Page 1 Agilent 5975 Series Troubleshooting and Maintenance Manual Agilent Technologies...
Page 2 Notices © Agilent Technologies, Inc. 2012 Warranty Safety Notices No part of this manual may be reproduced in The material contained in this docu- any form or by any means (including elec- ment is provided “as is,” and is sub-...
Page 3: Table Of Contents
Contents Introduction 5975 Series MSD Version Abbreviations Used The 5975 Series MSD MSD Hardware Description Electron Ionization (EI) systems Chemical Ionization (CI) systems Changing modes Important Safety Warnings Hydrogen Safety Safety and Regulatory Certifications Cleaning/Recycling the Product Moving or Storing the MSD General Troubleshooting Troubleshooting Tips and Tricks General Symptoms...
Page 4 CI Troubleshooting Common CI-Specific Problems Troubleshooting Tips and Tricks Air Leaks Pressure-Related Symptoms Signal-Related Symptoms Tuning-Related Symptoms General Maintenance Before Starting Maintaining the Vacuum System To Remove the MSD Covers To Connect the Micro-Ion Vacuum Gauge To Move or Store the MSD To Check and Add Foreline Pump Oil To Drain the Foreline Pump To Refill the Foreline Pump...
Page 5 To Remove the Micro-Ion Vacuum Gauge To Reinstall a Micro-Ion Vacuum Gauge To Lubricate the Side Plate O-Ring To Lubricate the Vent Valve O-Ring To Remove the Diffusion Pump To Replace the Diffusion Pump Fluid To Reinstall the Diffusion Pump To Remove the Foreline Gauge To Reinstall the Foreline Gauge Maintaining the Analyzer...
Page 6 Diffusion pump system Turbo pump system Analyzer Chamber Diffusion pump version Turbo pump version Side Plate Vacuum Seals Foreline Gauge Diffusion Pump and Fan Turbo Pump and Fan Calibration Valves and Vent Valve Micro-Ion Vacuum Gauge Analyzer Overview EI Ion Source CI Ion Source Filaments Other Source Elements...
Page 7 LAN/MS Control Card Power Supplies Back Panel and Connectors Interfacing to External Devices Parts To Order Parts Electronics Local Control Panel Vacuum System Analyzer EI GC/MSD Interface Consumables and Maintenance Supplies CI Parts Index 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 8 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 9 This manual describes the troubleshooting and maintenance of the Agilent Technologies 5975 Series Mass Selective Detector (MSD). It assumes familiarity with the procedures and information detailed in the 5975 Series MSD Operation Manual and with the Agilent MSD ChemStation software. Agilent Technologies...
Page 10: Introduction
1) that indicates what kind of MSD you have. Table 1 Available high vacuum pumps Model name Product number Description Ionization modes 5975C TAD VL MSD G3170A Diffusion Pump MSD Electron impact (EI) 5975C TAD inert MSD G3171A Standard Turbo MSD...
Page 11: Abbreviations Used
Introduction Abbreviations Used The abbreviations in Table 2 are used in discussing this product. They are collected here for convenience. Table 2 Abbreviations Abbreviation Definition Alternating current Automatic liquid sampler Bromofluorobenzene (calibrant) Chemical ionization Direct current DFTPP Decafluorotriphenylphosphine (calibrant) Direct insertion probe Diffusion pump Electron impact ionization Electron multiplier (detector)
Page 12 Introduction Table 2 Abbreviations (continued) Abbreviation Definition Negative CI Octafluoronaphthalene (calibrant) Positive CI PFDTD Perfluoro-5,8-dimethyl-3,6,9-trioxydodecane (calibrant) PFHT 2,4,6-tris(perfluoroheptyl)-1,3,5-triazine (calibrant) PFTBA Perfluorotributylamine (calibrant) Quad Quadrupole mass filter Radio frequency RFPA Radio frequency power amplifier Torr Unit of pressure, 1 mm Hg Turbo Turbomolecular (pump) 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 13: The 5975 Series Msd
Introduction The 5975 Series MSD The 5975 Series MSD is a stand-alone capillary GC detector for use with Agilent Gas Chromatographs (Table 3). The MSD features: • Local Control Panel (LCP) for locally monitoring and operating the MSD • One of three different high vacuum pumps •...
Page 14 Introduction The gauge is required for chemical ionization (CI) operation. Table 3 5975 series MSD models and features Model Feature G3170A G3171A G3172A G3174A G3175A G3176A High vacuum pump Diffusion Standard Performance Performance turbo turbo turbo Optimal He column flow mL/min 1 to 2 1 to 2 Maximum recommended gas flow...
Page 15: Msd Hardware Description
Introduction MSD Hardware Description Figure 1 is an overview of a typical GC/MSD system. 7890A GC CI gas flow module Local control panel 5975 Series MSD MSD power switch GC power switch Figure 1 5975 Series GC/MSD system 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 16: Electron Ionization (Ei) Systems
Introduction Electron Ionization (EI) systems EI systems ionize sample molecules by bombarding them with electrons. The ions, including fragments, are drawn into the quadrupole analyzer where they are separated by their mass-to-charge (m/z) ratios and detected. Chemical Ionization (CI) systems CI systems use a reagent gas as an intermediate between the electrons and the sample.
Page 17: Changing Modes
Introduction Changing modes Switching back and forth between CI and EI sources takes less than an hour, although a 1- to 2-hour wait is required to purge the reagent gas lines and bake out water and other contaminants. Switching from PCI to NCI requires about 2 hours for the ion source to cool.
Page 18: Important Safety Warnings
Introduction Important Safety Warnings There are several important safety notices to always keep in mind when using the MSD. Many internal parts of the MSD carry dangerous voltages If the MSD is connected to a power source, even if the power switch is off, potentially dangerous voltages exist on: •...
Page 19: Many Parts Are Dangerously Hot
Introduction Many parts are dangerously hot Many parts of the GC/MSD operate at temperatures high enough to cause serious burns. These parts include but are not limited to: • The inlets • The oven and its contents • The detector •...
Page 20: Hydrogen Safety
Introduction Hydrogen Safety The use of hydrogen as a GC carrier gas is potentially dangerous. WARNING When using hydrogen (H ) as the carrier gas or fuel gas, be aware that hydrogen WARNING gas can flow into the GC oven and create an explosion hazard. Therefore, be sure that the supply is turned off until all connections are made and ensure that the inlet and detector column fittings are either connected to a column or capped at all times when hydrogen gas is supplied to the instrument.
Page 21: Dangers Unique To Gc/Msd Operation
Introduction Dangers unique to GC/MSD operation Hydrogen presents a number of dangers. Some are general, others are unique to GC or GC/MSD operation. Dangers include, but are not limited to: • Combustion of leaking hydrogen. • Combustion due to rapid expansion of hydrogen from a high-pressure cylinder.
Page 22 Introduction Table 4 Hydrogen accumulation mechanisms (continued) Mechanism Results Mass spectrometer automated shutoff Some mass spectrometers are equipped with valves closed automated diffusion pump shutoff valves. In these instruments, deliberate operator action or various failures can cause the shutoff valves to close. shutoff valve closure does not shut off the flow of carrier gas.
Page 23: Precautions
Introduction Once hydrogen has accumulated in a mass spectrometer, extreme caution must be WARNING used when removing it. Incorrect startup of a mass spectrometer filled with hydrogen can cause an explosion. After a power failure, the mass spectrometer may start up and begin the pumpdown WARNING process by itself.
Page 24 Introduction Operating precautions • Turn off the hydrogen at its source every time you shut down the GC or MSD. • Turn off the hydrogen at its source every time you vent the MSD (do not heat the capillary column without carrier gas flow). •...
Page 25: Safety And Regulatory Certifications
The 5975 Series MSD is designed and manufactured under a quality system registered to ISO 9001. Information The Agilent Technologies 5975 Series MSD meets the following IEC (International Electro-technical Commission) classifications: Equipment Class I, Laboratory Equipment, Installation Category II, Pollution Degree 2.
Page 26: Symbols
Failure to comply with these precautions violates safety standards of design and the intended use of the instrument. Agilent Technologies assumes no liability for the customer’s failure to comply with these requirements.
Page 27: Electromagnetic Compatibility
Make sure that all peripheral devices are also certified. Make sure that appropriate cables are used to connect the device to peripheral equipment. Consult your equipment dealer, Agilent Technologies, or an experienced technician for assistance. Changes or modifications not expressly approved by Agilent Technologies could void the user’s authority to operate the equipment.
Page 28: Cleaning/Recycling The Product
Introduction Cleaning/Recycling the Product To clean the unit, disconnect the power and wipe down with a damp, lint-free cloth. For recycling, contact your local Agilent sales office. Moving or Storing the MSD The best way to keep your MSD functioning properly is to keep it pumped down and hot, with carrier gas flow.
Page 29 See the Troubleshooting section in the online help and the other chapters in this manual for more information. If the material in this chapter and in the online help proves insufficient to help you diagnose a problem, contact your Agilent Technologies service representative. Agilent Technologies...
Page 30: General Troubleshooting
General Troubleshooting Troubleshooting Tips and Tricks Rule 1: “Look for what has been changed.” Many problems are introduced accidentally by human actions. Every time any system is disturbed, there is a chance of introducing a new problem. • If the MSD was just pumped down after maintenance, suspect air leaks or incorrect assembly.
Page 31: General Symptoms
General Troubleshooting General Symptoms This section describes symptoms you might observe when first turning on the GC/MSD system. All of these symptoms would prevent operation of the system. GC does not turn on Nothing happens when the GC is switched on. The GC fans do not turn on and the keypad display does not light.
Page 32 General Troubleshooting MSD turns on but then the foreline pump shuts off MSDs will shut down both the foreline pump and the high vacuum pump if the system fails to pump down correctly. This is usually because of a large air leak: either the sideplate has not sealed correctly or the vent valve is still open.
Page 33: Chromatographic Symptoms
General Troubleshooting Chromatographic Symptoms These are symptoms you may observe in the chromatograms generated by data acquisition. In general, these symptoms do not prevent you from operating your GC/MSD system. They indicate, however, that the data you are acquiring may not be the best data obtainable. These symptoms can be caused by instrument malfunctions but are more likely caused by incorrect chromatographic technique.
Page 34 General Troubleshooting • Calibration valve is not working correctly • Bad signal cable connection • Filament has failed or is not connected correctly • Bad ion source wiring connection • Bad detector wiring connection • Failed electron multiplier horn Peaks are tailing •...
Page 35 General Troubleshooting Peaks have split tops • Bad injection technique • Injection is too large Baseline is rising • Column bleed • Other contamination Baseline is high • Column bleed • Other contamination • Electron multiplier voltage is too high Baseline is falling A falling baseline indicates contamination is being swept away.
Page 36 General Troubleshooting Baseline wanders • Insufficient carrier gas supply pressure* • Malfunctioning flow or pressure regulator* • Intermittent leak in the GC inlet* * These could cause a fault condition in the GC that would prevent the GC from operating. Retention times for all peaks drift –...
Page 37 General Troubleshooting Poor sensitivity • Incorrect tuning • Tune file that does not match the type of analysis • Repeller voltage is too low • Incorrect temperatures (oven, GC/MSD interface, ion source, or mass filter) • Incorrect sample concentration • Leaking GC inlet* •...
Page 38: Mass Spectral Symptoms
General Troubleshooting Mass Spectral Symptoms This section describes symptoms you might observe in mass spectra. Some of these symptoms will appear in the mass spectra of samples. Others you will observe only in a tune report. Some of these symptoms have causes that can be corrected by the operator.
Page 39 General Troubleshooting High abundances at m/z 18, 28, 32, and 44 or at m/z 14 and 16 • System was recently vented (residual air and water) • Air leak. Large peaks at m/z 14 and 16 are symptomatic of especially large leaks.
Page 40 General Troubleshooting Relative abundance of m/z 502 is less than 3% Autotune should give an m/z 502 relative abundance greater than 3%. The relative abundance of m/z 502 can, however, vary a great deal depending on column flow, ion source temperature, and other variables. As long as relative abundance is above 3%, the stability of the relative abundance is more important than the absolute value.
Page 41 General Troubleshooting High mass sensitivity is poor This refers to a condition where the absolute abundance at the upper end of the mass range is poor. Absolute abundance should not be confused with the relative abundance (percentage) of m/z 502 to m/z 69. Sensitivity at high masses can be excellent even if the relative abundance of m/z 502 is low.
Page 42: Pressure Symptoms
General Troubleshooting Pressure Symptoms This section describes unusual pressure readings and their possible causes. The symptoms in this section are based on typical pressures. At typical column flow rates (0.1 to 2.0 mL/minute), the foreline pressure will be approximately 20 to 100 mTorr. The analyzer chamber pressure will be approximately 1 ×...
Page 43 General Troubleshooting Foreline pressure is too low If the pressures you observe are below 20 mTorr, check for the following: • Column (carrier gas) flow is too low • Column plugged or crushed by an overtightened nut • Empty or insufficient carrier gas supply* •...
Page 44 General Troubleshooting Power indicator on the gauge controller does not light • Unplugged gauge controller power cord • Incorrect or inadequate line voltage (24 V supply) • Failed gauge controller fuse 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 45: Temperature Symptoms
General Troubleshooting Temperature Symptoms The MSD has three heated zones: • Ion source (Source in the MSD ChemStation software) • Mass filter (Quad in the MSD ChemStation software) • GC/MSD interface (in the MSD ChemStation software Thermal Aux #2 for the Agilent 7890A and 6890, Thermal Aux #1 for the Agilent 7820A, Thermal Aux for the Agilent 6850) Each heated zone has a heater and temperature sensor.
Page 46 General Troubleshooting • Mass filter heater failed (burned out or shorted to ground)* • Mass filter temperature sensor failed* • Source power cable is not connected to the sideboard* • MSD electronics are not working correctly * These will cause an error message. GC/MSD interface will not heat up •...
Page 47: Error Messages
General Troubleshooting Error Messages Sometimes, a problem in your MSD will cause an error message to appear in the MSD ChemStation software. Some error messages appear only during tuning. Other messages may appear during tuning or data acquisition. Some error messages are “latched.” These messages remain active in your data system even if the condition that caused the message has corrected itself.
Page 48 General Troubleshooting Difficulty with the HED supply The only time this error occurs is if the output of the supply cannot get to its destination (the HED). • Large peak, such as the solvent peak, eluted while the analyzer was on •...
Page 49 General Troubleshooting High foreline pressure • Excessive carrier gas flow (typically > 5 mL/min) • Excessive solvent volume injected • Large vacuum leak • Severely degraded foreline pump oil (standard foreline pump) • Collapsed or kinked foreline hose • Foreline pump is not working correctly •...
Page 50 General Troubleshooting • Electrical leads to the detector are not connected correctly • HED power supply output cable failed • Electrical leads to the ion source are not connected correctly • Filament shorted to the source body Temperature control disabled •...
Page 51 General Troubleshooting The high vacuum pump is not ready • Diffusion pump is on but has not had enough time (10-15 minutes) to reach its normal operating temperature • Turbo pump is on but has not had enough time (5 minutes) to reach 80% of its normal operating speed •...
Page 52 General Troubleshooting There is no emission current • Filament is not connected properly; try the other filament • Filament has failed; try the other filament • MSD electronics are not working correctly There is not enough signal to begin tune •...
Page 53: Air Leaks
General Troubleshooting Air Leaks Air leaks are a problem for any instrument that requires a vacuum to operate. Leaks are generally caused by vacuum seals that are damaged or not fastened correctly. Symptoms of leaks include: • Higher than normal analyzer chamber pressure or foreline pressure •...
Page 54: Contamination
General Troubleshooting Contamination Contamination is usually identified by excessive background in the mass spectra. It can come from the GC or from the MSD. The source of the contamination can sometimes be determined by identifying the contaminants. Some contaminants are much more likely to originate in the GC. Others are more likely to originate in the MSD.
Page 55 General Troubleshooting Table 5 Common contaminants Ions (m/z) Compound Possible source 18, 28, 32, 44 or 14, 16 0, N , CO or N, O Residual air and water, air leaks, outgassing from Vespel ferrules 31, 51, 69, 100, 119, 131, PFTBA and related ions PFTBA (tuning compound) 169, 181, 214, 219, 264, 376,...
Page 56 General Troubleshooting 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 57 Air Leaks Pressure-Related Symptoms Signal-Related Symptoms Tuning-Related Symptoms This chapter outlines the troubleshooting of 5975 Series MSDs equipped with the chemical ionization (CI) source. Most of the troubleshooting information in the previous chapter also applies to CI MSDs. Agilent Technologies...
Page 58: Ci Troubleshooting
CI Troubleshooting Common CI-Specific Problems Because of the added complexity of the parts required for CI, there are many potential problems added. By far the greatest number and most serious problems with CI are associated with leaks or contamination in the reagent gas introduction system.
Page 59: Troubleshooting Tips And Tricks
CI Troubleshooting Troubleshooting Tips and Tricks Rule 1: “Look for what has been changed.” Many problems are introduced accidentally by human actions. Every time any system is disturbed, there is a chance of introducing a new problem. • If the MSD was just pumped down after maintenance, suspect air leaks or incorrect assembly.
Page 60: Air Leaks
CI Troubleshooting Air Leaks How do I know if I have an air leak?  Large air leaks can be detected by vacuum symptoms: loud gurgling noise from the foreline pump, inability of the turbo pump to reach 95% speed, or, in the case of smaller leaks, high pressure readings on the high vacuum gauge controller.
Page 61 CI Troubleshooting There should not be any peak visible at m/z 32 (O ). This almost always indicates an air leak. Figure 2 Looking for air leaks Special NCI notes Since NCI is so extremely sensitive, air leaks that are not detectable in EI or PCI can cause sensitivity problems in NCI.
Page 62 CI Troubleshooting • If you just replaced the reagent gas bottle or gas purifier, check the fittings you just opened and refastened. Check for tightness of seals at GC inlet and interface column nuts. Ferrules for capillary columns often loosen after several heat cycles. Do not overtighten the interface nut.
Page 63 CI Troubleshooting CI ion source Gas A (methane) supply Gas A Mass select valve flow controller Shutoff valve Gas B Calibration (other gas) valve GC/MSD supply interface Restrictor Gas B select valve Calibration vial GC column Figure 3 Schematic of CI flow control module Table 6 Flow module valve state diagram Result...
Page 64: Pressure-Related Symptoms
CI Troubleshooting Pressure-Related Symptoms The following symptoms are all related to high vacuum pressure. Each symptom is discussed in more detail in the following pages. The mass flow controller is calibrated for methane and the high vacuum gauge controller is calibrated for nitrogen, so these measurements are not accurate in absolute terms (Table 7).
Page 65 For the standard foreline pump, replace the pump oil. If that does not help, or for the dry foreline pump, it may be necessary to replace the pump. Contact your local Agilent Technologies Customer Engineer. The turbo pump is not working properly Check the pump speed.
Page 66 CI Troubleshooting High pressure with reagent gas flow The reagent gas flow rate is too high On the flow controller, turn down reagent gas flow as appropriate. Verify that reagent ion ratios are correct. Air leak Run Methane Pretune. See the Operation Manual.
Page 67 CI Troubleshooting Pressure does not change when reagent flow is changed The reagent gas regulator is closed Check and, if necessary, open the reagent gas regulator. The reagent gas regulator is set to the wrong pressure Set the reagent gas regulator to 10 psi (70 kPa) for methane or to 3 to 10 psi (20 to 70 kPa) for isobutane or ammonia.
Page 68: Signal-Related Symptoms
CI Troubleshooting Signal-Related Symptoms This section describes symptoms related to the signal. The symptom may be too much signal, too little signal, a noisy signal, or an incorrect signal. Signal-related symptoms are generally observed during tuning but may also be observed during data acquisition.
Page 69 CI Troubleshooting No peaks When troubleshooting “no peaks” it is important to specify what mode of operation is being used and what expected peaks are not being seen. Always start with methane PCI and verify presence of reagent ions. No reagent gas peaks in PCI If MSD has been working well and nothing seems to have been changed •...
Page 70 CI Troubleshooting No reagent gas peaks in NCI • Reagent gases do not ionize in NCI; look for background ions instead • Verify tune parameters • If no background ions are visible, go back to methane PCI No PFDTD calibrant peaks in NCI •...
Page 71 CI Troubleshooting No or low reagent gas signal If you have just installed the CI ion source and have an air leak or large amounts of water in the system and have run one or more autotunes, the ion source is probably dirty now.
Page 72 CI Troubleshooting The signal cable is not connected. Check and, if necessary, reconnect the signal cable. The filament or filament support is shorted to the ion source body or repeller. Inspect the filament. If necessary, realign the filament support arms. The electron inlet hole is blocked.
Page 73 CI Troubleshooting No or low PFDTD signal, but reagent ions are normal You are using any reagent gas but methane in PCI. Switch to methane. Wrong or corrupted tune file loaded Check your tune file. No PFDTD in the calibrant vial Inspect the calibration vial on the back of the flow controller.
Page 74 CI Troubleshooting Excessive noise or low signal-to-noise ratio The GC inlet needs maintenance. Refer to the GC manual. The CI ion source is dirty. Clean the ion source. See “To Clean the CI Ion Source” on page 164 for more information.
Page 75 CI Troubleshooting Large peak at m/z 19 If the abundance of the peak at m/z 19 is more than half abundance of the peak at m/z 17, then there is probably too much water in the system. The system was not baked out sufficiently after it was last vented. Bake out the system as described in the Maintenance chapter of this manual.
Page 76 CI Troubleshooting Peak at m/z 32 A visible peak at m/z 32 in methane pretune often indicates air in the system. Residual air from recent venting — check for water indicated by a large peak at m/z 19. Bake out the system under vacuum to eliminate water. New or dirty reagent gas supply tubing Purge the reagent gas supply lines and flow module for at least 60 minutes.
Page 77: Tuning-Related Symptoms
CI Troubleshooting Tuning-Related Symptoms This section describes symptoms related to tuning. Most symptoms involve difficulties with tuning or with the results of tuning. The following symptoms are covered in this section: • CI ion ratio is difficult to adjust or unstable •...
Page 78 CI Troubleshooting Reagent gas ion ratio is difficult to adjust or unstable The interface tip seal is incorrectly placed, damaged, or missing. Inspect the interface tip seal. If necessary, remove and reinstall it to ensure a good seal with the CI ion source. Replace it if it is damaged. Install it if it is missing.
Page 79 CI Troubleshooting High electron multiplier voltage The electron multiplier voltage can range from a few hundred volts to 3000 V. If the CI autotune program consistently sets the electron multiplier voltage at or above 2600 V but can still find peaks and complete the tune, it may indicate a problem.
Page 80 CI Troubleshooting Cannot complete Autotune Wrong or corrupted tune file Check the tune parameters. The m/z 28/27 ion ratio (for methane) is incorrect. The correct ratio should be between 1.5 and 5.0. If the ion ratio is incorrect, adjust it. See the Operation Manual.
Page 81 CI Troubleshooting Peak widths are unstable Wrong or corrupted tune file Check the tune parameters. The CI ion source is dirty. Clean the ion source. See the “CI Maintenance” chapter of this manual for more information. Air leak Run Methane Pretune (in PCI). A visible peak at m/z 32 indicates air in the system.
Page 82 CI Troubleshooting 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 83: General Maintenance
To Lubricate the Vent Valve O-Ring To Remove the Diffusion Pump To Replace the Diffusion Pump Fluid To Reinstall the Diffusion Pump To Remove the Foreline Gauge To Reinstall the Foreline Gauge Maintaining the Analyzer Maintaining the GC/MSD Interface Maintaining the Electronics Agilent Technologies...
Page 84: Before Starting
General Maintenance Before Starting For your safety, read all of the information in this introduction before performing any maintenance tasks. Scheduled maintenance Common maintenance tasks are listed in Table 8. Performing these tasks when scheduled can reduce operating problems, prolong system life, and reduce overall operating costs.
Page 85 General Maintenance Tools, spare parts, and supplies Some of the required tools, spare parts, and supplies are included in the GC shipping kit, MSD shipping kit, or MSD tool kit. You must supply others yourself. Each maintenance procedure includes a list of the materials required for that procedure.
Page 86 General Maintenance Dangerous temperatures Many parts in the MSD operate at, or reach, temperatures high enough to cause serious burns. These parts include, but are not limited to: • GC/MSD interface • Analyzer parts • Vacuum pumps Never touch these parts while your MSD is on. After the MSD is turned off, give WARNING these parts enough time to cool before handling them.
Page 87 General Maintenance into a fume hood vented to the outdoors. For the standard foreline pump, this requires removing the oil trap. Be sure to comply with your local air quality regulations. The oil trap supplied with the standard foreline pump stops only foreline pump oil. It WARNING does not trap or filter out toxic chemicals.
Page 88 General Maintenance Take extra precautions, such as a grounded antistatic mat, if you must work on components or assemblies that have been removed from the MSD. This includes the analyzer. To be effective, an antistatic wrist strap must fit snugly (not tight). A loose strap CA UT IO N provides little or no protection.
Page 89: Maintaining The Vacuum System
General Maintenance Maintaining the Vacuum System Periodic maintenance As listed earlier in Table 8, some maintenance tasks for the vacuum system must be performed periodically. These include: • Checking the foreline pump fluid (every week) • Checking the calibration vial (every 6 months) •...
Page 90: To Remove The Msd Covers
General Maintenance To Remove the MSD Covers Materials needed • Screwdriver, Torx T-15 (8710-1622) If you need to remove one of the MSD covers, follow these procedures (Figure The color of the MSD cover will vary, depending upon the model type, but the installation NO T E and removal procedures are the same for all models.
Page 91 General Maintenance Analyzer window cover Latch Analyzer cover Left side cover Figure 4 Removing covers Do not use excessive force or the plastic tabs that hold the cover to the mainframe will CA UT IO N break off. 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 92: To Connect The Micro-Ion Vacuum Gauge
General Maintenance To Connect the Micro-Ion Vacuum Gauge required The Micro-Ion vacuum gauge is optional for EI operation. It is operating the MSD in CI mode. Materials needed • Micro-Ion vacuum gauge (G3397A) • Power cord • Micro-Ion vacuum gauge cable (G3170-60805) •...
Page 93 General Maintenance EI only MSDs CI and upgraded MSDs Figure 5 Micro-Ion vacuum gauge cables 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 94: To Move Or Store The Msd
General Maintenance To Move or Store the MSD Materials needed • Ferrule, blank (5181-3308) • Interface column nut (05988-20066) • Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510) Procedure Vent the MSD. Remove the column and install a blank ferrule and interface nut. Tighten the vent valve.
Page 95 The MSD must remain upright at all times. If you need to ship your MSD to another CA UT IO N location, contact your Agilent Technologies service representative for advice about packing and shipping. 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 96: To Check And Add Foreline Pump Oil
General Maintenance To Check and Add Foreline Pump Oil Standard foreline pump only Materials needed • Foreline pump oil (6040-0621) • Funnel (9301-6461) • Hex key, 5-mm, to remove drain plug (8710-1838) • Screwdriver, flat-blade, to remove top fill cap Procedure The foreline pump can cause burns if touched when operating.
Page 97 General Maintenance Reinstall the fill cap. Pump down the MSD. Oil level lines Oil mist filter Fill cap Drain plug Figure 7 Foreline pump (standard pump shown without safety cage) 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 98: To Drain The Foreline Pump
General Maintenance To Drain the Foreline Pump Standard foreline pump only Materials needed • Book or other solid object approximately 5 cm thick • Container for catching old pump oil, 500 mL • Gloves, oil- and solvent-resistant • Screwdriver, flat-blade, large (8730-0002) •...
Page 99 General Maintenance Replace the drain plug after draining the oil. Refill the foreline pump until the oil level is between the two fill marks in the site window. Replace the fill cap. 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 100: To Refill The Foreline Pump
General Maintenance To Refill the Foreline Pump Standard foreline pump only Materials needed • Foreline pump oil (6040-0621) – approximately 0.28 L required • Funnel (9301-6461) • Gloves, oil- and solvent-resistant • Screwdriver, flat-blade, large (8730-0002) • Drain plug O-ring (if required) (0905-1515) •...
Page 101: To Check The Diffusion Pump Fluid
General Maintenance To Check the Diffusion Pump Fluid Materials needed • Screwdriver, Torx T-15 (8710-1622) Procedure Remove the analyzer window cover. Do not remove any other covers. Removing other covers may expose hazardous WARNING voltages. Vent the MSD. Remove the side cover. Keep your hair away from the cooling fan if the MSD is turned on.
Page 102 General Maintenance Fluid level window (sight glass) Figure 8 Diffusion pump 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 103: To Separate The Msd From The Gc
General Maintenance To Separate the MSD from the GC Materials needed • Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510) Procedure Vent the MSD. Turn off the GC. Make sure the GC/MSD interface and GC oven have cooled before you remove the WARNING column.
Page 104 General Maintenance Agilent 7890A GC has a front and a back location for the MSD interface. Agilent 6890 GC has only one (front) location. Agilent 7820A GC has only one location for the MSD interface. Interface cable 5975 Series MSD and Agilent 7890A, 7820A and 6890 6850 GC has only one location for the MSD interface.
Page 105: To Reconnect The Msd To The 7890A Gc/7820A/6890 Gc
General Maintenance To Reconnect the MSD to the 7890A GC/7820A/6890 GC Materials needed • Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510) Procedure  Position the MSD so the end of the GC/MSD interface is near the GC (Figure Reconnect the GC/MSD interface cable. Slide the MSD to its regular position next to the GC.
Page 106: To Reconnect The Msd To The 6850 Gc
General Maintenance To Reconnect the MSD to the 6850 GC Materials needed • Wrench, open-end, 1/4-inch  5/16-inch (8710-0510) • Screwdriver, Torx T-15 (8710-1622) Procedure Position the MSD so that it is near the GC. If not installed, install the GC/MSD interstitial panel (part number G2589-00031) onto the midsupport and front-support legs of the right side of the MSD.
Page 107 General Maintenance Connect the GC and the MSD end of the GC/MSD interface cable. Figure GC/MSD interface cable, GC end GC/MSD interface cable, MSD end Figure 11 Interstitial panel installed, GC/MSD interface cable connected Carefully push the MSD and GC together. 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 108 General Maintenance When positioned properly, the end of the GC/MSD interface cover will touch the oven wall and the GC/MSD interface tip will protrude slightly into the GC oven. See Figure Figure 12 MSD and 6850 GC properly positioned The foreline pump may be located on the floor, on the lab bench next to or behind the MSD, or under the analyzer chamber at the back of the MSD.
Page 109: To Refill The Ei Calibration Vial
General Maintenance To Refill the EI Calibration Vial Materials needed • PFTBA (05971-60571) Procedure Stop any tuning or data acquisition. Turn off the analyzer. There are several ways to do this: • In the Tune and Vacuum Control view, select MS OFF from the Execute menu.
Page 110 General Maintenance Syringe or pipette PFTBA into the vial. With the vial vertical, the liquid should be just below the end of the internal tube, approximately 70 µL of sample. Push the calibration vial into the valve as far as possible. Withdraw the vial 1 mm.
Page 111: To Purge The Calibration Valves
General Maintenance To Purge the Calibration Valves After removing a calibrant vial, you must purge the calibration valve. Failure to do so CA UT IO N will result in damage to the filaments and the electron multiplier. EI calibration valve After adding new PFTBA to the calibrant vial, you must purge the air out of the vial and valve.
Page 112: To Remove The Ei Calibration And Vent Valve Assembly
General Maintenance To Remove the EI Calibration and Vent Valve Assembly Materials needed • Screwdriver, Torx T-15 (8710-1622) Procedure Vent the MSD.  Trace the calibration valve cable to the connector next to the fan and disconnect it. Loosen the collar and remove the calibration vial (Figure 13).
Page 113: To Reinstall The Ei Calibration And Vent Valve Assembly
General Maintenance To Reinstall the EI Calibration and Vent Valve Assembly Materials needed • Calibration valve (G3170-60204) • O-ring for calibration valve (0905-1217) • PFTBA (05971-60571) or other tuning compound • Screwdriver, Torx T-15 (8710-1622) Procedure  Remove the old valve assembly. See page 112 Figure Be sure the valve O-ring is in place.
Page 114: To Replace The Fan For The High Vacuum Pump
General Maintenance To Replace the Fan for the High Vacuum Pump Materials needed • Fan (G1099-60564) • Screwdriver, Torx T-15 (8710-1622) Procedure Vent the MSD. Remove the left side MSD cover. Disconnect the fan wiring from the connector on the MSD frame (Figure 14).
Page 115 General Maintenance Fan wiring connector Fan wiring Figure 14 Replacing the pump fan (turbo pump shown) 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 116: To Remove The Micro-Ion Vacuum Gauge
General Maintenance To Remove the Micro-Ion Vacuum Gauge Procedure Vent the MSD.  Disconnect the cable on the back of the Micro-Ion vacuum gauge. Unscrew the red plastic thumbnut on the gauge clamp. Remove the long screw from the clamp. While supporting the gauge body, remove the clamp from the mounting flange.
Page 117: To Reinstall A Micro-Ion Vacuum Gauge
General Maintenance To Reinstall a Micro-Ion Vacuum Gauge Material needed • KF16 O-ring 0905-1463 Procedure Place the KF16 O-ring in the groove on the analyzer chamber flange.  Replace it if it is worn or damaged. Hold the gauge flange against the chamber flange with the O-ring. Push the clamp over both flanges.
Page 118: To Lubricate The Side Plate O-Ring
General Maintenance To Lubricate the Side Plate O-Ring Materials needed • Cloths, clean (05980-60051) • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Grease, Apiezon L, high vacuum (6040-0289) The side plate O-ring needs a thin coat of grease to ensure a good vacuum seal. If the side plate O-ring appears dry or does not seal correctly, lubricate it using this procedure.
Page 119 General Maintenance Side plate O-ring Figure 15 Side plate O-ring 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 120: To Lubricate The Vent Valve O-Ring
General Maintenance To Lubricate the Vent Valve O-Ring Materials needed • Cloths, clean (05980-60051) • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Grease, Apiezon L, high vacuum (6040-0289) • O-ring, vent valve (0905-1217). Replace if the old O-ring is worn or damaged The vent valve O-ring needs a thin coat of lubrication to ensure a good vacuum seal and smooth operation.
Page 121 General Maintenance Vent valve O-ring Vent valve knob Figure 16 Vent valve O-ring Reinstall the vent valve knob. Be very careful when reinstalling the vent valve knob. It is possible to cross thread the CA UT IO N knob and damage the threads in the valve body. Be sure the O-ring stays in place. Pump down the MSD.
Page 122: To Remove The Diffusion Pump
General Maintenance To Remove the Diffusion Pump The diffusion pump fluid may contain traces of toxic chemicals. WARNING Materials needed • Aluminum foil, clean • Gloves, oil-resistant Procedure Vent the MSD. Separate the MSD from the GC. See “To Separate the MSD from the GC” page 103.
Page 123 General Maintenance Remove the KF50 clamp. See Figure Foreline gauge assembly KF50 clamp O-ring assembly Diffusion pump Diffusion pump outlet Figure 17 Removing the diffusion pump Lower the diffusion pump. Remove the O-ring assembly from the top of the diffusion pump. The O-ring will have diffusion pump fluid on it and will be very sticky.
Page 124: To Replace The Diffusion Pump Fluid
General Maintenance To Replace the Diffusion Pump Fluid Materials needed • Aluminum foil, clean • Cloths, clean, lint-free (05980-60051) • Container for old diffusion pump fluid • Diffusion pump fluid, 18.5 mL (6040-0809) – 2 required • Gloves • Oil- and solvent-resistant •...
Page 125 General Maintenance If the diffusion pump has been heated with insufficient pump fluid (or with a large air leak in the MSD), the remaining pump fluid may be severely charred and blackened. Blackened pump fluid may also be baked onto the internal parts (stack) of the pump.
Page 126 General Maintenance Preheat the new diffusion pump fluid following the instructions on the bottle. Pour new diffusion pump fluid into diffusion pump until the fluid level is within the FULL COLD range. The recommended charge for this pump is 30 mL. It will require approximately 1.5 of the bottles (18.5 mL each) of diffusion pump fluid.
Page 127: To Reinstall The Diffusion Pump
General Maintenance To Reinstall the Diffusion Pump Materials needed • Gloves, oil-resistant • Vacuum cleaner, non-ESD generating (92175V or equivalent) This procedure works best with two people, one to hold the pump and one to install the clamp. Procedure Vacuum the fan that cools the diffusion pump. Keeping the fan clean helps ensure maximum cooling.
Page 128 General Maintenance Foreline gauge assembly KF50 clamp O-ring assembly Diffusion pump Diffusion pump outlet Figure 19 Reinstalling the diffusion pump 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 129: To Remove The Foreline Gauge
General Maintenance To Remove the Foreline Gauge Materials needed • Screwdriver, flat-blade, large (8730-0002) Procedure Vent the MSD. Separate the MSD from the GC. See page 103. The foreline pump and diffusion pump may still be hot. WARNING Unplug the foreline gauge cable from the foreline gauge. Disconnect the foreline gauge assembly from the diffusion pump outlet.
Page 130: To Reinstall The Foreline Gauge
General Maintenance To Reinstall the Foreline Gauge Materials needed • Foreline gauge assembly (G1099-60545) • Screwdriver, flat-blade, large (8730-0002) Procedure Connect a new foreline gauge assembly to the foreline hose. Tighten the hose clamp. Reconnect the foreline gauge cable to the foreline gauge. Reconnect the foreline gauge assembly to the diffusion pump outlet.
Page 131: Maintaining The Analyzer
General Maintenance Maintaining the Analyzer Scheduling None of the analyzer components require periodic maintenance. Some tasks, however, must be performed when MSD behavior indicates they are necessary. These tasks include: • Cleaning the ion source • Replacing filaments • Replacing the electron multiplier horn “General Troubleshooting”...
Page 132 General Maintenance Some parts can be damaged by electrostatic discharge The wires, contacts, and cables connected to the analyzer components can carry electrostatic discharges (ESD) to the electronics boards to which they are connected. This is especially true of the mass filter (quadrupole) contact wires which can conduct ESD to sensitive components on the side board.
Page 133 General Maintenance To disassemble the EI ion source Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Hex ball driver, 1.5 mm (8710-1570) • Hex ball driver, 2.0 mm (8710-1804) • Wrench, open-end, 10 mm (8710-2353) Procedure Remove the ion source.
Page 134 General Maintenance Setscrew Source body Repeller Filament Interface socket Repeller insulator Source heater assembly Repeller insulator Washer Repeller nut Lens insulator Filament (1 of 2) Entrance lens Ion focus lens Drawout cylinder Drawout plate Figure 20 Disassembling the EI ion source 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 135 General Maintenance To clean the EI ion source Materials needed • Abrasive paper (5061-5896) • Alumina abrasive powder (8660-0791) • Aluminum foil, clean • Cloths, clean (05980-60051) • Cotton swabs (5080-5400) • Glass beakers, 500 mL • Gloves, clean, lint-free •...
Page 136 General Maintenance If insulators are dirty, clean them with a cotton swab dampened with reagent-grade CA UT IO N methanol. If that does not clean the insulators, replace them. Do not abrasively or ultrasonically clean the insulators. 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 137 General Maintenance Source body Repeller Interface socket Drawout plate Drawout cylinder Ion focus lens Entrance lens Figure 21 Source parts to be cleaned 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 138 General Maintenance Procedure The filaments, source heater assembly, and insulators cannot be cleaned CA UT IO N ultrasonically. Replace these components if major contamination occurs. If the contamination is serious, such as an oil backflow into the analyzer, seriously consider replacing the contaminated parts. ...
Page 139 General Maintenance Let the parts cool before you handle them. WARNING Take care to avoid recontaminating cleaned and dried parts. Put on new, clean gloves NO T E before handling the parts. Do not set the cleaned parts on a dirty surface. Set them only on clean, lint-free cloths.
Page 140 General Maintenance To reassemble the EI ion source Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Hex ball driver, 1.5 mm (8710-1570) • Hex ball driver, 2.0 mm (8710-1804) • Wrench, open-end, 10 mm (8710-2353) Procedure ...
Page 141 General Maintenance Source body Setscrew Repeller Repeller insulator Filament (1 of 2) Source heater assembly Repeller insulator Washer Repeller nut (do not over-tighten) Interface socket Ion focus lens Drawout cylinder Drawout plate Lens insulator (1 of 2) Entrance lens Figure 22 Assembling the ion source 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 142 General Maintenance To remove a filament Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Hex ball driver, 1.5-mm (8710-1570) Procedure Vent the MSD. Open the analyzer chamber. Remove the ion source. See the Operation Manual. Remove the filament(s) to be replaced (Figure 23).
Page 143 General Maintenance Filament 1 Filament 2 Figure 23 Replacing filaments 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 144 General Maintenance To reinstall a filament Materials needed • Filament assembly (G2590-60053) • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Hex ball driver, 1.5 mm (8710-1570) Procedure  Install the new filament (Figure 23). Remove the screw holding the filament to the ion source body. Slide off the filament assembly.
Page 145 General Maintenance To remove the heater and sensor from the ion source Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Hex ball driver, 1.5 mm (8710-1570) • Hex ball driver, 2.0 mm (8710-1804) • Hex nut driver, 5.5 mm (8710-1220) Procedure Vent the MSD.
Page 146 General Maintenance Source body Filament Repeller Repeller insulator Source heater assembly Repeller nut, washer, insulator Filament Figure 24 Replacing the heater and sensor 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 147 General Maintenance To reinstall the heater and sensor in the ion source Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Hex ball driver, 1.5 mm (8710-1570) • Hex ball driver, 2.0 mm (8710-1804) • Hex nut driver, 5.5 mm (8710-1220) •...
Page 148 General Maintenance To remove the heater and sensor from the mass filter Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Hex ball driver, 1.5 mm (8710-1570) • Hex ball driver, 2.0 mm (8710-1804) Procedure Vent the MSD. Open the analyzer chamber.
Page 149 General Maintenance To reinstall the heater and sensor in the mass filter Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Hex ball driver, 1.5 mm (8710-1570) • Hex ball driver, 2.0 mm (8710-1804) • Mass filter heater assembly (G1099-60172) Procedure Unpack the new mass filter heater assembly (Figure...
Page 150 General Maintenance Heater/sensor assembly Mass filter radiator Figure 25 Mass filter heater and sensor 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 151 General Maintenance To replace the electron multiplier horn Materials needed • Electron multiplier horn (G3170-80103) • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) Procedure Vent the MSD. Open the analyzer chamber.  Open the retaining clip (Figure 26). Lift the arm of the clip up and then swing the clip away from the electron multiplier horn.
Page 152 General Maintenance Pump down the MSD. Electron multiplier horn Retaining clip Figure 26 Replacing the electron multiplier horn 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 153: Maintaining The Gc/Msd Interface
General Maintenance Maintaining the GC/MSD Interface The GC/MSD interface requires no periodic maintenance Rarely, the heater cartridge in the GC/MSD interface fails. In those cases, it is necessary to replace the heater and sensor. This section contains procedures for removing the heater and sensor and installing new ones. See Figure Insulation Analyzer chamber...
Page 154 General Maintenance To remove the GC/MSD interface heater and sensor Materials needed • Screwdriver, Torx T-15 (8710-1622) • Hex driver, 1.5 mm (8710-1570) Procedure Vent the MSD. Make sure you turn off the GC/MSD interface heater. This heater is controlled and powered by the GC. Separate the MSD from the GC.
Page 155 General Maintenance Installing a new heater and sensor in a damaged heater sleeve will result in poor CA UT IO N performance of the heated zone and could reduce the lifetime of the new parts. Heater sleeve Setscrew Heater Temperature sensor Tip of interface Insulation Cover...
Page 156 General Maintenance To reinstall the GC/MSD interface heater and sensor Materials needed • GC/MSD interface heater assembly (G1099-60107) • Heater sleeve (G1099-20210); replace the old sleeve if it is damaged • Screwdriver, Torx T-15 (8710-1622) • Hex driver, 1.5 mm (8710-1570) Procedure Slide the new heater and temperature sensor into the heater sleeve (Figure...
Page 157: Maintaining The Electronics
The RF coils can be adjusted by the operator. All other maintenance of the electronics should be performed by your Agilent Technologies service representative. Improper use of these procedures could create a serious safety hazard. Improper use...
Page 158 General Maintenance precautions. The wrist strap should be connected to a known good earth ground. If that is not possible, it should be connected to a conductive (metal) part of the assembly being worked on, but to electronic components, exposed wires or traces, or pins on connectors. Take extra precautions, such as a grounded antistatic mat, if you must work on components or assemblies that have been removed from the MSD.
Page 159 General Maintenance To adjust the quad frequency Materials needed • Screwdriver, flat-blade, large (8730-0002) Procedure Make sure the MSD is at thermal equilibrium. It takes at least 2 hours after all heated zones have reached their setpoints for the MSD to reach thermal equilibrium.
Page 160 General Maintenance Side board RF cover Quad frequency adjustment screws Figure 29 Adjusting the quad frequency Repeat steps 4 through 7 for m/z 650. The minimum voltage is typically between 300 and 340 mV. Exit the Set Optimize Quadrupole Frequency program. 10 Select MS OFF from the Execute menu.
Page 161 General Maintenance To replace the primary fuses Materials needed • Fuse, T8 A, 250 V (2110-0969) – 2 required • Screwdriver, flat-blade (8730-0002) The most likely cause of failure of the primary fuses is a problem with the foreline pump. If the primary fuses in your MSD fail, check the foreline pump. Procedure Vent the MSD and unplug the power cord from the electrical outlet.
Page 162 General Maintenance Primary fuses in holders Figure 30 Primary fuses (turbo model shown) Repeat steps 3 through 6 for the other fuse. Always replace both fuses. Reconnect the MSD power cord to the electrical outlet. Pump down the MSD. 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 163 To Replace the Methane/Isobutane Gas Purifier To Clean the Reagent Gas Supply Lines To Refill the CI Calibrant Vial This chapter describes maintenance procedures and requirements that are unique to 5975 Series MSDs equipped with the Chemical Ionization hardware. Agilent Technologies...
Page 164: Ci Maintenance
CI Maintenance To Clean the CI Ion Source The CI ion source has slightly different cleaning requirements than the EI ion source. See the video clip in the 5975 Series MSD User Information DVD. Frequency of cleaning Because the CI ion source operates at much higher pressures than the EI ion source, it will probably require more frequent cleaning than the EI ion source.
Page 165 CI Maintenance CI source radiator Setscrew CI repeller CI repeller washer CI filament CI heater assembly CI dummy filament CI interface tip seal CI ion focus lens CI drawout cylinder CI drawout plate CI lens insulator (1 of 2) Entrance lens Figure 31 Exploded view of the CI ion source 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 166: To Minimize Foreline Pump Damage From Ammonia (Standard Pump)
CI Maintenance To Minimize Foreline Pump Damage from Ammonia (Standard Pump) Air ballasting for an hour every day removes most of the ammonia from the pump oil. This will greatly increase the life of the pump. Only perform this procedure if the pump is at normal operating temperature. The water CA UT IO N vapor in air can cause condensation of the ammonia at the ballast valve if the pump is cold.
Page 167: To Replace The Methane/Isobutane Gas Purifier
CI Maintenance To Replace the Methane/Isobutane Gas Purifier Materials needed • Methane/Isobutane gas purifier (G1999-80410) • Front ferrule for 1/8-inch tubing (5180-4110) • Rear ferrule for 1/8-inch tubing (5180-4116) • Tubing cutter (8710-1709) The methane/isobutane gas purifier needs to be replaced after four tanks of reagent gas.
Page 168: To Clean The Reagent Gas Supply Lines
CI Maintenance To Clean the Reagent Gas Supply Lines Materials needed • Clean, dry nitrogen • Heat gun • Tubing cutter (8710-1709) Procedure If the reagent gas lines become contaminated, they can be cleaned. Disconnect the reagent gas tubing from the gas supply, the gas purifier, and the MSD.
Page 169: To Refill The Ci Calibrant Vial
CI Maintenance To Refill the CI Calibrant Vial Materials needed • PFDTD calibrant (8500-8510) Procedure  Set the reagent gas flow to Gas Off. Vent the MSD. Remove the capillary column from the GC/MSD interface. Pull the MSD away from the GC to expose the calibration vial and valve. page 103.
Page 170 CI Maintenance Calibration valve Collar Calibration vial Figure 33 CI calibration valve and vial 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 171 Face seals KF (NW) seals Compression seals High voltage feedthrough seal Foreline Gauge Diffusion Pump and Fan Turbo Pump and Fan Calibration Valves and Vent Valve Micro-Ion Vacuum Gauge This chapter describes components of the MSD vacuum system. Agilent Technologies...
Page 172: Vacuum System
Vacuum System Overview The vacuum system creates the high vacuum (low pressure) required for the MSD to operate. Without the vacuum, the molecular mean free path would be very short and ions would collide with air molecules before they could reach the detector.
Page 173: Vacuum System Components
Vacuum System Vacuum System Components The parts of the vacuum system are identified in Figure • Foreline (rough) pump • High vacuum pump (diffusion or turbo pump) • Analyzer chamber • Side plate (analyzer door), and front and rear end plates •...
Page 174: Common Vacuum System Problems
Vacuum System Common Vacuum System Problems Air leak symptoms The most common problems associated with any vacuum system are air leaks. Symptoms of air leaks include: • Loud gurgling noise from the foreline pump (very large leak.) • Inability of the turbo pump to reach 95% speed •...
Page 175: Foreline Pump
Vacuum System Foreline Pump The foreline pump (Figure 35) reduces the pressure in the analyzer chamber so the high vacuum pump can operate. It also pumps away the gas load from the high vacuum pump. The foreline pump is connected to the high vacuum pump by a 130-cm hose called the foreline hose.
Page 176 Vacuum System The standard foreline pump is a two-stage rotary-vane pump. An optional dry pump is also available. The pump turns on when the MSD power is turned on. The foreline pump has a built-in antisuckback valve to help prevent backstreaming in the event of a power failure.
Page 177 Vacuum System The oil pan under the foreline pump can be a fire hazard (standard pump) Oily rags, paper towels, and similar absorbents in the oil pan could ignite and damage the pump and other parts of the MSD. Combustible materials (or flammable/non-flammable wicking material) placed WARNING under, over, or around the foreline (roughing) pump constitutes a fire hazard.
Page 178: High Vacuum Pump
Vacuum System High Vacuum Pump Diffusion pump system The diffusion pump supports a maximum flow rate into the MSD of 1.5 mL/min. The diffusion pump uses baffling to prevent vapor from migrating into the analyzer chamber. Foreline pressure is monitored by the foreline gauge.
Page 179: Analyzer Chamber
Vacuum System Analyzer Chamber The analyzer chamber (Figure 36) is where the analyzer operates. The manifold is extruded and machined from an aluminum alloy. Large openings in the side, front, and rear of the analyzer chamber are closed by plates. O-rings provide the seals between the plates and the manifold.
Page 180: Side Plate
Vacuum System Side Plate The side plate (Figure 37) covers the large opening in the side of the analyzer chamber. It is attached to the manifold with a hinge. The analyzer assembly is attached to the side plate inside the analyzer chamber. The hinge allows the side plate to swing away from the manifold for easy access to the analyzer.
Page 181 Vacuum System EM voltage Signal (detector output) Mass filter (quadrupole) Screws for radiator mounting brackets (2 of 4) Ion source and heater Detector focus High voltage (HED) Figure 37 Side plate feedthroughs 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 182: Vacuum Seals
Vacuum System Vacuum Seals Vacuum seals are shown in Figure Several types of Viton elastomer O-ring seals are used to prevent air leaks into the analyzer chamber. All these O-rings, and the surfaces to which they seal, must be kept clean and protected from nicks and scratches. A single hair, piece of lint, or scratch can produce a serious vacuum leak.
Page 183: Compression Seals
Vacuum System Compression seals A compression fitting consists of a threaded fitting on the analyzer chamber and a threaded collar with a ferrule and O-ring. A cylindrical part fits inside the collar. Tightening the collar presses the ferrule, compressing the O-ring around the part.
Page 184: Foreline Gauge
Vacuum System Foreline Gauge The foreline gauge monitors the pressure (vacuum) at the exit of the diffusion pump. The primary function of the foreline gauge is diffusion pump control. When the foreline pump has reduced the pressure in the analyzer chamber to below 300 mTorr (0.3 Torr), the diffusion pump is automatically switched on.
Page 185: Diffusion Pump And Fan
Vacuum System Diffusion Pump and Fan The diffusion pump in the MSD is an air-cooled vapor diffusion pump with 90 L/s capacity. It mounts with a KF50 fitting to a baffle adapter clamped to the bottom of the analyzer chamber. The diffusion pump has a cylindrical body surrounded by fins to help dissipate heat.
Page 186 Vacuum System Diffusion pump outlet Foreline gauge assembly KF10/16 seal KF10/16 clamp Foreline gauge cable – part of high vacuum control cable Foreline hose and hose clamp Figure 39 Diffusion pump parts The diffusion pump transports gas by momentum transfer. The heater boils a special fluid (a polyphenyl ether) inside the stack.
Page 187 Vacuum System A cooling fan is located between the diffusion pump and the front cover of the MSD. The fan draws air through the cover and blows it over the pump. Without this cooling, the pump fluid vapor would not condense correctly, but would diffuse into the analyzer chamber.
Page 188 Vacuum System Table 10 Diffusion pump thermal switches (continued) Changes at 170 °C rising; 140 °C 365 °C rising falling Function Keeps analyzer turned Shuts off diffusion pump off until the pump is hot and analyzer if the pump enough to for adequate overheats.
Page 189 Vacuum System Diffusion pump outlet Inlet Cooling fins Too hot sensor Too cold sensor Fluid level window Diffusion pump heater cable Cold fluid level marker Hot fluid level marker Figure 40 The diffusion pump 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 190 Vacuum System Diffusion pump fluid that is exposed to air at operating temperature will break down and turn dark brown or black. This reaction is called cracking. Cracked pump fluid gives two symptoms: higher manifold pressure and high background with a large peak at m/z 446. See also •...
Page 191: Turbo Pump And Fan
Vacuum System Turbo Pump and Fan The turbo pump is clamped directly to the bottom of the analyzer chamber. The turbo pump has a cylindrical body with its inlet open to the interior of the analyzer chamber. Inside the pump body is a central shaft or cylinder. Sets of small blades (airfoils) radiate from the central shaft.
Page 192: Calibration Valves And Vent Valve
Vacuum System Calibration Valves and Vent Valve Calibration valves A calibration valve (Figure 41) is an electromechanical valve with a vial to hold the tuning compound. When a calibration valve is opened, tuning compound in the vial diffuses into the ion source. EI MSDs have one calibration valve;...
Page 193 Vacuum System EI CALIBRATION above analyzer window EI calibration vial Vent valve knob EI calibration valve CI CALIBRATION right side of MSD CI calibration valve CI calibration vial Figure 41 Calibration valves 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 194 Vacuum System Vent valve knob O-ring Air passage Valve closed Valve open Valve open too far Figure 42 Vent valve 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 195: Micro-Ion Vacuum Gauge
Vacuum System Micro-Ion Vacuum Gauge The G3397A Micro-Ion vacuum gauge is standard on CI MSDs and optional on EI MSDs. It consists of the sensing element (an ionization-type gauge) and the necessary electronics to support it. Both parts are mounted in a single package.
Page 196 Vacuum System 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 197 Quadrupole Mass Filter AMU gain AMU offset 219 width DC polarity Mass (axis) gain Mass (axis) offset Quadrupole maintenance Detector Detector ion focus High energy dynode EM horn Analyzer Heaters and Radiators This chapter describes the parts of the analyzer. Agilent Technologies...
Page 198: Analyzer
Analyzer Overview The analyzer (Figure 43) is the heart of the MSD. It ionizes the sample, filters the ions, and detects them. The sample components exiting the GC column flow into the ion source. In the ion source, the sample molecules are ionized and fragmented.
Page 199 Analyzer Detector Mass filter heater assembly Mass filter contact Feedthrough board Ion source (inside radiator) Mass filter (inside radiator) Mass filter contact cable Figure 43 The analyzer 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 200: Ei Ion Source
Analyzer EI Ion Source The EI ion source (Figure 44) operates by electron ionization. The sample enters the ion source from the GC/MSD interface. Electrons emitted by a filament enter the ionization chamber, guided by a magnetic field. The high-energy electrons interact with the sample molecules, ionizing and fragmenting them.
Page 201 Analyzer Lens insulation Entrance lens Ion focus lens Drawout cylinder Drawout plate Filament Repeller Figure 44 Ion source structure The CI ion source is similar in design, but critical dimensions are different. Do not interchange parts. 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 202: Ci Ion Source
Analyzer CI Ion Source The CI ion source (Figure 45 Figure 46) is similar to the EI source, but only has one part in common with the EI source — the entrance lens. The single CI filament has a straight wire and a reflector. A “dummy” filament provides connections for the other wires.
Page 203 Analyzer Setscrew CI repeller CI repeller insulator CI filament CI ion source heater assembly CI dummy filament CI interface tip seal CI lens insulator (1 of 2) CI ion focus lens CI drawout cylinder CI drawout plate Entrance lens Figure 46 CI ion source exploded view 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 204: Filaments
Analyzer Filaments Two filaments (Figure 46) are located on opposite sides of the outside of the active EI ion source. The filament carries an adjustable AC emission current. The emission current heats the filament causing it to emit electrons which both ionize the sample molecules.
Page 205: Filament Care
Analyzer Filament care Like the filaments in incandescent light bulbs, the ion source filaments will eventually burn out. Certain practices will reduce the chance of early failure: • If you have an optional G3397A Micro-Ion vacuum gauge, use it to verify that the system has an adequate vacuum before turning on the analyzer, especially after any maintenance was performed.
Page 206: Other Source Elements
Analyzer Other Source Elements Magnet The field created by the magnet directs the electrons emitted by the filament into and across the ionization chamber. The magnet assembly is a permanent magnet with a charge of 350 gauss in the center of the field. Repeller The repeller (Figure...
Page 207: Entrance Lens
Analyzer Entrance lens The entrance lens (Figure 46) is at the entrance to the quadrupole mass filter. This lens minimizes the fringing fields of the quadrupole which discriminate against high-mass ions. There is a permanent +4.4 volt voltage added to the entrance lens.
Page 208: Quadrupole Mass Filter
Analyzer Quadrupole Mass Filter The mass filter separates ions according to their mass-to-charge ratio (m/z). At a given time, only ions of a selected mass-to-charge ratio can pass through the filter to the detector. The mass filter in the MSD is a quadrupole (Figure 47).
Page 209: Amu Gain
Analyzer Figure 47 Quadrupole mass filter AMU gain AMU gain (AmuGain) affects the ratio of DC voltage to RF frequency on the mass filter. This controls the widths of the mass peaks. • Higher gain yields narrower peaks. • AMU gain affects peaks at high masses more than peaks at low masses. AMU offset AMU offset (AmuOffs) also affects the ratio of DC voltage to RF frequency on the mass filter.
Page 210: Dc Polarity
If necessary (that is, if the only alternative is replacement), the quadrupole can be cleaned. Cleaning must be performed by Agilent Technologies service personnel. Never put the quadrupole in an ultrasonic cleaner. CA UT IO N Never change the physical orientation of the quadrupole mass filter.
Page 211: Detector
Analyzer Detector The detector (Figure 48) in the MSD analyzer is a high energy conversion dynode (HED) coupled to an electron multiplier (EM). The detector is located at the exit end of the quadrupole mass filter. It receives the ions that have passed through the mass filter.
Page 212 Analyzer As the EM horn ages, the voltage (EMVolts) required increases over time. If the EM voltage must always be set at or near –3000 VDC to complete Autotune, with no other probable cause, it may need to be replaced. Check your tune charts for gradual degradation, which indicates wearing out.
Page 213: Analyzer Heaters And Radiators
Analyzer Analyzer Heaters and Radiators The ion source and mass filter are housed in cylindrical aluminum tubes called radiators (Figure 49). The radiators control the distribution of heat in the analyzer. They also provide electrical shielding for analyzer components. The source heater and temperature sensor are mounted in the source heater block.
Page 214 Analyzer Mass filter radiator Mass filter heater assembly Ion source radiator Ion source heater assembly Figure 49 Heaters and radiators 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 215 MSD. It may be of interest to persons responsible for servicing the MSD (Figure 50). Dangerous voltages are present under the safety covers. Do not remove safety WARNIN G covers. Refer servicing to your Agilent Technologies service representative. Agilent Technologies...
Page 216: Electronics
Electronics Cooling fan Log amplifier LAN/MS control card Main board HED power supply Cooling fan Low voltage power supply Toroid transformer AC board Figure 50 The electronics module 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 217: Local Control Panel And Power Switch
Electronics Local Control Panel and Power Switch Local Control Panel (LCP) You can view MSD system status and perform some control functions from the local control panel on the front of the instrument. Functions available through the local control panel include: •...
Page 218: Side Board
Electronics Side Board The side board is mounted on the side plate. It performs these functions: • Provides the 1 MHz reference clock for the RF amplifier. • Generates the RF component of the voltage applied to the quadrupole mass filter according to a signal from the main board.
Page 219: Electronics Module
Electronics Electronics Module Most of the electronics in the MSD are contained in the electronics module. The whole electronics module can be replaced, if necessary, by your Agilent Technologies service representative. The electronics module contains: • Main board • Signal amplifier board •...
Page 220 Electronics • Supplies and controls the power for the ion source and quadrupole (mass filter) heaters. • Provides 24 VDC power for the cooling fans. Signal amplifier board The signal amplifier board amplifies the output of the detector. It produces an output voltage of 0 to 10 volts DC, proportional to the logarithm of the input current of 3 picoamps to 50 microamps.
Page 221 Electronics Diffusion pump control The power regulator ensures that the diffusion pump heater receives constant power, even if there are fluctuations in the AC line voltage. It measures the voltage across the heater and the current through it, multiplies them together, and compares the result with a standard value.
Page 222 Electronics Pumpdown failure shutdown The AC board will shut down both the high vacuum and the foreline pump if the system fails to pump down correctly. One condition that triggers shutdown is turbo pump speed below 80% after 7 minutes, or it the foreline pressure is above 300 mTorr after 7 minutes.
Page 223: Lan/Ms Control Card
Electronics LAN/MS Control Card The LAN/MS control card is located to the left of the main board on the electronics panel. The LAN/MS control card has two main functions: • Providing a communication interface between the MSD and the data system.
Page 224: Power Supplies
Electronics Power Supplies Low voltage (AC-DC) power supply The low voltage power supply is mounted next to the toroid transformer in the electronics module. A universal input power supply, it converts AC line voltage into the DC voltages used by the rest of the electronics. The power supply generates the following DC voltages: •...
Page 225: Back Panel And Connectors
Electronics Back Panel and Connectors The back panel (Figure 52) contains several connectors, the primary fuses, and several status LEDs. Most of these components are part of the AC board or the LAN/MS control card and extend through the back panel. High vacuum control (HIVAC SIGNAL) connector The high vacuum signal connector is on the AC board.
Page 226 Electronics RS-232 Serial A connector Not currently used. RS-232 Serial B connector The RS-232 Serial B connector goes to the CI flow module or to the Micro-Ion vacuum gauge, depending on the accessories installed on the MSD. It handles data communication between the GC and the MSD. LAN (I/O) connector The LAN cable from the data system is connected to the I/O LAN connector.
Page 227 Electronics Remote start High vacuum control Primary fuses High vacuum power Power cord RS-232 Serial B Foreline pump RS-232 Serial A power cord Figure 52 Back panel connections 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 228: Interfacing To External Devices
Electronics Interfacing to External Devices Remote control processor The remote control processor on the LAN/MS control card synchronizes start-run signals with GCs and other devices. The functions of the remote control processor are extended to the remote start (Remote) connector (Figure 53) on the back panel of the MSD.
Page 229 Electronics signal. On receipt of the ready signal, the desorbtion cycle begins. When a specific temperature is reached, the purge-and-trap closes a contact to indicate the run has started. The ready pin on the remote start connector on the GC is held low at all times except when the GC, MSD, and data system are all ready.
Page 230 Electronics 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 231 5975 Series MSD. It includes most of the parts or assemblies in the MSDs. This chapter is organized so that related parts are grouped together. Some of the parts listed are not user-replaceable. They are listed here for use by Agilent Technologies service representatives. Agilent Technologies...
Page 232: Parts
To Order Parts To order parts for your MSD, address the order or inquiry to your local Agilent Technologies office. Supply them with the following information: Model and serial number of your MSD, located on a label on the lower left side near the front of the instrument.
Page 233: Electronics
Parts Electronics The printed circuit boards in the MSD are available only as complete assemblies. Individual electronic components are not available. This section contains the following parts: cables (Tables and 12), printed circuit boards (Table 13 Figure 54), and fuses and switches (Table 14).
Page 234 Parts Table 12 Internal cables Description Part number AC board control cable (AC board to main board) G1099-60422 Chassis ground wire G1099-60433 Local control panel ribbon cable G3170-60830 Electronics module fan cable G1099-60560 Diffusion pump control cable G3170-60437 Fan (high vacuum) cable G1099-60561 Feedthrough board G1099-60425...
Page 235: Printed Circuit Boards
Parts Printed circuit boards Table 13 Printed circuit boards (Figure Description Part number AC board G3170-65006 Fan for electronics module 3160-1038 Snap-on rivets (4) may be required if old ones are broken by 0361-1341 the removal process HED power supply G3170-80017 Bipolar HED power supply G3170-80018...
Page 236 Parts HED power supply Cooling fan Low voltage power supply Toriod transformer AC board Cooling fan Signal amplifier board LAN/MS control card Main board Figure 54 Electronics module 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 237: Fuses And Power Switch
Parts Fuses and power switch Table 14 Fuses and power switches Description Part number Fuse 8A, 250V 2110-0969 Power button 5041-1203 Power switch extender rod G3170-40050 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 238: Local Control Panel
Parts Local Control Panel This section lists replaceable parts for the LCP and related covers. See Table Table 15 LCP and related parts (Figure Item Description Part number LCP fascia • for 5975C VL MSD G3170-60081 • for 5975C inert MSD G3170-60082 •...
Page 239 Parts LCP fascia LCP assembly and fascia Figure 55 LCP replacement parts 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 240: Vacuum System
Parts Vacuum System This section lists replacement parts available for the vacuum system. It includes clamps, O-rings and seals (Table 16), standard foreline pump and related components (Table 17 Figure 56), dry foreline pump and related components (Table 18 Figure 57), diffusion pump and related components (Table 19 Figure...
Page 241: Standard Foreline Pump And Related Parts
Parts Standard foreline pump and related parts Table 17 Standard foreline pump and related parts (Figure Item Description Part number Foreline hose assembly (hose and internal spring) 05971-60119 • Hose Clamp used with 05971-60119 1400-3241 Standard foreline pump – 120V – Pfeiffer Duo 2.5 G3170-89025 Standard foreline pump –...
Page 242 Parts Table 17 Standard foreline pump and related parts (Figure Item Description Part number M6 Acorn Cap Hex nut Qty. 2 0535-0041 M4 Internal Star washer Qty. 2 2190-0009 Hose clamps are interchangeable, but give an optimum fit if they are matched 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 243 Parts Safety cage removed for clarity Figure 56 Foreline pump and related parts 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 244 Parts Dry foreline pump and related parts Table 18 Dry foreline pump and related parts (Figure Description Part number Foreline hose assembly (hose and internal spring) 05971-60119 • Hose Clamp used with 05971-60119 1400-3241 Dry foreline pump G3170-80028 Dry foreline pump (exchange) G3170-89028 Foreline pump inlet seal (KF10/16) 0905-1463...
Page 245: Diffusion Pump And Related Parts
Parts Foreline hose assembly Hose clamp Dry pump Figure 57 Dry foreline pump and related parts Diffusion pump and related parts Table 19 Diffusion pump MSD vacuum system components (Figure Item Description Part number Claw clamps for baffle adapter G3170-60590 Diffusion pump 120V G1099-80500...
Page 246 Parts Table 19 Diffusion pump MSD vacuum system components (Figure 58) (continued) Item Description Part number Diffusion pump packaging cap G3170-40540 Fan (for high vacuum pump) 3160-1037 Foreline gauge assembly G1099-60545 Foreline gauge seal 0905-1463 KF10/16 clamp (diffusion pump outlet) 0100-1397 KF10/16 seal (diffusion pump outlet) 0905-1463...
Page 247: Turbo Pump And Related Parts
Parts Figure 58 Diffusion pump and related parts Turbo pump and related parts Table 20 Turbo pump MSD vacuum system components (Figure Item Description Part number Claw clamps for baffle adapter, standard turbo G3170-60590 Clamp for vacuum gauging 0100-1397 Fan (for high vacuum pump) G1099-60564 KF25 clamp (for turbo pump outlet) 0100-0549...
Page 248 Parts Table 20 Turbo pump MSD vacuum system components (Figure 59) (continued) Item Description Part number KF25 O-ring assembly (for turbo pump outlet) 0100-1551 Micro-Ion Vacuum Gauge vacuum gauging electronics G3170-80001 Performance turbomolecular pump G3170-89062 Standard turbomolecular pump G3170-89061 Turbo pump seal with shield 0905-1613 Turbo power supply only G3170-60600...
Page 249 Parts Figure 59 Turbo pump and related parts 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 250: Analyzer
Parts Analyzer Table 21 Figure 60 show the analyzer chamber and associated parts. Table 21 Analyzer chamber and related parts (Figure Item Description Part number Shield/plate for ion gauge port G3170-00003 Micro-Ion Vacuum Gauge Baffle G3170-00015 • M3X12 TX T10 PN SQ Cone SS (qty 2) 0515-0664 EI Calibration valve assembly Turbo pump MSDs...
Page 251 Parts Figure 60 Analyzer chamber and related parts Table 22 Figure 61 show the replacement parts for the analyzer. Analyzer screws (Table 23) and the individual ion source parts (Table 24) are listed in the tables that follow. Table 22 Analyzer parts (Figure Item...
Page 252 Parts Table 22 Analyzer parts (Figure 61) (continued) Item Description Part number EI 350 ion source, new Turbo - inert G3170-65760 Diffusion - stainless steel G3170-65750 EI 350 ion source, rebuilt Turbo - inert G3170-69760 Diffusion - stainless steel G3170-69750 Magnet assembly 05971-60160 Low gauss magnet assembly...
Page 253 Parts 7 (under clips) Figure 61 Analyzer parts 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 254 Parts Table 23 Analyzer screws Description Part number Heater/Sensor (quad) setscrew 0515-1446 Ion source thumbscrew G1099-20138 Magnet mounting screws 0515-1046 Screw – magnet bracket to source radiator 0515-1602 Screws – source radiator and detector to quad radiator G3170-20123 Screws – mass filter contact assembly/heater block G3170-20122 Screws –...
Page 255: Ei Source
Parts EI source Table 24 EI ion source (Figure Description Part number Ion source, new Turbo - inert G3170-65760 Diffusion - stainless steel G3170-65750 Ion source, rebuilt Turbo - inert G3170-69760 Diffusion - stainless steel G3170-69750 Drawout cyclinder G1072-20008 Drawout plate – 3 mm Inert G2589-20100 Drawout plate - 3 mm Stainless Steel - Standard 05971-20134...
Page 256 Parts Figure 62 EI source 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 257: Repeller Assembly
Parts Repeller assembly Table 25 Repeller assembly Description Part number EI 350 Anodized Repeller assembly G3170-60172 Inert EI 350 Anodized Repeller assembly G3170-60171 Insulator (2 required) G1099-20133 Nut, 5.5-mm 0535-0071 Repeller - Inert G2589-20044 Repeller - Stainless Steel G1099-20132 Setscrew 0515-1446 Anodized Source Heater Assembly G3169-60177...
Page 258 Parts Table 26 Heater sensor block assembly Description Part number Heater, Repeller, Japan G3170-60103 High Temp Source Sensor G3170-60104 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 259: Ei Gc/Msd Interface
Parts EI GC/MSD Interface Table 27 lists the replacement parts related to the EI GC/MSD interface. Table 27 EI GC/MSD interface Description Part number GC/MSD interface (complete) G1099-60300 Interface column nut 05980-20066 Heater sleeve G1099-20210 Heater/Sensor assembly G1099-60107 Insulation G1099-20301 Setscrew for heater/sensor assembly 0515-0236 Screws, M4x0.7 panhead, for heater sleeve...
Page 260: Consumables And Maintenance Supplies
Parts Consumables and Maintenance Supplies This section (Tables through 31) lists parts available for cleaning and maintaining your MSD. Table 28 EI maintenance supplies Description Part number Abrasive paper, 30 µm 5061-5896 Alumina powder, 1 kg 8660-0791 Cloths, clean (qty 300) 05980-60051 Cloths, cleaning (qty 300) 9310-4828...
Page 261 Parts Table 29 Tools Description Part number Column installation tool G1099-20030 Funnel 9301-6461 Hex key, 5 mm 8710-1838 Tool Kit G1099-60566 Ball drivers, 1.5-mm 8710-1570 Ball drivers, 2.0-mm 8710-1804 Ball drivers, 2.5-mm 8710-1681 Hex nut driver, 5.5-mm 8710-1220 Pliers, long-nose (1.5-inch nose) 8710-1094 Screwdrivers Flat-blade, large 8730-0002...
Page 262 Parts Table 30 Ferrules Description Part number For the GC/MSD interface • Blank, graphite-vespel 5181-3308 • 0.3-mm id, 85%/15% for 0.10-mm id columns 5062-3507 • 0.4-mm id, 85%/15%, for 0.20 and 0.25-mm id columns 5062-3508 • 0.5-mm id, 85%/15%, for 0.32-mm id columns 5062-3506 •...
Page 263 Parts Table 31 Miscellaneous EI and CI parts and samples Description Part number EM Horn G3170-80103 Filament assembly (EI) G2590-60053 Filament assembly (High temperature EI for GCMS) G3170-60050 Filament assembly (CI) G1099-80053 Foreline pump oil (1 liter), P3 6040-0621 Foreline exhaust oil mist trap G1099-80039 Heater/Sensor GC/MSD interface G1099-60107...
Page 264 Parts Table 31 Miscellaneous EI and CI parts and samples (continued) Description Part number Tubing cutter replacement blades 8710-1710 CI shipping kit G3170-60505 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 265: Ci Parts
Parts CI Parts Tables through and Figures show parts that may be required to maintain the 5975 Series MSD with CI. The parts in this section are related directly to the CI accessory; other parts for the MSD can be found in the previous sections of this chapter.
Page 266 Parts Table 32 CI flow control module (Figure 63) (continued) Item Description Part number Swagelok nut, for 1/8-inch fitting, 20/package 5080-8751 Swagelok nut and ferrules, 20 sets/package 5080-8751 Not set up Figure 63 CI flow control module 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 267 Parts Table 33 CI ion source (Figure Item Description Part number Box for ion source G1999-65001 350 CI ion source, new G3170-65403 CI drawout cylinder G1999-20444 CI drawout plate G1999-20446 CI filament G1099-80053 CI heater block G3170-20431 350 CI repeller block G3170-20133 CI interface tip seal G1999-60412...
Page 268 Parts Figure 64 Exploded view of the CI ion source 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 269 Parts Table 34 CI GC/MSD interface Description Part number CI GC/MSD interface Assembly G3170-65400 Heater clamp G1999-20410 Heater/Sensor assembly G1099-60107 Transfer line cup (cover) G3170-00405 Interface insulation G1999-20401 Screws for heater clamp 0515-0383 Screws to attach interface to manifold 0515-0380 Welded interface G3170-60401 Interface tip seal...
Page 270 Parts 5975 Series MSD Troubleshooting and Maintenance Manual...
Page 271: Index
Index Numerics Autotune CI ion source relative abundances of m/z 502 repeller, 19, large peak at m/z, in CI MSD, produced by different autotunes, CI maintenance, 219 width, CI MSD maintenance, 32, visible peak at, in CI MSD, installing the CI interface tip seal, 164, 166, 167, CI spectra Back panel and connectors,...
Page 272 Index See also Foreline pump oil Detector focus lens, foreline pressure has exceeded 300 Diffusion pump mTorr, Foreline pump oil effect of low fluid level in, internal MS communication fault, draining, error messages related to, latched, refilling the pump with, Diffusion pump fluid lens supply fault, replace every 6 months,...
Page 273 Index HED power supply, filament, reinstalling, High electron multiplier voltage in CI foreline pump in CI, LAN (I/O) connector, MSD, foreline pump oil, draining, High energy dynode. See HED LAN/MS control card, foreline pump, refilling, interfacing to external devices, High vacuum gauge GC/MSD interface, RAM on, installing,...
Page 274 Index mass (axis) offset, O-rings and O-ring assemblies, Ion source, for CI, parameters, symptoms indicating malfunctions, radiator, too high in analyzer chamber with RF voltage, reagent gas flow, Mass gain, Parts, too high in analyzer chamber without Mass offset, analyzer, reagent gas flow, Mass spectra consumables,...
Page 275 Index high abundances at m/z 18, 28, 32, 44 relative abundance of m/z 502 less than Septum, leaking, or at m/z 14 and 16, Side plate lubricating the O-ring, high analyzer chamber pressure with retention time drifts (all peaks), O-ring, reagent gas flow, signal-related symptoms, overview, thumbscrews,...
Page 276 Index Vacuum seals, Vacuum system, part numbers, turbo pump system overview, Valve CI calibration, Voltages, dangerous, Water detecting in CI, Wid219 parameter, Wiring, dangerous voltages on, 5975 Series MSD Troubleshooting and Maintenance Manual...

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Agilent Technologies 5975C TAD VL MSD Troubleshooting And Maintenance Manual

Table of Contents

2 General Troubleshooting

3 CI Troubleshooting

4 General Maintenance

5 CI Maintenance

6 Vacuum System

7 Analyzer

8 Electronics

9 Parts

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