valve. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 60 CAUTION INSTRUMENT DAMAGE. Do not withdraw the I/R tool beyond the point where the guide ball reaches the first stop in the guide bar until the inlet valve is closed. Otherwise, the system vents to the atmosphere and cleaning may be required. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 61 Remove the guide bar by rotating it 90-degrees counter-clockwise and sliding it out of the entry housing. b. Replace the inlet valve plug. c. In Xcalibur’s Insert/Remove Probe window, click the Close button. Figure 27. Insert/Remove Probe Window Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 62 • Wrench, open-ended, 5/16-in. • Wrench, Allen, 4 mm 1. Close the inlet valve by pulling the inlet valve lever down, as shown in Figure Figure 28. Inlet Valve Seal Inlet Valve Seal Inlet Valve Lever Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 63 30) into the inlet valve. Figure 30. Inlet Valve Seal Removal Tool (PN 119283-0001) b. Press the button on the tool to engage the seal. c. Pull out the seal and discard it. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 64 Remove the four hex-socket screws that hold the Inlet valve entry housing to the vacuum manifold. e. Remove the inlet valve from the vacuum manifold and place it on a clean surface. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 65 Remove the vacuum manifold cover, as described in “Removing the Vacuum Manifold Cover” page 28. Note Wear clean, lint- and powder- free gloves when you handle parts inside the vacuum manifold. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 66 Turn the ion volume tool handle 30° counter-clockwise to engage the ion volume holder. c. Use the ion volume tool to pull the ion volume straight back and through the opening in the ion source PCB. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 67 Use a dental pick or old syringe needle to clean the hole. 4. Replace the ion volume. a. Insert the ion volume holder onto the end of the ion volume tool, as shown in Figure Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 68 CAUTION INSTRUMENT DAMAGE. Make sure the arrows on the ion volume tool and ion volume are aligned to avoid damaging the ion source. 5. Restore the mass spectrometer for operation. a. Replace the vacuum manifold cover. b. Replace the covers. c. Restart the system. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 69 Remove the ion source and ion trap (“To disassemble/assemble the ion source and ion trap, you will need:” page 30). b. Remove the two thumbscrews holding the ion trap and ion source together, as shown Figure Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 70 Ion Source Springs Ion Source Lenses Two thumbscrews holding the Ion Ion Trap Trap and Ion Source c. Remove the magnet yoke and ion source. d. Remove the lenses from the ceramic lens holder. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 71 “To disassemble/assemble the ion source and ion trap, you will need:” page 5. Restore the mass spectrometer for operations. a. Replace the vacuum manifold cover. b. Replace the covers. c. Restart the system. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 72 “Removing the Vacuum Manifold Cover” page Figure 36. Removing the ion source and ion trap Magnet Yoke Ion Source Two Springs Ion Source Lenses Two thumbscrews holding the Ion Trap Ion Trap and Ion Source Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 73 Gently remove the ion source PCB from the ion source by sliding the three cartridge heaters and temperature sensor off the ion source and pulling the filament straight away from the three filament connectors on the ion source block PCB. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 74 “To disassemble/assemble the ion source and ion trap, you will need:” page 4. Restore the mass spectrometer for operation. a. Replace the vacuum manifold cover. b. Replace the covers. c. Restart the system. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 75 “Removing the Covers” page d. Remove the vacuum manifold cover. e. Remove the ion source and ion trap. Note Wear clean, lint- and powder- free gloves when you handle parts inside the vacuum manifold. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 76 Insert the ion source and ion trap into the vacuum manifold. 5. Restore the mass spectrometer for operation. a. Replace the vacuum manifold cover. b. Replace the covers. c. Restart the system. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 77: Cleaning The Ion Trap

    Cleaning frequency depends on the type and quantity of the compounds that you analyze. With normal use, you do not have to clean the ion trap more than once every two years. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 78 Remove the front cover, top cover, and vacuum manifold cover, as described in “Removing the Covers” page d. Remove the ion source and ion trap. Note Wear clean, lint- and powder- free gloves when you handle parts inside the vacuum manifold. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 79 Place the components in a beaker and cover them with acetone. b. Place the beaker in an ultrasonic bath for about 10 minutes. c. Pour the acetone out of the beaker. d. Rinse the components with fresh acetone. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 80 “To disassemble/assemble the ion source and ion trap, you will need:” page 7. Restore the mass spectrometer for operation. a. Replace the vacuum manifold cover. b. Replace the covers. c. Restart the system. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 81: Maintaining The Ion Detector System

    Pull up on right side of electron multiplier c. Slide electron multiplier out of the clip on the left side 3. Install new electron multiplier a. Slide electron multiplier into the clip on the left side Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 82 16). WARNING - ELECTRICAL SHOCK HAZARD. Unplug the mass spectrometer before proceeding. c. Remove the front and top covers as described in “Removing the Covers” page d. Remove the vacuum manifold cover. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 83 Shut down and vent the mass spectrometer (“Shutting Down” page 16). WARNING - ELECTRICAL SHOCK HAZARD. Unplug the mass spectrometer before proceeding. c. )Remove the front, top, and left covers as described in “Removing the Covers” page Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 84 Remove the two nuts and two hex-socket screws holding the electrometer PCB cover in place (Figure 43) and then remove the cover. c. Remove the screw holding the electrometer PCB wire to the anode feedthrough, which is shown in Figure Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 85 Use the two nuts and two screws to reattach the electrometer PCB cover to the vacuum manifold. d. Reconnect the electrometer PCB cable. 6. Restore the mass spectrometer for operation. a. Replace the vacuum manifold cover. b. Replace the covers. c. Restart the system. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 86: Maintaining A High-Vacuum Pump

    The high-vacuum pump is located directly under the vacuum manifold. It provides the high vacuum that is necessary for ion detection. There are two types of high-vacuum pumps available for the Ion Trap Series—a 250 L/s or a 70 L/s turbomolecular pump. Each contains a lifetime supply of lubricant for the bearings.

  • Page 87: Maintaining A Rotary-Vane Pump

    MIN Mark Inlet Port Oil Level Sight Glass Gas Ballast Control Mode Selector Oil Filler Plugs On/Off Switch Outlet Port Lifting Handle Every 1,000 hours if using ammonia as a reagent gas for CI. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 88 If the oil level goes above the MAX level mark, remove the drain plug and drain the excess oil into a suitable container. 4. Insert the oil filler plug back into the rotary-vane pump. 5. Plug in the rotary-vane pump and mass spectrometer. 6. Restart the system. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 89 Be careful, however, as the oil can still be very hot at this time. 1. Shut down and vent the mass spectrometer system described in “Shutting Down” page WARNING - ELECTRICAL SHOCK HAZARD. Shut down and unplug the mass spectrometer and rotary-vane pump before adding oil. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 90 Remove the oil drain plug and allow the oil to drain into a suitable container. iii. Dispose of the spent oil according to local environmental regulations. iv. Replace the oil drain plug. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 91: Finding Components And Assemblies

    Technical Support, or a Thermo Fisher Scientific Customer Service Engineer. CAUTION INSTRUMENT DAMAGE. Avoid damaging the PCBs with electrostatic discharge by attaching a properly grounded electrostatic discharge (ESD) strap to your wrist before replacing fuses. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 92 “Replacing the Vent Valve Solenoid” page 120 As needed means you should only replace the part when instructed by Tune Diagnostics, Thermo Fisher Scientific Technical Support or a Thermo Fisher Scientific Customer Service Engineer. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 93 Figure 51. Replaceable Parts behind the Left Cover CI Reagent Gas Flow Module Balun PCB Calibration Gas Flow Module RF Generator PCB RF Detector PCB (covered) Conversion Dynode and Electron Multiplier Power Supply Low Pass Filter PCB (covered) Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 94 Digital PCB Analog PCB Figure 53. Replaceable Parts behind the Right Cover Lens Interface PCB High-Vacuum Pump Transfer Line Convectron Gauge and Foreline Adapter Damping Gas Flow Module 6 Turbo Pump Power Supply Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 95: Replacing The Analog Pcb

    To get access to the analog PCB, you must remove the digital PCB. The removal process is described in “Replacing the Digital PCB” page b. Disconnect the remaining cables from the analog PCB. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 96 Vacuum Control PCB Cable Connector Connector GC Start Cable Six nuts holding the Analog PCB to the left Connector cover Lens Interface PCB Fuse Cable Connector CI Reagent Gas Flow Digital PCB Cable Connector Module Cable Connector Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 97: Replacing A Fuse On The Analog Pcb

    2 A, very fast 76339-0008 Heater microfuse, 125 V 3. Restore the mass spectrometer for operation. a. Replace the covers. b. Restart the system. c. Run Tune diagnostics to verify that your system is operational. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 98: Balun Pcb

    Disconnect all the cables from the balun PCB. Figure 56. Balun PCB (Side View) FRONT Lens Interface PCB Cable Analog PCB Cable Connections Connector Low Pass Filter PCB Cable Three screws holding the balun Connector PCB to the chassis Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 99: Replacing The Calibration Gas Flow Module

    Remove the front, top, and left covers as described in “Removing the Covers” page 2. If you have the optional CI module then turn off the CI reagent gas supply. 3. Remove the calibration gas flow module. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 100 Reconnect the tubing and the cables. e. Turn on the CI reagent gas supply (if present). Add a calibration compound to the vial. 5. Restore the mass spectrometer for operation. a. Replace the covers. b. Restart the system. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 101: Adding Calibration Compound

    Use a 9/16-in. wrench to remove the nut from the calibration compound vial. b. Slide the vial away from the calibration valve fitting with the ferrule and nut attached. c. Remove the ferrule and nut. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 102 Place the 1/4-in. ferrule over the neck of the vial and into the nut. c. Connect the vial to the calibration valve fitting with the nut and ferrule. 5. Restore the mass spectrometer for operation. a. Replace the covers. b. Restart the system. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 103: Replacing The Ci Reagent Gas Flow Module

    2. Remove the CI reagent gas flow module. Figure 59. CI Reagent Gas Flow Module (Left Side) Two gas fittings Analog PCB Cable Connector Two screws holding the CI Reagent Foreline Adapter Tubing Gas Flow Module Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 104: Replacing The Conversion Dynode/Electron Multiplier Power Supply

    Shut down and vent the mass spectrometer (“Shutting Down” page 16). WARNING - ELECTRICAL SHOCK HAZARD. Unplug the mass spectrometer before proceeding. c. Remove the front, top, and left covers as described in “Removing the Covers” page Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 105 Connector b. Disconnect the conversion dynode cable from the vacuum manifold. c. Disconnect the electron multiplier cable from the vacuum manifold. d. Remove the two screws holding the power supply to the chassis. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 106: Replacing The Convectron Gauge And Foreline Adapter

    Remove the front, top, and left covers as described in “Removing the Covers” page 2. Remove the convectron gauge and foreline adapter. a. Disconnect the convectron gauge cable from the foreline adapter. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 107 Reconnect the tubing and the convectron gauge cable. 4. Restore the mass spectrometer for operation. a. Replace the covers. b. Restart the system. c. Run Tune Diagnostics to verify that your system is operational. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 108: Replacing The Digital Pcb

    Analog PCB Digital PCB Ethernet Cable Digital PCB Cable Connector Connector Three screws holding the Digital Four screws holding the Digital PCB Cover to the Left Side Panel PCB Cover to the Analog PCB Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 109: Replacing The Electrometer Pcb

    Shut down and vent the mass spectrometer (“Shutting Down” page 16). WARNING - ELECTRICAL SHOCK HAZARD. Unplug the mass spectrometer before proceeding. c. Remove the front, top, and left covers as described in “Removing the Covers” page Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 110 Remove the electrometer PCB cover and set it aside. Figure 64. Electrometer PCB with Cover Removed (Left Side) Screw holding the Electrometer Nut holding the Electrometer PCB Wire to the Anode PCB to the Anode Feedthrough Feedthrough Electrometer PCB Anode Feedthrough Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 111: Replacing The Variable Damping Gas Regulator

    Remove the front, top, and left covers as described in “Removing the Covers” page Note If the mass spectrometer and gas chromatograph share a gas line, you must also shut down the gas chromatograph. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 112 Use the wrench to reconnect the orange gas line to the variable damping gas regulator. 4. Test the gas line fitting for leaks. a. Use an electronic leak detector to check each fitting for leaks. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 113: Replacing The Damping Gas Flow Module

    “Removing the Covers” page Note If the mass spectrometer and gas chromatograph share a single Helium gas line, you must also shut down the gas chromatograph. d. Turn off the damping gas supply. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 114 Use an electronic leak detector to check each fitting for leaks. CAUTION INSTRUMENT DAMAGE. Do not use liquid soap leak detectors (such as Snoop) to check for leaks. They may contaminate your system. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 115: Replacing The Ion Gauge

    WARNING - ELECTRICAL SHOCK HAZARD. Unplug the mass spectrometer before proceeding. c. Remove the front, top, and left covers as described in “Removing the Covers” page 2. Remove the ion gauge. a. Disconnect the ion gauge control PCB cable. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 116 Use the three screws to attach the new ion gauge to the vacuum manifold. d. Reconnect the ion gauge control PCB cable. 4. Restore the mass spectrometer for operation. a. Replace the covers. b. Restart your system. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 117: Replacing The Lens Interface Pcb

    Reconnect the lens interface PCB cable to the analog and balun PCBs. Figure 68. Lens Interface PCB (Right Side View) Lens Interface PCB Lens Interface PCB Cable Connector Four screws holding the lens interface PCB to the chassis Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 118: Replacing The Low Pass Filter Pcb

    Shut down and vent the mass spectrometer (“Shutting Down” page 16). WARNING - ELECTRICAL SHOCK HAZARD. Unplug the mass spectrometer before proceeding. c. Remove the front, top, and left covers as described in “Removing the Covers” page Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 119 Low-Pass Filter PCB Cable connector 3. Remove the RF coil cover. a. Remove the 12 screws holding the RF coil cover to the RF module. b. Remove the RF coil cover and set it aside. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 120 Two screws holding the RF module to the front of the chassis c. Remove the two screws holding the RF module to the front of the chassis. d. Remove the RF module from the chassis. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 121 Reconnect the terminal lugs to the low pass filter PCB. b. Reconnect the balun PCB cable. c. Use the four screws to attach the new low pass filter PCB to the RF module. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 122: Replacing The Power Module

    Shut down and vent the mass spectrometer (“Shutting Down” page 16). WARNING - ELECTRICAL SHOCK HAZARD. Unplug the mass spectrometer before proceeding. c. Remove the front, top, and left covers as described in “Removing the Covers” page Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 123 Use the two screws to attach the new power module to the chassis. 4. Restore the mass spectrometer for operation. a. Replace the covers. b. Restart the system. c. Run Tune Diagnostics to verify that your system is operational. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 124: Replacing The Rear Cooling Fans

    Remove the front, top, and left covers as described in “Removing the Covers” page 2. Remove the fan bracket. a. Remove the two screws holding the fan bracket to the chassis. b. Remove the rear cooling fans and the fan bracket. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 125 3. Remove the rear cooling fans from the fan bracket. a. Disconnect the two fan cables. b. Remove the four nuts holding the rear cooling fans to the fan bracket. c. Remove the fans and set them aside. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 126 Insert the rear cooling fans and fan bracket in the chassis. d. Use the screws to attach the fan bracket to the chassis. 5. Restore the mass spectrometer for operation. a. Replace the covers. b. Restart the system. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 127: Replacing The Rf Detector Pcb

    Figure 75. RF Module (Left Side View) RF Module 15-pin RF Detector PCB Cable Connector 9-pin RF Detector PCB Cable RF Detector PCB Cover Connector Two screws holding the RF Detector PCB Cover to the RF Module and chassis Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 128 5. Use the two screws to reattach the RF detector PCB cover to the RF module. 6. Reconnect the RF detector PCB cables. 7. Restore the mass spectrometer for operation. a. Replace the covers. b. Restart your system. c. Run Tune diagnostics to verify your system is operational. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 129: Replacing The Rf Generator Pcb

    Remove the top two screws and loosen the bottom two screws holding the RF generator PCB to the chassis. c. Disconnect the 50-pin ribbon cable from the RF generator PCB. d. Remove the RF generator PCB from the chassis. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 130: Replacing A Fuse On The Rf Generator Pcb

    Remove the top two screws and loosen the bottom two screws holding the RF generator PCB to the chassis. c. Disconnect the 50-pin ribbon cable from the RF generator PCB. d. Remove the RF generator PCB from the chassis. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 131: Replacing The Transfer Line

    To replace the transfer line, you will need: • Gloves, clean, lint- and powder-free • Screwdriver, Phillips #2 • Transfer Line (PN 119640-1005) • Wrench, Allen, 3 mm • Wrench, open-ended, 5/16-in. • Wrenches, two, open-ended, 7/16-in. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 132 Check the O-ring for damage and replace, if necessary. b. Insert the new transfer line into the vacuum manifold. c. Use the three screws to reattach the transfer line to the vacuum manifold. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 133: Replacing The Turbomolecular Pump Power Supply

    Remove the two screws from the metal safety cover. Remove the cover and set it aside. 2. Remove the turbomolecular pump power supply. a. Unscrew the P2-1 (-), P2-2 (+), P1-2N and P1-2L terminal lugs from the turbomolecular pump power supply. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 134 Use the two screws to reattach the metal safety cover. b. Replace the front cover. c. Reconnect the GC column to the transfer line. d. Restart the system. e. Run Tune diagnostics to verify that your system is operational. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 135: Replacing The Vacuum Control Pcb

    8-pin Power Cable Connector Control PCB to the chassis 4-pin Cable Connector 8-pin Cable Connector 15-pin Cable Connector (if 30-pin Ribbon Cable Connector present) 3-pin Cable Connector 6-pin Cable Connector Ion Gauge Control PCB Connector Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 136: Replacing The Vent Valve Solenoid

    Shut down and vent the mass spectrometer (“Shutting Down” page 16). WARNING - ELECTRICAL SHOCK HAZARD. Unplug the mass spectrometer before proceeding. c. Remove the front and top covers as described in “Removing the Covers” page Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 137 3. Replace the vent valve solenoid. a. Screw in the new vent valve solenoid. b. Reconnect the vent valve cable. 4. Restore the mass spectrometer for operation. a. Replace the covers. b. Restart the system. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 138 Maintenance Replacing the Vent Valve Solenoid Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 139: Troubleshooting

    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 Diagnostics. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 140: Running Diagnostics

    From the Xcalibur Home-Page, select Instrument Setup. b. Open the mass spectrometer Method Editor and click the Tune button. c. From Tune, select Diagnostics | Run Tests to display the Diagnostics window, which is shown in Figure Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 141: Communication Symptoms

    • Data transfer between the mass spectrometer and the data system • Mass spectrometer, gas chromatograph and autosampler current status readbacks • Instrument control, method downloading and uploading • Start, stop, pause and initialize functions • Error messages Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 142 • The incorrect ethernet cable is used for the MS. Use the supplied 10 Base-T Category 5 crossover cable. Note The length of the ethernet cable may be extended by plugging a standard Category 5 cable in series with the supplied crossover cable. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 143 • The autosampler did not start. Verify autosampler methods and configuration. Verify that the sample is present. • The heated zone did not reach the set temperature. Refer to section on “Heated Zone Symptoms” page 133. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 144 • The cable between the data system and GC is disconnected or damaged. Verify connection and cable integrity. • The communication port on the data system is not configured properly. Verify communication port configuration. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 145: Contamination Symptoms

    Always wear clean, lint- and powder- free gloves when handling ion source and mass analyzer components, and assure that the carrier gas filter, carrier gas lines, and gas regulators are free of contamination and leaks. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 146 43, 57, 71, 85, 99). Possible Solution • Carrier gas tubing is contaminated. • Isolate source of hydrocarbon contamination and remedy. • Replace carrier gas tubing. • Change carrier gas filters. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 147 Acetone (m/z 43, 58, 59) Hexane (m/z 41, 43, 56, 57, 58, 85, 86) Methanol (m/z 31) Methylene chloride (m/z 84/86) Toluene (m/z 91, 92) Trichloroethane (m/z 151, 153) Xylene (m/z 105, 106) Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 148: Filament And Lens Control Symptoms

    • The filament is near the end of its life span. Replace the filament. • There is a fault in the source heater PCB. Replace the source heater PCB. • There is a problem with the analog PCB. Replace if necessary. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 149: Heated Zone Symptoms

    Component failures are less common, but can occur. These are usually related to open circuits in heater cartridges or faulty temperature sensors. Heated zones in the gas chromatograph are not discussed in this manual. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 150 • The source temperature sensor (RTD) is defective. Vent the system and check the resistance of the RTD. The resistance should be 108 Ω at 20 °C. Replace the source heater PCB if necessary. • There is a problem with the analog PCB. Replace if necessary. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 151: High Vacuum Symptoms

    EI. Argon produces m/z 40. Alternatively, compressed electronic dusting spray containing an HFC can be used. For example, Falcon ® Dust-Off ® and MicroCare ® Micro-Blast ™ contain tetrafluoroethane, which produces ions at m/z 69 and 83. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 152 • The laboratory environment is too hot. Bring the laboratory environment to within mass spectrometer specifications. • The line voltage is out of tolerance. Check the line voltage; correct as necessary. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 153: Linearity Symptoms

    Perform routine injector and column maintenance to minimize linearity problems. Keep the injected sample concentration within the system’s working range. Usually, a hardware fault that affects linearity will show different symptoms than those which might be attributed to concentration. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 154: Power Supply Symptoms

    WARNING - ELECTRICAL SHOCK HAZARD. Use extreme care when replacing a fuse or electrical component. Turn off and unplug the mass spectrometer before removing the covers. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 155 • If there is no + 28 V current, -28 V, or +36 V, then the system may be off. Turn on the system by going to the Tune window and selecting Instrument | System On. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 156: Rf Control Symptoms

    Begin troubleshooting ion trap control problems by using Tune Diagnostics. Diagnostics helps you identify whether the fault is due to a power supply problem, a break in the RF signal path, or a faulty component. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 157 • There is high voltage arcing within the ion trap. Vent the system and disassemble the ion trap. Check for burn marks or evidence of arcing. Clean components and carefully reassemble. Replace the components if problems persist. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 158: Sensitivity Symptoms

    Improper GC maintenance is another cause of diminished sensitivity. It is important to establish a routine maintenance program for the GC. See the maintenance manual for your GC for more information on establishing a maintenance program. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 159 PCB. • Reagent gas is leaking into the analyzer, suppressing EI signal. Check for the presence of CI reagent ions in spectrum. Replace the CI gas flow module if necessary. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 160 • The filament is not aligned. Remove the ion volume and check if the ion burn is centered around the small electron entrance hole. Be sure the filament is properly inserted into the connector. Carefully bend the filament wire to better align it with the ion volume. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 161: Stability Symptoms

    Unstable mass assignment. Possible Solution • There is a problem with the RF control. See “RF Control Symptoms” page 140 more information. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 162: Tuning Symptoms

    • The tune file settings are out of the usable range. Restore the default tune and calibration settings. Run automatic tune. • The calibration gas vial is empty. Add 100 μL (max) of the calibration compound to calibration gas vial. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 163 • No helium buffer gas. Replace helium tank and remove air from the gas lines. • No resonant ejection signal on endcap electrodes. Check all cables between analog PCB, balun PCB, and lens interface PCB. Replace the analog PCB. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 164 Because calibration gas levels are sensitive to instrument parameters, the ion ratios you see on your instrument may be different. However, if you use the experimental parameters found in Table 8, then your ion ratios should be similar to those found in Table Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 165 6. Turn on EI/NICI calibration gas and allow it to stabilize for several minutes. 7. Run the automatic tune selecting all available options. It is very important to run all the automatic tune procedures including multiplier gain calibration. 8. Turn off the calibration gas. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 166 • CI reagent gas is leaking into the analyzer, which suppresses the EI signal. Check for presence of CI reagent ions in the spectrum. Replace the CI reagent gas flow module if necessary. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 167 • CI reagent gas is leaking into the analyzer, which suppresses the EI signal. Check for presence of CI reagent ions in the spectrum. Replace the CI reagent gas flow module if necessary. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 168 Troubleshooting Tuning Symptoms Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 169: Vacuum System And Gas Inlets

    166 Vacuum System Components The vacuum system includes these components: • Convectron gauge • High-vacuum pump (turbomolecular) • Ion gauge (upgrade option) • Rotary-vane pump (and optional expansion volume) • Vacuum manifold Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 170 The vacuum manifold, which houses the ion source, ion trap, and ion detector system, is pumped (or evacuated) by the high-vacuum pump. The rotary-vane pump reduces the foreline pressure enough for the high-vacuum pump to operate. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 171: Convectron Gauge And Foreline Adapter

    If the foreline pressure inside becomes too high, the vacuum control PCB removes power to the high-vacuum pump. The foreline adapter connects the foreline hose from the rotary-vane pump to the high-vacuum pump outlet. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 172: High Vacuum Pump

    The 250 L/s turbomolecular pump is optimized for molecular flow conditions and requires the use of a rotary-vane pump to exhaust to atmosphere. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 173 This design allows for operation even with high foreline pressures. Figure 88. 70 L/s Turbomolecular Pump (left side view) Turbo Pump Power Supply Backing Port (Outlet Flange) Connector Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 174: Ion Gauge (Upgrade Option)

    An ion gauge measures the pressure inside the vacuum manifold. The ion gauge measures pressures up to 1 x 10 If you have an ion gauge, it must measure a pressure below 1x10 Torr for the filament, electron multiplier, or conversion dynode to be turned on. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 175: Rotary-Vane Pump

    Always plug the rotary-vane pump power cord into the outlet on the rear of the mass spectrometer and never into a wall outlet. This prevents the rotary-vane pump from operating when the mass spectrometer is switched off. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 176: Expansion Volume (Upgrade Option)

    91). This reduces a device foreline pressure surges when an inlet valve is evacuated. The smoothing of the foreline pressure prevents the vacuum control PCB from temporarily removing power from the high-vacuum pump when the inlet valve is evacuated. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 177: Vacuum Manifold

    The vacuum manifold is a thick walled, aluminum chamber that encases the ion source, the ion trap, and the ion detector system. The vacuum manifold has a removable cover, machined flanges on the front and rear, and various electrical feedthroughs and gas inlets. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 178: Gas Inlets

    These components allow for the control of gases into the vacuum manifold to allow for tuning, the proper operation of the ion trap, the proper venting of the vacuum manifold, and optionally the creation of a CI region. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 179: Calibration Gas Flow Module

    EI and negative ion CI. The higher flow is used for positive ion CI. The module permits calibration compound to enter the ion source through 1/8 in. o.d. tubing. The module is factory charged with 0.1 mL of perfluorotributylamine, which is adequate for approximately one year of operation. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 180: Ci Reagent Gas Flow Module (Upgrade Option)

    The flow is under computer control for repeatable CI experiments. Figure 95. CI Reagent Gas Flow Module (Left Side) Two gas fittings Analog PCB Cable Connector (not shown) Two screws holding the Module Foreline Adapter Tubing Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 181: Damping Gas Flow Module

    The damping gas flow module regulates helium flow into the ion trap. Helium in the ion trap improves the analytical performance of the mass spectrometer as well as providing a gas for collision induced dissociation (CID) if your system is equipped with the MSn upgrade. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 182: Vent Valve Solenoid

    Approximately three seconds after the main power is turned off, air is allowed into the manifold. The manifold will be completely filled with air about four minutes after the main power is turned off. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 183: Chapter 5 Ion Source Components And Inlet Valve

    174 • “Ball Valve” page 177 • “Guide Bar Housing” page 178 • “I/R Tool and Guide Bar” page 179 • “Inlet Valve Plug” page 180 • “Inlet Valve Seal” page 181 Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 184: Ion Source Components

    CI reagent gas molecules to form ions. Once formed, these ions are then focused by the ion source lenses into the ion trap for mass analysis. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 185: Filament Assembly

    The electrons emitted by the filament are accelerated by the potential difference into the ion volume. The filament spacer is a ceramic ring that aligns the filament with the electron entrance hole in the ion source and ion volume. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 186: Ion Source Block Assembly

    Three base studs hold the ion source PCB to the ion source block. These studs slip into the magnet support and position the ion source block between two permanent magnets. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 187: Ion Volume Assembly

    EI and CI without changing ion volumes. A closed exit ion CEI volume is made from a special metal. This ion volume is used in the analysis of highly acidic compounds, such as nitrophenols. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 188: Ion Source Lenses

    The electrical connections are made through stainless steel pins protruding from the edge of the lenses. A small connector attaches to these pins and carries the voltage from the electrical feedthrough. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 189: Magnets And Magnet Support

    For optimal sensitivity, position both magnets so the south pole is on top. Electrons are focused into the ion volume only when opposite poles face each other (N faces S). Figure 103. Magnets and Magnet Support Magnets Magnet Support Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 190: Inlet Valve (Upgrade Option)

    Guide Bar Housing Inlet Valve Knob Inlet Valve Block Inlet Valve Plug Foreline Hose Connection Ball Valve Lever Ball Valve Housing Figure 105 illustrates a cross section of internal and external inlet valve components. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 191 Inlet Valve Solenoid Inlet Valve Block Inlet Valve Chamber Ball Valve Lever Inlet Valve Seal Guide Bar Housing Inlet Valve Knob Vacuum Manifold Figure 106 illustrates an exploded view of the inlet valve components. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 192 The inlet valve mounts onto the front port of the vacuum manifold and is the vacuum interlock mechanism for the mass spectrometer. The inlet valve is a vacuum sealed valve through which you insert and remove the ion volume assembly using an I/R (insertion/removal) tool. Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 193: Ball Valve

    Ball Valve Lever Ball Valve Housing When the ball valve is open, the I/R tool can enter the vacuum manifold. When the ball valve is closed, the vacuum manifold is sealed from atmospheric pressure. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 194: Guide Bar Housing

    The guide bar housing, shown in Figure 108, is an aluminum chamber mounted on the vacuum manifold. The guide bar housing has an opening for the guide bar. Figure 108. Guide Bar Housing Entry Housing Guide Bar Housing Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 195: I/R Tool And Guide Bar

    Once the ball valve is opened, the I/R tool is slid along the guide bar track all the way into the vacuum manifold. Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 196: Inlet Valve Plug

    The plug is etched with “EI” on one side and “CI” on the other to help you remember what kind of ion volume is installed. Figure 110. Inlet Valve Plug Inlet Valve Plug Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 197: Inlet Valve Seal

    You should replace the inlet valve seals periodically. Replacement instructions are in “To replace the ball valve seal and O-ring, you will need:” page Figure 111. Inlet Valve Seal Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 198 Ion Source Components and Inlet Valve Inlet Valve Seal Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 199: Chapter 6 Ion Trap System

    Ion Trap System This chapter discusses the ion trap, also called a mass analyzer. Contents • “Components” page 184 • “Description” page 184 • “Theory of Operations” page 185 Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 200: Components

    The ring electrode is separated from the endcaps by two spacer rings. These spacers are used to electrically isolate and precisely separate the endcaps from the ring electrode. The exit lens shields the ion trap from the electric fields created by the ion detector system. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 201 Sample ions formed in the ion source are trapped in the ion trap only if the ions have mass-to-charge ratios greater than the minimum storage mass and the ions are not rejected by the injection waveform voltage. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 202 Ion Trap System Components Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 203: Ion Detector Systems

    Ion Detector Systems The mass spectrometer has an electron multiplier. Contents • “Description” page 188 • “Theory of Operations” page 189 Figure 113. Ion Detector Systems Electron multiplier Vacuum Manifold Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 204: Electron Multiplier

    The multiplier is designed to snap into the vacuum manifold mount without the need for additional tools. The electron multiplier system is located towards the back of the vacuum manifold. Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 205 After going through the entire multiplier, there will be about 3 x 10 electrons generated per initial ion, depending on the gain of the system. This pulse of electrons is then sent to the electrometer by way of the anode feedthrough. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 206 Ion Detector Systems Electron Multiplier Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 207: Appendix A Replaceable Parts

    “Gas Inlets and Gauges” page 202 • “PCBs and Cables” page 206 • “Turbomolecular Pump” page 214 • “Inlet Valve (Upgrade Option)” page 216 • “Installation Kit” page 218 • “Miscellaneous Items” page 219 Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 208: Vacuum Manifold

    3814-6501 O-ring, # 274 Viton 3814-6500 Rear Endplate 119605-0040 RF Feedthrough Assembly 119615-60169 Screws, Electron Multiplier Assembly A0452-20000 Transfer Line Bellows 92001-20155 Transfer Line Nozzle 119640-0400 Vacuum Manifold 119605-0020 Vent Valve Solenoid 76461-1003 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 209 Rear Endplate (119605-0040) O-ring, # 256 Viton (3814-6501)* Electron Multiplier (76022-0002) O-ring, # 110 Viton (A0107-07000)* RF Feedthrough Assembly (119615-60169) O-ring, # 126 Viton (A0107-10400)* O-ring, # 214 Viton (A0107-11500)* - Not Shown Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 210: Analyzer Assembly

    Replaceable Parts Analyzer Assembly Analyzer Assembly Table 10. Analyzer Assembly Description Part Number Analyzer Assembly (Complete) 119650-0750 Magnet 70001-98195 Magnet Yoke 119650-0710 Setscrew 76905-0405 Spring 76485-0032 Thumbscrew 76483-0125 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 211 Replaceable Parts Analyzer Assembly Magnet Yoke (119650-0710) Magnet (70001-98195) Analyzer Assembly Complete (119650-0750) Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 212: Ion Source

    Heater Ring 119650-0422 Ion Source PCB 96000-60087 Ion Source Block (does not include ball plunger or setscrew) 119650-0205 Ion Volume Key Thumbscrew 119650-0206 Ion Volume Holder 70001-20532 Setscrew 119573-0001 Spring 96000-20176 Spring Thumbscrew 119650-0208 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 213 Ion Volume Holder (70001-20532) EI Ion Volume (119650-0220) Filament (119701-60287) Filament Spacer (119650-0235) Setscrew (119573-0001) Heater Ring (119650-0422) Spring Thumbscrew (119650-0208) Spring (96000-20176) Ball Plunger (119572-0001) Ion Volume Key Thumbscrew (119650-0206) Ion Source Block 119650-0205 Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 214: Ion Source Lenses

    Ion Source Lenses Ion Source Lenses Table 12. Ion Source Lenses Parts List Description Part Number Lens 1 119650-0414 Lens 2 119650-0416 Lens 3 119650-0418 Lens Clip 119650-0428 Lens Holder 119650-0420 Lens Spacer 119650-0426 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 215 Replaceable Parts Ion Source Lenses Lens Clip (119650-0428) Lens Spacers (119650-0426) Lens 1 (119650-0414) Lens 2 (119650-0416) Lens 3 (119650-0418) Lens Holder (119650-0420) Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 216: Ion Trap

    Replaceable Parts Ion Trap Ion Trap Table 13. Ion Trap Parts List Description Part Number Endcap Electrode 119650-0520 Exit Lens 119650-0530 Exit Lens Spacer 119650-0515 Helium Inlet 119650-0532 Ring Electrode 119650-0525 Spacer 119650-0540 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 217 Replaceable Parts Ion Trap Exit Lens (119650-0530) Exit Lens Spacer (119650-0515) Helium Inlet (119650-0532) Endcap Electrode (119650-0520) Spacer (119650-0540) Ring Electrode (119650-0525) Spacer (119650-0540) Endcap Electrode (119650-0520) Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 218: Gas Inlets And Gauges

    CI Reagent Gas Flow Module (Upgrade Option) 23331-0091 Ferrule, Glass Filled Teflon 95001-20310 Ion Gauge A0105-06003 O-ring, # 116 Viton A0107-10056 Union, Elbow, 1/8-in., SS (Without CI) 4030-0602 Union, Tee, 1/8-in., SS (With CI) 4032-0182 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 219 Calibration Gas Flow Module (119246-0001) Cable, Vacuum Control PCB to Cal Gas and Vent Valves (119378-0019)* Ferrule, Glass Filled Teflon (95001-20310) Calibration Gas Vial (96000-40013) Ion Gauge (A0105-06003) O-ring, # 116 Viton (A0107-10056)* - Not Shown Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 220 76458-2009 • Reducing Union, 1/8-1/16-in., SS A0101-03151 • Transfer Line 119640-1005 • Transfer Line Bellows 92001-20155 • Transfer Line Nozzle 119640-0400 Vent Valve Solenoid 76461-1003 Helium Inlet Adapter 119605-0011 Union, 1/8-in., SS 4035-0702 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 221 Ferrule, 1/8-in., No hole, Graphite/Vespel (76458-2009)* Reducing Union, 1/8-1/16-in. SS (A0101-03151)* O-ring, # 124 Viton (A0107-10404)* Union, 1/8-in., SS (4035-0702)* Helium Inlet Fitting (76480-0014) Helium Inlet Sleeve (76480-0015) - Not Shown Helium Inlet Ferrule (76458-5001) Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 222: Pcbs And Cables

    Cable, Ribbon, Analog PCB to Multiplier/Dynode Power 119378-0009 Supply Digital PCB 119590-0010 Multiplier/Dynode Power Supply 119377-0001 Multiplier/Dynode Power Supply (PPINICI) Upgrade option. 119377-0002 RF Generator PCB 119590-0060 Spacer, Analog PCB 76350-0056 Spacer, Digital to Analog PCB 119567-0001 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 223 Spacer, Digital to Analog PCB (119567-0001)* Digital PCB (119590-0010)* Spacer, Analog PCB (76350-0056) Cable, Analog to Balun PCB (119378-0003) Cable, Analog to Balun PCB (119378-0011) Cable, Main System Power (119378-0001) - Not Shown Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 224 Ion Gauge Control PCB (Upgrade option) 119590-0120 Ion Gauge Control PCB Standoff (Upgrade option) 76350-1007 Low Pass Filter PCB 119590-0080 Power Module 115 V 119655-1115 Power Module 230 V 119655-1230 RF Coil 119670-0001 Vacuum Control PCB 119590-0031 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 225 Low Pass Filter PCB (119590-0080)* Cable, Vacuum Control PCB to Convectron Gauge (119378-0015)* Ion Gauge Control PCB (119590-0120)* Ion Gauge Control PCB Standoff (76350-1007)* Vacuum Control PCB (119590-0031) RF Coil (119670-0001) - Not Shown Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 226 Replaceable Parts PCBs and Cables Table 18. PCB’s and Cables Parts List (right cover) Description Part Number Lens Interface PCB 119590-0110 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 227 Replaceable Parts PCBs and Cables Lens Interface PCB (119590-0110) Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 228 Replaceable Parts PCBs and Cables Table 19. PCBs Parts List (under the RF Detector PCB cover) Description Part Number RF Detector PCB 119590-0070 RF Capacitor Assembly 119669-0002 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 229 Replaceable Parts PCBs and Cables RF Detector PCB (119590-0070) RF Capacitor Assembly (119669-0002) Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 230: Turbomolecular Pump

    O-ring, 70 L/s Turbo Pump, w/centering ring, NW16 76505-0005 Oil, Rotary-Vane Pump, 1 L A0301-15101 Rotary-Vane Pump 76505-3007 Turbomolecular Pump, 250 L/s 119268-0001 Turbomolecular Pump, 70 L/s 76505-3006 Turbomolecular Pump Controller 76505-3005 Turbomolecular Pump Power Supply 119254-1000 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 231 Cable, Turbo Pump Power Supply to Main Power (119378-0006)* Cable, Turbo Pump Power Supply to Vacuum Control PCB (119378-0017)* Turbomolecular Pump, 250 L/s (119268-0001) Turbomolecular Pump, 70 L/s (76505-3006) * Foreline Hose (76505-0003)* * Not Shown Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 232: Inlet Valve (Upgrade Option)

    Ferrule, Inlet Valve 119684-0001 Guide Bar 119687-0010 I/R Tool 96000-60057 Inlet Valve Housing Seal 119682-0100 Inlet Valve Seal Replacement Kit 119265-0003 Inlet Valve Solenoid 119262-0001 Knob 119685-0010 Lever 119554-0001 Plug 119273-0001 Tubing 76433-0107 Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 233 Ball Valve Seal Replacement Kit (76461-2002) Lever (119554-0001) Ball Valve (A0101-02530) Inlet Valve Solenoid (119262-0001) Tubing (76433-0107) Inlet Valve Seal Replacement Kit (119265-0003) Ferrule Inlet Valve (119684-0001) Knob (119685-0010) Plug (119273-0001) Guide Bar (119687-0010) Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 234: Installation Kit

    A0006-04550 • Fuse, 0.8 A SB A0006-06075 • Fuse, 0.5 A A0006-07608 • Fuse, 1.0 A A0006-07610 • Ion Trap Series User’s Guide 120425-USER • Ion Volume Tool 119270-0001 • Methods and Manuals CD 120150-CDMANS • Nut, 1/8-in., Brass A0101-15500 •...

  • Page 235: Miscellaneous Items

    Capillary Column, TR-5MS A0012-08143 Injector Ferrule, for 0.25 mm i.d. Column 29013488 Transfer Line Ferrule, 1/16-in. to 0.4 mm, Graphite/Vespel for A0101-18100 0.25 mm i.d. Column Syringe, 10 L w/70 mm Needle 36500103 μ Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 236 Replaceable Parts Miscellaneous Items Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 237: Appendix B Functional Block Diagrams

    This appendix contains functional block diagrams for the mass spectrometer system and its subsystems. Contents • “Vacuum System and Gas Inlets” page 222 • “Electronic Assemblies” page 223 • “Power Distribution” page 224 • “Cable Connections” page 225 Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 238: Vacuum System And Gas Inlets

    Variable Damping Gas Glow Regulator (Upgrade Option) Vent Valve Inlet Valve Solenoid Ion Trap Ion Source (Upgrade Option) Ion Gauge (Upgrade Helium Inlet Vacuum Manifold Option) (Rear Panel) High Vacuum Pump Convectron Gauge Exhaust Rotary Vane Pump Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 239: Electronic Assemblies

    Functional Block Diagrams Electronic Assemblies Electronic Assemblies Figure 116. Electronic Assemblies Thermo Scientific Ion Trap Series Hardware Manual...

  • Page 240: Power Distribution

    Functional Block Diagrams Power Distribution Power Distribution Figure 117. Power Distribution Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 241: Cable Connections

    GC Start. Use these connections to determine which connection to plug the remote start cable into. Plug one end of the remote start cable into the back of the mass spectrometer and the other end into the device you intend to use to start injections. Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 242 Functional Block Diagrams Cable Connections Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 243: Abbreviations

    Mandatory european marking for certain product groups to indicate conformity with essential eV electron volt health and safety requirements set out in european directives. EN european conformity cfm cubic feet per minute Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 244 , mass spectrometer m/z mass-to-charge ratio interactive chemical information system ™ ICIS IEC international electrotechnical commission n nano (10 IEEE institute of electrical and electronics engineers in. inch p pico (10 I/O input/output Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 245 ROM read-only memory RS-232 industry standard for serial communications s second SCSI small computer system interface SIM selected ion monitoring SI international system of units S/N signal to noise ratio TIC total ion current Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 246 Abbreviation: Ion Trap Series Hardware Manual Thermo Scientific...

  • Page 247: Index

    178, removing the top cover covers, removing high-vacuum pumps Damping Gas Flow Module 78, 97, 97, 98, 162, 165, 204, standard or adjustable I/R tool diagnostics Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 248 Power Module maintenance anode power module, replacing column removal power supplies GC column installation pumping down non-routine schedule shutting down reader survey starting up reagent gas mass analysis Ion Trap Series Hardware Manual Thermo Scientific...
  • Page 249 Spectrum, calibration gas stainless steel, cleaning tetrafluoroethane transfer line, replacing troubleshooting communication contamination filament and lens control heated zones high vacuum linearity power supply Thermo Scientific Ion Trap Series Hardware Manual...
  • Page 250 Index: X Ion Trap Series Hardware Manual Thermo Scientific...

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