Page 1 Agilent 5977B Series MSD Troubleshooting and Maintenance Manual Agilent Technologies...
Page 2: Safety Notices
Notices Warranty Safety Notices © Agilent Technologies, Inc. 2016 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
Moving or Storing the MSD To Replace the Primary Fuses General Troubleshooting Instrument State Troubleshooting Tips and Tricks General Symptoms Chromatographic Symptoms Mass Spectral Symptoms Pressure Symptoms Temperature Symptoms Error Messages Air Leaks Contamination 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 4 To Change the Blue Oil Mist Filter on the Foreline Pump To Install the Exhaust Filter on the IDP3 Dry Pump To Change the Filter Cartridge on the IDP3 Dry Foreline Pump To Check the DP Fluid To Remove the DP 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 5 To Replace the Primary Fuses CI Maintenance To Replace the Methane/Isobutane Gas Purifier To Clean the Reagent Gas Supply Lines To Refill the CI Calibrant Vial Vacuum System Overview Vacuum System Components Common Vacuum System Problems 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 6 Turbo Pump and Fan Calibration Valves and Vent Valve Micro-Ion Vacuum Gauge Analyzer Overview EI Ion Source HES EI Ion Source CI Ion Source Filaments Other Source Elements Quadrupole Mass Filter Detector Analyzer Heaters and Radiators 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 7 Side Board Electronics Module LAN/MS Control Card Power Supplies Back Panel and Connectors High vacuum gauge connector Interfacing to External Devices Parts To Order Parts Electronics Vacuum System Analyzer Consumables and Maintenance Supplies 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 8 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 9 This manual describes the troubleshooting and maintenance of the Agilent Technologies 5977B Series Mass Selective Detector (MSD).It assumes familiarity with the procedures and information detailed in the 5977B Series MSD or 5975/77 Series for OpenLAB CDS Operation Manual, and with the accompanying software.
Page 10: Introduction
Turbo pump MSD Electron ionization (EI)/Extractor Electron ionization  5977B Inert+ EI/CI MSD Turbo G7078B Turbo pump MSD (EI) /Extractor Chemical ionization /PCI, NCI 5977B HES MSD G7079B Turbo pump Electron ionization (EI)/High Efficiency 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 11: Abbreviations Used
Electron multiplier (detector) Electron multiplier voltage Electronic pneumatic control Electron volt Firmware Gas chromatograph High-energy dynode (refers to detector and its power supply) High efficiency source Inside diameter Inert+ Extractor source Local Area Network 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 12 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) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 13: The 5977B Series Msd
Introduction The 5977B Series MSD The 5977B Series MSD is a stand-alone capillary GC detector. The MSD features: • GC Compatibility includes the new Agilent Intuvo 9000 GC, Agilent 7890 Series GC, the Agilent 7820 GC, or the Agilent 6850 MSD •...
Page 14 Total gas flow into the MSD: column flow plus reagent gas flow (if applicable). Based on helium gas use. For other gases the maximum flow will vary. Expect degradation of spectral performance and sensitivity. ‡ Turbo pump models are field upgradeable to CI. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 15 The 5977B HES Series MSD may be equipped with an ion vacuum gauge. The Data Acquisition software can be used to read the pressure (high vacuum) in the vacuum manifold. The gauge is required for chemical ionization (CI) operation. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 16: Msd Hardware Description
Figure 1 is an overview of a typical GC/MSD system. GC control panel 7890 GC 5977B Series MSD power switch Front panel LED GC power switch Figure 1 Agilent 5977B Series GC/MS system 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 17: Electron Ionization (Ei) Systems
In this manual, the term CI MSD refers to the upgraded G7077B, the upgraded G7078B, or the upgraded G7079B MSD. It also applies, unless otherwise specified, to the flow modules for these instruments. The 5977B Series GC/MS CI system adds the following to the 5977B Series MSD: • An EI/CI GC/MSD interface •...
Page 18: Changing Modes
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. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 19: Important Safety Warnings
Do not touch any of the boards unless it is absolutely necessary. If you must handle them, wear a grounded wrist strap and take other antistatic precautions. Wear a grounded wrist strap any time you remove the MSD right side cover. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 20 The oil pan under the standard foreline pump can be a fire hazard Oily rags, paper towels, and similar absorbents in the oil pan could ignite and damage the pump and other parts of the MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 21 WA R N I N G under, over, or around the foreline (roughing) pump constitutes a fire hazard. Keep the pan clean, but do not leave absorbent material such as paper towels in it. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 22: Hydrogen Safety
• Hydrogen burns with a nonluminous flame which can be invisible under bright light. Additional information can be found in the Hydrogen Safety Guide which is included on this Agilent 5977B HES Series MSD User Information media. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 23 There is a safety feature that will shutdown the flow of carrier gas in the event of an MSD foreline pump shutdown. However, if this feature fails, hydrogen may slowly accumulate in the mass spectrometer. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 24 If the mass spectrometer is shut off at the same time, the accumulation can be fairly rapid. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 25 You must remove the analyzer window cover on the front of a 5977B HES MSD. In the unlikely event of an explosion, this cover may dislodge. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 26 Environmental Health and Safety (EHS) requirements. Always check for leaks after changing a tank or servicing the gas lines. Always make sure the vent line is vented into a fume hood. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 27: Safety And Regulatory Certifications
This ISM device complies with Canadian ICES-001. Cet appareil ISM est conforme a la norme NMB—001 du Canada. The 5977B Series MSD is designed and manufactured under a quality system registered to ISO 9001. The 5977B HES Series MSD is RoHS compliant.
Page 28 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 29: 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 30: Cleaning/Recycling The Product
If you plan to move or store your MSD, a few additional precautions are required. The MSD must remain upright at all times; this requires special caution when moving. The MSD should not be left vented to the atmosphere for long periods. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 31 33) counterclockwise until it pops out. The fuse holders are spring loaded. Remove the old fuse from the fuse holder. Install a new fuse in the fuse holder. Reinstall the fuse holder. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 32: To Replace The Primary Fuses
Introduction Primary fuses in holders Figure 2 Primary fuses Repeat steps through for the other fuse. Always replace both fuses. Reconnect the MSD power cord to the electrical outlet. Pump down the MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 33 Introduction 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 34 Introduction 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 35: General Troubleshooting
If the material in this chapter and in the online help does not to help you diagnose your problem, contact your Agilent Technologies service representative. Agilent Technologies...
Page 36: Instrument State
Not connected to DS Blinking yellow (<2 sec) Ready and not connected to DS Solid yellow for 3 sec, quick double blink Start up (prior to FW load) Blinking red (<2 sec) Fault Solid red 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 37: Troubleshooting Tips And Tricks
• To determine whether an air leak is in the GC or the MSD, you can vent the MSD, remove the column, and install the blank interface ferrule. If the leak goes away, it was in the GC. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 38: General Symptoms
“Pumpdown failure shutdown” on page 156. You must power cycle the MSD to recover from this state. • Disconnected foreline pump power cord • Malfunctioning foreline pump • Check power switch on foreline pump 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 39 “Pumpdown failure shutdown” on page 156. You must power cycle the MSD to recover from this state. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 40: Chromatographic Symptoms
† This could cause a fault condition in the GC that would prevent the GC from operating. Does not pass tune • Calibration vial is empty • Excessive foreline or analyzer chamber pressure 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 41 • Insufficient column flow Peaks have flat tops • Insufficient solvent delay • Incorrect scale on the display • Injection is too large • Electron multiplier voltage is too high • Gain is too high 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 42 • Residual water air and water from a recent venting • Column bleed • Septum bleed • Splitless injection time too long (inlet is not properly swept, resulting in excess solvent on the column and slow solvent decay) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 43 • Initial oven temperature was decreased • Active sites in the sample path † • Leaks in the GC inlet † This could cause a fault condition in the GC that would prevent the GC from operating. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 44 • Variations in pressure, column flow, and temperature • Dirty ion source • Loose connections in the analyzer • Ground loops † This could cause a fault condition in the GC that would prevent the GC from operating. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 45: Mass Spectral Symptoms
• Electron multiplier voltage is too high • Repeller voltage is too high • High background • Dirty ion source High background • Pressure in the analyzer chamber is too high • Air leak • Contamination 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 46 • MSD has not had enough time to reach thermal equilibrium • Large variations in the temperature of the laboratory • Incorrect tuning • Calibration vial(s) empty or almost empty • Calibration valve(s) not working correctly • Dirty ion source 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 47 • Incorrect DC polarity on the quadrupole mass filter Spectra look different from those acquired with other MSDs Ion ratios are different from those in older models MSDs. This is due to the HED detector, and is normal. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 48 • Poor filament operation • Dirty ion source • Air leak • Incorrect DC polarity on the quadrupole mass filter • No voltage to the extractor lens (is using an extractor EI ion source) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 49: Pressure Symptoms
• Column (carrier gas) flow is too high • Air leak • Foreline pump is not working correctly (see Foreline pressure is too high) • Turbo pump is not working correctly 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 50 • Solvent peak from an on-column injection • MSD has not had enough time to pump down • Excessive foreline pressure • Vacuum gauge has failed • Line voltage too low • Turbo pump is not working correctly 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 51 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 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 52: Temperature Symptoms
• Mass filter has not had enough time to reach temperature setpoint † • Mass filter heater cartridge is not connected † • Mass filter temperature sensor is not connected † • Mass filter heater failed (burned out or shorted to ground) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 53 † • GC/MSD sensor failed † • GC electronics are not working correctly † These will cause a GC error message. GC error messages are described in the documentation supplied with your GC. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 54: Error Messages
“The system is in vent state” on page 58 for precautions to take. • One of the fans is disconnected • One of the fans has failed • MSD electronics are not working correctly 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 55 • Severely degraded foreline pump oil (standard foreline pump) • Collapsed or kinked foreline hose • Foreline pump is not working correctly Internal MS communication fault • MSD electronics are not working correctly 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 56 • Calibration vial(s) empty or almost empty • Excessive pressure in the analyzer chamber • Air leak • Signal cable is not connected • Electrical leads to the detector are not connected correctly 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 57 • Turbo pump is on but has not had enough time (5 minutes) to reach 80% of its normal operating speed • Turbo pump is not working correctly • MSD electronics are not working correctly 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 58 • Corrupted tune file • Poor mass axis calibration • Amu gain or offset is too high • Calibration vial(s) empty or almost empty • Excessive pressure in the analyzer chamber • Air leak 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 59 • Electrical leads to the detector are not connected correctly • Electrical leads to the ion source are not connected correctly • Filament shorted to the source body • Column inserted too far into source 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 60: Air Leaks
• Side plate O-ring (all the way around) • Vent valve O-ring • Calibration valve(s) • GC/MSD interface O-ring (where the interface attaches to the analyzer chamber) • Front and rear end plate O-rings • Turbo pump O-ring 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 61: Contamination
• Foreline pump oil (standard foreline pump) • Fingerprints (improper handling of clean parts) Table 6 on page 62 lists some of the more common contaminants, the ions characteristic of those contaminants, and the likely sources of those contaminants. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 62 73, 147, 207, 221, 281, 295, 355, Dimethylpolysiloxane Septum bleed or methyl silicone column bleed Plasticizer (phthalates) Vacuum seals (O-rings) damaged by high temperatures, vinyl gloves Peaks spaced 14 m/z apart Hydrocarbons Fingerprints, foreline pump oil 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 63: Ci Troubleshooting
Troubleshooting Tips and Tricks Air Leaks Pressure-Related Symptoms Signal-Related Symptoms Tuning-Related Symptoms This chapter outlines troubleshooting 5977B Series MSDs equipped with the chemical ionization (CI) ion source. Most of the troubleshooting information in the previous chapter also applies to CI MSDs. Agilent Technologies...
Page 64: Common Ci-Specific Problems
CI Troubleshooting Common CI-Specific Problems Because of the added complexity of the parts required for CI, there are many potential problems added. The greatest number of, and most serious problems with CI are associated with leaks or contamination in the reagent gas introduction system.
Page 65: 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 66: 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 67 CI Troubleshooting There should not be any peak visible at m/z 32 (O ). This almost always indicates an air leak. Figure 3 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 68 CI Troubleshooting 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. If any of the fittings inside the flow module (VCR fittings) were loosened and then retightened, the gasket must be replaced.
Page 69 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 4 Schematic of CI flow control module Table 7 Flow module valve state diagram ...
Page 70: 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 8).
Page 71 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 72 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 73 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 74: 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 75 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 the MSD has been working well and nothing seems to have been changed •...
Page 76 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 77 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 after running one or more autotunes, the ion source is probably dirty.
Page 78 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 79 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 80 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. Poor vacuum Check the pressure on the high vacuum gauge controller. Air leak Run Methane Pretune (in PCI).
Page 81 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, there probably is 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 82 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. To eliminate water, bake out the system under vacuum. New or dirty reagent gas supply tubing Purge the reagent gas supply lines and flow module for at least 60 minutes.
Page 83: 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 ratio is difficult to adjust or unstable •...
Page 84 CI Troubleshooting Reagent gas ion ratio is difficult to adjust or unstable The interface tip seal is incorrectly placed, damaged, or missing. Inspect the Isolation tip. 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. Residual air and water in the MSD or in the reagent gas supply lines Run the methane pretune.
Page 85 CI Troubleshooting High electron multiplier voltage The electron multiplier voltage can range from a few hundred volts to 3,000 V. If the CI autotune program consistently sets the electron multiplier voltage at or above 2,600 V but can still find peaks and complete the tune, it may indicate a problem.
Page 86 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 87 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. Air leak Run Methane Pretune (in PCI). A visible peak at m/z 32 indicates air in the system.
Page 88 CI Troubleshooting...
Page 89 To Install the EI Calibration and Vent Valve Assembly To Replace the Fan for the High Vacuum Pump To Remove the Ion Vacuum Gauge To Install an Ion Vacuum Gauge To Lubricate the Side Plate O-Ring To Lubricate the Vent Valve O-Ring Agilent Technologies...
Page 90: General Maintenance
General Maintenance Maintaining the Electronics To Adjust the Quad Frequency To Replace the Primary Fuses 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 91: Before Starting
Every 3 months for CI MSDs using ammonia reagent gas. Vacuum seals other than the side plate O-ring and vent valve O-ring do not need to be lubricated. Lubricating other seals can interfere with their correct function. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 92 Some procedures in this chapter require access to the inside of the MSD while the power switch is on. Do not remove any of the electronics safety covers in any of these procedures. To reduce the risk of electric shock, follow the procedures carefully. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 93 As a result, the exhaust from the foreline pump will contain traces of the carrier gas and your samples. Exhaust from the standard foreline pump also contains tiny droplets of foreline pump oil. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 94: Electrostatic Discharge
The wrist strap should be connected to a known good earth 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 95 Antistatic precautions are not 100% effective. Handle electronic circuit boards as little as possible and then only by the edges. Never touch components, exposed traces, or pins on connectors and cables. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 96: Maintaining The Vacuum System
If you need more information about the locations or functions of vacuum system components. (See “Vacuum System” on page 153.) Most of the procedures in this chapter are illustrated with video clips on the 5977B Series MSD User Information media. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 97: To Separate The Msd From The 7890 Gc
MSD interface. The Agilent 7820A GC has only one location for the MSD interface. Interface cable LVDS cable Figure 5 Separating and connecting the MSD and GC 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 98 Disconnect the GC/MSD interface cable and the LVDS cable (if applicable). Disconnecting either cable with the GC on can cause a fault condition. Continue to move the MSD until you have access to the part requiring maintenance. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 99: To Separate The Msd From The 9000 Gc
WA R N I N G the 9000 GC/MSD Tail. Separate the MSD and 9000 GC Remove the 9000 GC/MSD Tail. Refer to the Agilent 5977B Series MSD Operating Manual. Power off the GC. Using a T-20 Torx screwdriver, loosen the lock plate by turning the lock plate screw clockwise.
Page 100 Disconnecting the interface heater cables with the GC on can cause a fault condition. Continue to move the MSD until you have access to the part requiring maintenance. Interface cables LVDS cable Figure 6 GC/MSD interface heater cables and LVDS cable 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 101: To Reconnect The Msd To The 7890 Gc
MSD, or under the analyzer chamber at the back of the MSD. Reinstall the capillary column. Pump down the MSD. Turn on the MS and GC. Enter appropriate temperature setpoints for the GC/MSD interface and GC oven. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 102: To Reconnect The Msd To The 9000 Gc
Be careful not to damage the GC/MSD interface as it passes into the GC. Open the GC front door. Slide the MS forward until the GC/MSD interface lightly contacts the bus. (See Figure 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 103 During pumpdown, do not push on the filament board safety cover while pressing on C A U T I O N the analyzer boards. This cover was not designed to withstand this type of pressure. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 104 Ensure your MSD meets all the conditions listed in the Pump Down section of the WA R N I N G Agilent 5977B Series MSD Operating Manual before starting up and pumping down the MSD. Failure to do so can result in personal injury.
Page 105: To Move Or Store The Msd When Connected To A 7890 Gc
Plug the MSD power cord in. Switch the MSD on for 5 minutes to establish a rough vacuum. Switch the MSD off. Close the analyzer cover. 10 Disconnect the LAN, remote, and power cables. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 106 The MSD must remain upright at all times. If you need to ship your MSD to another C A U T I O N location, contact your Agilent Technologies service representative for advice about packing and shipping. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 107: To Move Or Store The Msd When Connected To A 9000 Gc
Plug the MSD power cord in. Switch the MSD on for 5 minutes to establish a rough vacuum. Switch the MSD off. Close the analyzer cover. 10 Disconnect the LAN, remote, and power cables. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 108 The MSD must remain upright at all times. If you need to ship your MSD to another C A U T I O N location, contact your Agilent Technologies service representative for advice about packing and shipping. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 109: To Check The Foreline Pump Fluid
(See “To Refill the Foreline Pump” on page 112, starting at step four.) Never add oil while the foreline pump is on. WA R N I N G 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 110 General Maintenance Oil mist filter Fill cap Oil level line Drain plug Figure 10 Pfeiffer Duo 2.5 foreline pump 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 111: To Drain The Foreline Pump
If necessary, you can place a book or other object under the pump motor to tilt it up slightly. The old pump oil may contain toxic chemicals. Treat it as hazardous waste. WA R N I N G Replace the drain plug after draining the oil. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 112: To Refill The Foreline Pump
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. Pump down the MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 113: To Change The Blue Oil Mist Filter On The Foreline Pump
Unscrew the filter from the top of pump. Screw the replacement filter on to the pump and replace the exhaust hose. Pump exhaust Oil mist filter Figure 11 Foreline Pump with oil mist filter 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 114: To Install The Exhaust Filter On The Idp3 Dry Pump
Disconnect the foreline pump exhaust hose from the adapter. Unscrew the adapter from the pump. Screw the filter on to the pump. Exhaust hose Hose adapter Exhaust filter Figure 12 IDP3 pump with exhaust filter 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 115: To Change The Filter Cartridge On The Idp3 Dry Foreline Pump
Figure 12 on page 114.) Pull the filter cartridge out of the filter cap. Replace the filter cartridge. Align the cap onto the filter and the cap counter clockwise to lock in place. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 116: To Check The Dp Fluid
Then, check for an air leak. The DP fluid should be replaced at least once a year, or more often if the pump fluid level is low, or if the fluid is dark or cloudy. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 117 General Maintenance Fluid level window (sight glass) Figure 13 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 118: To Remove The Dp
MSD. (This is the thick black cable that emerges near the bottom of the pump.) Disconnect the DP temperature sensor wires from the wiring harness. Support the DP with one hand. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 119 Do not tilt the pump past 45 degrees if the pump is warm. 10 Disconnect the foreline gauge assembly from the DP outlet. The foreline gauge cable can be disconnected or can remain connected to the foreline gauge. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 120: To Replace The Dp Fluid
Methylene chloride is a hazardous solvent. Work in a fume hood and take all WA R N I N G appropriate precautions. Check the color of the pump fluid. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 121 Only use about half of the second bottle Figure 15 Filling the DP with fluid Clean the DP flange on the analyzer chamber. Preheat the new DP fluid following the instructions on the bottle. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 122 1.5 of the bottles (18.5 mL each) of DP fluid. Pour the fluid between the center stack and the side wall. Watch the sight glass while pouring. Do not overfill. Reinstall the DP. (See “To Install the DP” on page 123.) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 123: To Install The Dp
Reconnect the foreline gauge fitting to the outlet of the DP. If you disconnected the foreline gauge cable, reconnect it to the foreline gauge. Move the MSD back to its normal position.  5977B Series MSD Troubleshooting and Maintenance Manual...
Page 124 General Maintenance Foreline gauge assembly KF50 clamp O-ring assembly DP outlet Figure 16 Installing the DP 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 125: To Remove The Foreline Gauge
C A U T I O N gauge. Never vent the MSD at the pump end; use the vent valve. Pull the foreline gauge assembly out of the foreline hose. (See Figure 17 page 126.) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 126 General Maintenance Foreline gauge Figure 17 Foreline gauge assembly 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 127: To Install The Foreline Gauge
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. Pump down the MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 128: To Refill The Ei Calibration Vial
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. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 129 12 Purge the EI calibration valve. (See “To Purge the Calibration Valves” page 130.) Failure to purge the calibration valve will result in damage to the filaments and C A U T I O N detector. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 130: To Purge The Calibration Valves
Verify that PCICH4.U is loaded. In Tune and Vacuum Control view, select Purge Calibrant Valve under the Vacuum menu. This will open the CI calibration valve for several minutes with all analyzer voltages turned off. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 131: To Remove The Ei Calibration And Vent Valve Assembly
Liquid in the restrictor will prevent diffusion of PFTBA into the analyzer chamber for tuning. Replace the valve if this happens. Remove the two screws holding the valve assembly to the top of the analyzer chamber. Do not lose the O-ring under it. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 132: To Install The Ei Calibration And Vent Valve Assembly
128.) The valve is supplied with a vial already installed. Fill and reinstall the calibration vial. Pump down the MSD. Failure to purge the calibration valve will damage the filaments and detector. C A U T I O N 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 133: To Replace The Fan For The High Vacuum Pump
Ensure the safety grill that shields the fan blades is in place. WA R N I N G Connect the fan wiring to the fan connector on the MSD frame. Reinstall the MSD covers. Pump down the MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 134 General Maintenance Fan wiring Fan wiring connector Figure 19 Replacing the pump fan (DP shown) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 135: To Remove The Ion Vacuum Gauge
While supporting the gauge body, remove the clamp from the mounting flange. Remove the gauge. If you will not be replacing the gauge soon, install the blanking plate provided with the gauge and secure it with the clamp, screw, and thumbnut. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 136: To Install An Ion Vacuum Gauge
Insert the long screw, add the thumbnut, and tighten. Attach the communication cable to the back of the gauge and connect the other end to the back of the MS. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 137: To Lubricate The Side Plate O-Ring
Use a clean, lint-free cloth or glove to wipe away excess grease. If the O-ring looks shiny, there is too much grease on it. Close the analyzer chamber. Pump down the MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 138 General Maintenance Side plate O-ring Figure 20 Side plate O-ring 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 139: To Lubricate The Vent Valve O-Ring
Use a clean, lint-free cloth or glove to wipe away excess grease. If the O-ring looks shiny, there is too much grease on it 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 140 Be very careful when reinstalling the vent valve knob. It is possible to cross thread the C A U T I O N knob and damage the threads in the valve body. Ensure the O-ring stays in place. Pump down the MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 141: Maintaining The Electronics
When you work on or near printed circuit boards, or when you work on components with wires, contacts, or cables connected to printed circuit boards, always use a grounded antistatic wrist strap and take other antistatic 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 142 More information about the functions of electronic components section is found later in this manual. (See Chapter “Electronics” on page 211.) Most of the procedures in this chapter are illustrated with video clips. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 143: To Adjust The Quad Frequency
Do not use a coin to adjust the screws. If you drop it, it could fall into the electronics C A U T I O N fan and cause significant damage. When the voltage is minimized, click Stop. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 144 Adjusting the quad frequency Repeat steps 4 through 7 for m/z 650. Exit the Set Optimize Quadrupole Frequency program. 10 Select MS OFF from the Execute menu. 11 Close the analyzer cover. 12 Tune the MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 145: To Replace The Primary Fuses
Turn one of the fuse holders counterclockwise until it pops out. (See Figure 23 on page 146.) The fuse holders are spring loaded. Remove the old fuse from the fuse holder. Install a new fuse in the fuse holder. Reinstall the fuse holder. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 146 Figure 23 Primary fuses (turbo model shown) Repeat steps 2 through 5 for the other fuse. Always replace both fuses. Reconnect the MSD power cord to the electrical outlet. Pump down the MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 147: Ci Maintenance
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 5977B Series MSDs equipped with the Chemical Ionization hardware. Agilent Technologies...
Page 148: To Replace The Methane/Isobutane Gas Purifier
Install the new filter. Purge the new filter. Cap the old filter and prepare it to be sent for regeneration. See the instructions on the label. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 149: To Clean The Reagent Gas Supply Lines
Do not heat the gas tubing when reagent gas is flowing. WA R N I N G Do not put liquids into the tubing. Do not heat the tubing when it is connected to the C A U T I O N MSD. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 150: To Refill The Ci Calibrant Vial
After removing the calibrant vial, you must purge the calibration valve. Failure to do so C A U T I O N will result in severe contamination of the ion source and damage to the filament and electron multiplier. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 151 CI Maintenance Calibration valve Collar Calibration vial Figure 24 CI calibration valve and vial 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 152 CI Maintenance 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 153: Vacuum System
Agilent 5977B Series MSD Troubleshooting and Maintenance Manual Vacuum System Overview Vacuum System Components Common Vacuum System Problems Foreline Pump High Vacuum Pump Analyzer Chamber Side Plate Vacuum Seals Face seals KF (NW) seals Compression seals High voltage feedthrough seal...
Page 154: Overview
Operation at high pressures also would damage analyzer components. The 5977B Series MSDs use two vacuum pumps to obtain the vacuum levels needed. One of two foreline pumps (standard or dry) creates a low vacuum, then a high vacuum pump engages to create the vacuum needed for operation.The 5977B Series MSD uses one of two kinds of high vacuum pumps:...
Page 155: Vacuum System Components
Ion vacuum gauge (if present) CI flow control Vent valve (not shown) Analyzer chamber GC/MSD interface High vacuum pump High vacuum pump cooling fan Figure 25 Example vacuum system components (MSD with turbo pump shown) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 156: Common Vacuum System Problems
• High foreline pressure in diffusion pump MSDs • Higher than normal high vacuum gauge controller readings The 5977B Series MSD will not pump down successfully unless you press on the side plate (analyzer door) when you turn on the MSD power. Continue to press until the sound from the foreline pump becomes quieter.
Page 157: Foreline Pump
MSDs Exhaust outlet with oil mist filter Hose to vacuum pump Power switch Fill cap Ballast control Oil level window Drain plug (on front) Figure 26 Pfeiffer DUO foreline pump 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 158 Power cord Figure 28 IDP3 dry foreline pump Agilent does not recommend using hydrogen as a carrier gas on systems equipped C A U T I O N with an IDP3 rough pump. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 159 There are two marks next to the window. The level of the pump oil should never be above the upper mark or below the lower mark. If the level of pump oil is near the lower mark, add foreline pump oil. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 160 WA R N I N G under, over, or around the foreline (roughing) pump constitutes a fire hazard.  Keep the pan clean, but do not leave absorbent material such as paper towels in it. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 161: High Vacuum Pump
The AC board controls the diffusion pump heater. Turbo pump system The 5977B Series MSD supports a turbo pump. The turbo pump has a screen to keep debris out of the pumpbut no baffle is necessary. Pump speed is controlled by the turbo controller; there is no foreline gauge.
Page 162: Analyzer Chamber
The turbo pump and the mounting bracket for the turbo controller are clamped directly to the manifold. Observation window Calibration and vent valves Side plate O-ring Vacuum gauge baffle GC/MSD interface To high vacuum pump Figure 29 Analyzer chamber 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 163: Side Plate
When you turn on the power to pump down the MSD, press on the side board to ensure C A U T I O N a good seal. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 164 Vacuum System EM voltage Signal (detector output) Mass Filter (quadrupole) Ion source and heater PE1, PE2, and Ext feedthroughs Detector focus High voltage (HED) Figure 30 Side plate feedthroughs (HES version) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 165 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 31 Side plate feedthroughs (non-HES version) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 166: Vacuum Seals
KF seals. KF seals have an O-ring supported by a centering ring. The centering ring can be either on the inside or outside of the O-ring. The clamp presses two flanges against the O-ring, making a seal. KF clamps must not be overtightened. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 167 Side plate O-ring seal KF seal with internal centering ring (clamp not shown) KF seal with external centering ring (clamp not shown) Compression seal Figure 32 Vacuum seals 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 168: Foreline Gauge
If the foreline pressure rises above 400 mTorr (0.4 Torr), the AC board switches off the diffusion pump heater and the analyzer electronics. Monitor the foreline pressure from the data system or the LCP. The foreline gauge is used only with diffusion pump MSDs. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 169: Diffusion Pump And Fan
A structure called the stack is located at the center of the pump body. An electric heater is located at the bottom of the stack. Figure 33 on page 169 and Figure 34 on page 170. Figure 33 Diffusion pump with fan 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 170 The vapor condenses on the sides of the pump, and the liquid drains down to the bottom. The liquid is boiled again, and is reused continuously. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 171 Two thermal switches monitor diffusion pump operational readiness. See Table Table 11 Diffusion pump thermal switches Thermal switch Too cold Too hot Normal state Normally open Normally closed Changes at 170 °C rising; 140 °C 365 °C rising falling 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 172 If the level drops below the appropriate marker (there are separate ranges for hot and cold conditions) or if the fluid turns dark brown or black, replace the fluid. Otherwise, replace the fluid once a year. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 173 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 35 The diffusion pump 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 174 Cracked pump fluid gives two symptoms: higher manifold pressure and high background with a large peak at m/z 446. See also • “Maintaining the Vacuum System” on page 96. • The troubleshooting sections of the MSD Data Acquisition online help. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 175: Turbo Pump And Fan
5 to 10 minutes. See Also • To pump down the MSD in the Operating Manual • To vent the MSD in the Operating Manual • See “Turbo pump control” on page 217. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 176: Calibration Valves And Vent Valve
The threaded end of the knob has an air passage inside it, allowing air to flow into the manifold when the knob is partially unscrewed. If you turn the knob too far, the O-ring can come out of its slot. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 177 Vacuum System EI calibration above analyzer window Vent valve knob EI calibration vial EI calibration valve CI calibration right side of MSD CI calibration valve CI calibration vial Figure 36 Calibration valves 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 178 Vacuum System Vent valve knob O-ring Air passage Valve closed Valve open Valve open too far Figure 37 Vent valve 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 179: Micro-Ion Vacuum Gauge
These changes can indicate air leaks or other problems with the vacuum system. All the pressures listed in this manual are indicated pressures for helium carrier gas. The gauge controller setpoints are also indicated pressures. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 180 Vacuum System 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 181: Analyzer
Agilent 5977B Series MSD Troubleshooting and Maintenance Manual Analyzer Overview EI Ion Source HES EI Ion Source CI Ion Source Filaments Other Source Elements Magnet Repeller Drawout plate and cylinder Ion focus Entrance lens Quadrupole Mass Filter AMU gain AMU offset...
Page 182: Overview
The analyzer has four basic components The analyzer consists of the following components (See Figure 39 on page 184) or (See Figure 38 on page 183): • Ion source • Mass filter • Detector • Heaters and radiators 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 183 Analyzer Detector Mass filter heater assembly Feedthrough board Ion source (inside radiator) Mass filter (inside radiator) Figure 38 The analyzer with an HES 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 184 Analyzer Detector Mass filter contact Mass filter heater assembly Feedthrough board Ion source (inside radiator) Mass filter (inside radiator) Mass filter contact cable Figure 39 The analyzer with an XTR source 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 185: Ei Ion Source
The ionization chamber is the space where the ions are formed. Slots in the source body help the vacuum system to pump away carrier gas and unionized sample molecules or fragments. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 186 Analyzer Lens insulation Entrance lens Ion focus lens Drawout cylinder Drawout plate Filament Repeller Figure 40 SST/Inert ion source structure 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 187 Analyzer Lens insulation Entrance lens Ion focus lens Extractor lens Ceramic insulator Filament Repeller Figure 41 Extractor ion source structure 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 188 Item number Item description Part number (SSL) Part number (Inert) Gold plated set screw G1999-20022 G1999-20022 Gold plated screw G3870-20021 G3870-20021 Interface socket G1099-20136 G1099-20136 Source body G1099-20130 G2589-20043 Drawout cylinder G1072-20008 G1072-20008 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 189 05971-20143 05971-20143 Repeller insulator G1099-20133 G1099-20133 Repeller G3870-60172 G3870-60173 Flat washer 3050-0627 3050-0627 Belleville spring washer 3050-1301 3050-1301 Repeller nut 0535-0071 0535-0071 Source heater block assembly G3870-60180 G3870-60179 Repeller block insert G3870-20135 G3870-20135 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 190 Parts list for extractor ion source (Figure 43 on page 190) Item number Item description Part number Setscrews G3870-20446 Screws G3870-20021 Source body G3870-20440 Extractor lens G3870-20444 Extractor lens insulator G3870-20445 Filaments G7005-60061 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 191 Flat washer 3050-0891 Belleville spring washer 3050-1301 Repeller nut 0535-0071 Source heater block assembly G3870-60177 Insulator G1099-20133 The CI ion source is similar in design, but critical dimensions are different. Do not interchange parts. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 192: Hes Ei Ion Source
The ionization chamber is the space where the ions are formed. Slots in the source body help the vacuum system to pump away carrier gas and un-ionized sample molecules or fragments. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 193 Source finger grip G7002-20008 Filament block G7005-60061 † Extractor lens (5) , with 3 mm opening G7002-20061 Ceramic insulator for extractor G7002-20064 † Entrance lens (1) G7002-20065 † Ion focus lens (2) G7002-20068 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 194 Locking ring lens insulator G7002-20126 High efficiency dual filament G7002-60001 Ring heater/sensor assembly G7002-60043 Source mount 1.5 mm G7002-60053 Repeller assembly G7002-67057 † The number in parenthesis is the number engraved on the lens 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 195: Ci Ion Source
196) ensures a leak-tight seal and electrical isolation between the CI interface and ion source. Ion source body Filament Lens insulation Entrance lens Ion focus lens Drawout cylinder Drawout plate Repeller Dummy filament Figure 45 CI ion source structure 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 196 Analyzer Interface tip seal Figure 46 Interface tip seal 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 197 (Figure 47 on page 197) Item number Item description Part number Setscrew G1999-20022 Filament screw G1999-20021 CI interface tip seal G3870-20542 CI repeller insulator G1999-20433 CI lens insulator G3170-20540 CI drawout cylinder G1999-20444 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 198 G3870-60415 Entrance lens G3170-20126 CI ion source body G3170-20430 CI ion focus lens G1999-20443 CI repeller G1999-20432 CI filament G7005-60072 Dummy filament G1999-60454 Not labeled Curved washer 3050-9082 Not labeled Flat washer 3050-1374 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 199: Filaments
–70 eV (electron volts). This value is adjustable from –5 to –241 VDC, but for normal operation, set this parameter to 70 for a non-HES source and 120 for the HES. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 200 NO. • Higher emission current reduces filament life. • Higher electron energy reduces filament life. • Leaving the filament on for short times (1 minute) during data acquisition reduces filament life. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 201: Other Source Elements
These are used in the standard, inert, and CI ion sources only. Extractor lens A voltage is applied to the extractor lens to increase ion focusing through the source. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 202 Entrance lens gain (EntLens) controls the variable voltage applied to the entrance lens. It determines how many volts are applied for each m/z. It can be varied from 0 to –128 mV/(m/z). A typical range is 0 to –40 mV/amu. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 203: Quadrupole Mass Filter
Parameters dialog. • AMU gain (AmuGain) • AMU offset (AmuOffs) • 219 width (Wid219) • DC polarity (DC Pol) • Mass (axis) gain (MassGain) • Mass (axis) offset (MassOffs) • MS quad temp 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 204 PFTBA, there may not be an ion at m/z 219. In that case, set the 219 width to the last value found for it by Autotune, or set it to 0. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 205 The fused-quartz quadrupole is fragile and will break if dropped or handled roughly. The material in the cusps of the quadrupole is very hygroscopic. If exposed to water, the quadrupole must be dried very slowly to prevent damage. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 206: Detector
0 to –3,000 VDC. Use the EM voltage found in autotune as a baseline for the EM voltage setting. • To increase signal gain, increase the EM voltage. • For concentrated samples where less signal gain is needed, decrease the EM voltage. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 207 See Also • Troubleshooting in the online help for more information about symptoms that may indicate EM problems. HED high voltage EM horn Figure 49 The detector 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 208: Analyzer Heaters And Radiators
The GC/MSD interface, ion source, and mass filter (quad) heated zones interact. The analyzer heaters may not be able to accurately control temperatures if the setpoint for one zone is much lower than that of an adjacent zone. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 209 Analyzer Mass filter radiator Mass filter heater assembly Ion source radiator Ion source heater assembly Figure 50 Heaters and radiators with an XTR source 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 210 Analyzer Mass filter radiator Mass filter heater assembly Ion source radiator Ion source heater/sensor wires (gray and purple) Figure 51 Heaters and radiators with an HES 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 211 MSD. Dangerous voltages are present under the safety covers. Do not remove safety WA R N I N G covers. Refer servicing to your Agilent Technologies service representative. Agilent Technologies...
Page 212: Electronics
C A U T I O N shutdown can seriously damage the MSD. Front Panel LED The front panel LED shows the current instrument status through a color code, as shown in Table 16 on page 213. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 213 Not connected to DS (system idle) Solid blue Ready and not connected to DS Solid yellow for 3 sec, quick double blink Start up (prior to FW load) Blinking red Fault Solid red 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 214: Side Board
• Generates and adjusts filament emission current and electron energy as controlled by the main board. • Switches the filament power from one filament to the other. • Monitors for RF faults and shuts down the analyzer if one is detected. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 215: Electronics Module
HV fault and RF fault signals from the side board. Activates the shutdown line when the analyzer electronics must be disabled. • Generates the control signals (on and off) used by the AC board for the high vacuum pump and calibration valve. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 216 Controls the foreline gauge. • Turns on the diffusion pump once the foreline pressure is low enough, as directed by the main board. • Regulates the AC power to the diffusion pump heater. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 217 HI VAC Power heater cable Heater Harness Fore- Sensors line Diffusion pump gauge harness valve Figure 52 Diffusion pump control Turbo pump control Your MSD is equipped with a turbo pump with an integrated controller. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 218 To correct the problem, power cycle the MSD and troubleshoot. You have 7 minutes to find and correct the air leak before the system shuts down again. Press on the side plate when turning on the MSD power to ensure a good seal. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 219: Lan/Ms Control Card
The flashing heartbeat LED indicates that the operating system of the MSD is functioning. In case of catastrophic loss of flash memory, the heartbeat flashes in an SOS (•••– – – •••) pattern. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 220: Power Supplies
200 to 260 VAC from the AC board. The AC board samples the line voltage and uses a relay to appropriately strap the toroid primary. The output wires connect to the main board. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 221: Back Panel And Connectors
If the power switch is off, no power is supplied to the foreline pump. REMOTE The remote start connector is the external connector for the remote start circuitry on the LAN/MS control card. It receives remote start signals from the 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 222: High Vacuum Gauge Connector
The two upper LEDs indicate network communication. The two bottom LEDs are the power and the heartbeat indicator. GC COMM This RS-232 cable connector is used for LVDS communication with a supported GC. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 223 Remote start High vacuum gauge connector High vacuum control Primary fuses High vacuum power GC communication Power cord RS-232 Serial B Foreline pump RS-232 Serial A power cord Figure 53 Back panel connections 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 224: Interfacing To External Devices
When interfacing to an external device, it is often desirable to send a system-ready signal to the device. In the case of a multisample Tekmar purge-and-trap, each sample is purged onto a trap where it waits for a ready 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 225 If necessary, the remote start connector on the back of the MSD can be used to send the start run signal. A contact closure between the start and ground pins will start the run, if the system is ready. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 226 Electronics 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 227 Consumables and Maintenance Supplies This chapter lists parts that can be ordered for use in maintaining your 5977B Series MSD. It includes most of the parts or assemblies in the MSDs.  This chapter is organized so that related parts are grouped together.
Page 228: To Order Parts
Parts To Order Parts To order parts for your MSD, contact 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 229: 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: fuses (Table 17). Fuses Table 17 Fuses Description Part number Fuse T12.5A, 250 V 2110-1398 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 230: Vacuum System
KF10/16 seal (foreline pump inlet), Micro-Ion vacuum KC16AV gauge KF10/16 seal (foreline pump inlet and diffusion pump KC16AV outlet), Micro-Ion vacuum gauge KF50 seal (diffusion pump inlet) 0100-1884 Side plate O-ring 0905-1442 Vent valve O-ring (1/4-inch) 5180-4182 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 231: Standard Foreline Pump And Related Parts
O-ring for oil mist filter and hose barb adapter 0905-1193 Foreline pump oil 6040-0621 5 mm hex key 8710-1838 † Hose clamps are interchangeable, but give an optimum fit if they are matched 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 232 Parts Figure 55 Pfeiffer DUO pump 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 233: Mvp-070 Foreline Pump And Related Parts
(Figure Description Part number Dry pump, MVP 070-3 G3870-80051 Dry pump, MVP 070-3C G3870-80061 Dry pump, MVP 070-3 - Rebuilt G3870-80052 Dry pump, MVP 070-3C - Rebuilt G3870-89052 Figure 56 MVP-070 foreline pump 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 234: Idp3 Dry Foreline Pump And Related Parts
Vibration Isolation kit IDP3VIBISOKIT Exhaust hose G3170-60100 Exhaust adapter G3170-80029 Barbed fitting G3170-80006 Exhaust hose for oil-less pump G3170-60100 † Hose clamps are interchangeable, but give an optimum fit if they are matched 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 235 Parts Figure 57 IDP3 Dry foreline pump Agilent does not recommend using hydrogen as a carrier gas on systems equipped C A U T I O N with an IDP3 rough pump. 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 236: Diffusion Pump And Related Parts
Fan (for high vacuum pump) G7005-60564 Foreline gauge assembly G1099-60545 KF50 clamp 0100-1395 High vacuum fan Foreline gauge assembly Diffusion pump Figure 58 Diffusion pump removed from analyzer chamber connection and related parts 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 237: Turbo Pump And Related Parts
Part number Turbomolecular pump G3170-80162 Pfeiffer HiPace 300 turbo pump- Rebuilt G3170-89162 Turbo power assembly G3170-60600 Centering ring seal with screen 0905-1613 Ion gauge assembly Turbo Pump Figure 59 Turbo pump and related parts 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 238: Analyzer
Table 25 Analyzer parts Description Part number TAD assembly (Detector, HED, bracket) G7002-80105 Detector (Electron multiplier horn) G7002-80103 EI 350 ion source, new Turbo - inert G3870-67700 Diffusion - stainless steel G3870-67750 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 239 Part number EI 350 extractor ion source G3870-67720 HES ion source G7002-67055 CI ion source G7077-67404 Tip Seal G3870-20542 Detector Electron multiplier horn (under clips) Ion source Figure 61 Analyzer parts (non-HES version) 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 240 Parts Detector Electron multiplier horn (under clips) Ion source Figure 62 Analyzer parts (HES version) Table 26 Analyzer screws Description Part number Ion source thumbscrew G1099-20138 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 241: Ei Ion Source
Parts EI ion source 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 242 3050-0982 Lens insulator G3870-20530 Entrance lens G3170-20126 Ion focus lens 05971-20143 Repeller insulator G3870-20133 Repeller G3870-60171 Flat washer 3050-0891 Belleville spring washer 3050-1301 Repeller nut 0535-0071 Source heater block assembly G3870-60177 Insulator G1099-20133 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 243 Parts Figure 63 Extractor EI ion source 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 244: Ci Ion Source
CI ion source heater block assembly G3870-60415 Entrance lens G3170-20126 CI ion source body G3170-20430 CI ion focus lens G1999-20443 CI repeller G1999-20432 CI filament G7005-60072 Dummy filament G1999-60454 Curved washer 3050-9082 Flat washer 3050-1374 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 245 Parts Figure 64 The CI ion source 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 246: The Hes Ion Source
Locking ring lens insulator G7002-20126 High efficiency dual filament G7002-60001 Ring heater/sensor assembly G7002-60043 Source mount 1.5 mm G7002-60053 Repeller assembly G7002-67057 † The number in parenthesis is the number engraved on the lens 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 247: Ei Gc/Msd Interface
248 illustrates the parts. Table 30 EI GC/MSD interface Item Description Part number Not shown EI Transferline Assembly G7077-67300 Transferline tip cap, threaded G3870-20547 1/16 Ferrule no hole (qty 10) 5181-3308 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 248 Transfer tip G3870-20542 Column nut 05988-20066 M3 screw G1999-20022 M4 X 0.7 16MM-LG 0515-0383 Heater clamp G7077-20210 Transfer line spring G1999-20023 Welded interface assembly G3870-60301 Heater/sensor assembly G1099-60109 Figure 66 EI GC/MSD interface 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 249: Ci Msd Interface
Transfer tip G3870-20542 Column nut 05988-20066 M3x3L screw-set, gold plated G1999-20022 M4 X 0.7 16MM-LG screws for heater clamp 0515-0383 Heater clamp G7077-20410 Transfer line spring G1999-20023 Welded interface assembly G3870-67401 Heater/sensor assembly G1099-60107 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 250 Parts Figure 67 CI GC/MSD interface 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 251: Consumables And Maintenance Supplies
Foreline pump oil, D545, 0.5 L 6040-0621 ,IDP-3 foreline pump replacement tip seal kit IDP3TS IDP-3 foreline pump 24V Power Supply G3870-60600 Gloves, clean – Large 8650-0030 Gloves, clean – Small 8650-0029 Grease, Apiezon L, high vacuum 6040-0289 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 252 Pliers, long-nose (1.5-inch nose) 8710-1094 Screwdrivers Flat-blade, large 8730-0002 Screwdrivers Torx, T-6 8710-2548 Screwdrivers Torx, T-10 8710-1623 Screwdrivers Torx. T-20 8710-1615 Tweezers, nonmagnetic 8710-0907 Wrenches, open-end 1/4-inch x 5/16-inch 8710-0510 Wrenches, open-end 10-mm 8710-2353 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 253 • 0.5-mm id, 85%/15% for 0.32-mm id columns 5062-3506 • 0.8-mm id, 85%/15% for 0.53-mm id columns 5062-3512 GC/MSD interface with self-tightening nut Figure 68 GC/MSD interface with a self tightening column nut 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 254 • 0.40-mm id, 90%/10%, for 0.25-mm id columns 5181-3323 • 0.47-mm id, 90%/10%, for 0.32-mm id columns 5062-3514 GC inlet with self tightening nut Figure 69 GC inlet with self tightening column nut 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 255 PFDTD calibrant 8500-8510 Foreline pump tray (Pfeiffer pump) G1099-00015 Duo 2.5s and DS-42 foreline pump oil pan G3870-00015 Eval A, hydrocarbons 05971-60045 Ion gauge electronics G3870-80030 Methane/isobutane gas purifier G1999-80410 Wipes (qty 300) 9310-4828 5977B Series MSD Troubleshooting and Maintenance Manual...
Page 256 Parts 5977B Series MSD Troubleshooting and Maintenance Manual...

Agilent Technologies 5977B series Troubleshooting And Maintenance Manual

Table of Contents

Introduction

General Troubleshooting

CI Troubleshooting

General Maintenance

CI Maintenance

Vacuum System

Analyzer

Electronics

9 Parts

Quick Links

Chapters

Troubleshooting

Need help?

Questions and answers

Related Manuals for Agilent Technologies 5977B series

Summary of Contents for Agilent Technologies 5977B series

Table of Contents