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Agilent Technologies 5977B Series, Troubleshooting And Maintenance Manual

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166

5977B Series MSD Troubleshooting and Maintenance Manual

6

Vacuum System

Vacuum Seals

Vacuum seals are shown in 

Figure 32

 on page 167.

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. Two of the O-rings, 
the side plate O-ring and the vent valve O-ring, are 

lightly

 lubricated with 

Apiezon-L vacuum grease.

Face seals

A face seal is an O-ring that fits in a shallow groove. The sealing surface is 
usually a flat plate. The manifold side plate and end plate O-rings fit into 
grooves around the large openings in the analyzer chamber. The side plate 
swings into place against the side plate O-ring, and must be held in place when 
the MSD is turned on for pump down to ensure a good seal.

The front and rear end plates are screwed onto the manifold and should not 
need to be removed. The GC/MSD interface fastens to the manifold with three 
screws.

The calibration valve assembly is fastened onto the front end plate by two 
screws. The vent valve knob threads into the front end plate. Small O-rings in 
grooves in the front end plate provide vacuum seals.

The diffusion pump baffle adapter has a groove for its O-ring. The baffle 
adapter is clamped to the manifold with four claw grips.

KF (NW) seals

Most of the seals for the high vacuum pumps, foreline gauge, and foreline 
pump are 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.

Summary of Contents for 5977B Series

Page 1: ...Agilent Technologies Agilent 5977B Series MSD Troubleshooting and Maintenance Manual ...

Page 2: ...ity and fitness for a par ticular purpose Agilent shall not be liable for errors or for incidental or consequential damages in connec tion with the furnishing use or per formance of this document or of any information contained herein Should Agilent and the user have a separate written agreement with warranty terms covering the material in this document that conflict with these terms the warranty ...

Page 3: ...anging modes 18 Important Safety Warnings 19 Hydrogen Safety 22 Safety and Regulatory Certifications 28 Cleaning Recycling the Product 31 Moving or Storing the MSD 31 To Replace the Primary Fuses 32 2 General Troubleshooting Instrument State 36 Troubleshooting Tips and Tricks 37 General Symptoms 38 Chromatographic Symptoms 40 Mass Spectral Symptoms 45 Pressure Symptoms 49 Temperature Symptoms 52 E...

Page 4: ... Separate the MSD from the 9000 GC 99 To Reconnect the MSD to the 7890 GC 101 To Reconnect the MSD to the 9000 GC 102 To Move or Store the MSD when Connected to a 7890 GC 105 To Move or Store the MSD when Connected to a 9000 GC 107 To Check the Foreline Pump Fluid 109 To Drain the Foreline Pump 111 To Refill the Foreline Pump 112 To Change the Blue Oil Mist Filter on the Foreline Pump 113 To Insta...

Page 5: ...alve Assembly 132 To Replace the Fan for the High Vacuum Pump 133 To Remove the Ion Vacuum Gauge 135 To Install an Ion Vacuum Gauge 136 To Lubricate the Side Plate O Ring 137 To Lubricate the Vent Valve O Ring 139 Maintaining the Electronics 141 To Adjust the Quad Frequency 143 To Replace the Primary Fuses 145 5 CI Maintenance To Replace the Methane Isobutane Gas Purifier 148 To Clean the Reagent ...

Page 6: ... 162 Turbo pump version 162 Side Plate 163 Vacuum Seals 166 Foreline Gauge 168 Diffusion Pump and Fan 169 Turbo Pump and Fan 175 Calibration Valves and Vent Valve 176 Micro Ion Vacuum Gauge 179 7 Analyzer Overview 182 EI Ion Source 185 HES EI Ion Source 192 CI Ion Source 195 Filaments 199 Other Source Elements 201 Quadrupole Mass Filter 203 Detector 206 Analyzer Heaters and Radiators 208 ...

Page 7: ...nt Panel LED 212 Side Board 214 Electronics Module 215 LAN MS Control Card 219 Power Supplies 220 Back Panel and Connectors 221 High vacuum gauge connector 222 Interfacing to External Devices 224 9 Parts To Order Parts 228 Electronics 229 Vacuum System 230 Analyzer 238 Consumables and Maintenance Supplies 251 ...

Page 8: ...8 5977B Series MSD Troubleshooting and Maintenance Manual ...

Page 9: ... foreline pump can be a fire hazard 20 Hydrogen Safety 22 Dangers unique to GC MSD operation 23 Hydrogen accumulation in an MSD 23 Precautions 26 Safety and Regulatory Certifications 28 Information 28 Symbols 29 Electromagnetic compatibility 30 Sound emission declaration 30 Cleaning Recycling the Product 31 Moving or Storing the MSD 31 To Replace the Primary Fuses 32 This manual describes the trou...

Page 10: ...able 1 that indicates what type of MSD you have Table 1 Available high vacuum pumps Model name Product number Description Ionization mode Type 5977B MSD Diff Pump G7080B Diffusion pump Electron ionization EI Stainless Steel 5977B MSD Turbo Pump G7081B Turbo pump Electron ionization EI Stainless Steel 5977B Inert EI MSD Turbo G7077B Turbo pump MSD Electron ionization EI Extractor 5977B Inert EI CI ...

Page 11: ...omofluorobenzene calibrant CI Chemical ionization DC Direct current DFTPP Decafluorotriphenylphosphine calibrant DIP Direct insertion probe DP Diffusion pump DS Data system EI Electron impact ionization EM Electron multiplier detector EMV Electron multiplier voltage EPC Electronic pneumatic control eV Electron volt FW Firmware GC Gas chromatograph HED High energy dynode refers to detector and its ...

Page 12: ...CI Negative CI OFN Octafluoronaphthalene calibrant PCI 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 RF Radio frequency RFPA Radio frequency power amplifier Torr Unit of pressure 1 mm Hg Turbo Turbomolecular pump Table 2 Abbreviations continued Abbre...

Page 13: ...ump with a Pfeiffer DUO 2 5 foreline pump A high efficiency ion source HES Three different non HES types of independently heated MSD electron ionization EI sources available standard source in both stainless steel and inert material and an extractor source Inert ion sources available Field upgradeable to chemical ionization PCI NCI modes that add a chemical ionization CI source reagent gas flow co...

Page 14: ...nded gas flow mL min 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 4 Maximum gas flow mL min Expect degradation of spectral performance and sensitivity 6 5 Max column id 0 53 mm 30 m CI capability Turbo pump models are field upgradeable to CI Yes Foreline pumps available Pfeiffer Duo 2 5 MVP 070 3 MVP ...

Page 15: ...6 kg The foreline pump is usually located on the floor behind the MSD The basic components of the instrument are the Frame cover assemblies Vacuum system GC interface Electronics Analyzer Front Panel LED The front panel LED allows the operator to monitor the MSD The LED displays the instrument status with color codes and patterns described in GC Control Panel Power Switch and Front Panel LED on pa...

Page 16: ...ntenance Manual 1 Introduction MSD Hardware Description Figure 1 is an overview of a typical GC MSD system Figure 1 Agilent 5977B Series GC MS system ALS GC control panel 7890 GC 5977B Series MSD MSD power switch GC power switch Front panel LED ...

Page 17: ...riety of reagent gases can be used 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 A reagent gas flow control module A bipolar HED power supply for PCI a...

Page 18: ...nging modes Switching back and forth between CI and EI ion 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 19: ... cables connected to these boards The wires for any heater oven detector inlet or valve box Electrostatic discharge is a threat to MSD electronics The printed circuit boards in the MSD can be damaged by electrostatic discharge 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 wr...

Page 20: ...aintenance on hot parts use a wrench and wear gloves Whenever possible cool the part of the instrument that you will be maintaining before you begin working on it 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 WARNING Be careful when working behind the instrum...

Page 21: ...intenance Manual 21 WARNING Combustible materials or flammable nonflammable wicking material placed 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 ...

Page 22: ...und in the Hydrogen Safety Guide which is included on this Agilent 5977B HES Series MSD User Information media WARNING The use of hydrogen as a GC carrier gas is potentially dangerous WARNING When using hydrogen H2 as the carrier gas or fuel gas be aware that hydrogen can flow into the GC oven and create an explosion hazard Therefore ensure that the supply is turned off until all connections are m...

Page 23: ...mechanisms by which hydrogen can accumulate Table 4 and know what precautions to take if they know or suspect that hydrogen has accumulated Note that these mechanisms apply to all mass spectrometers including the MSD WARNING The MSD cannot detect leaks in inlet or detector gas streams For this reason it is vital that column fittings should always be either connected to a column or have a cap or pl...

Page 24: ...e equipped with manual shutoff valves In these instruments the operator can close the shutoff valves Closing the shutoff valves does not shut off the flow of carrier gas As a result hydrogen may slowly accumulate in the mass spectrometer GC off A GC can be shut down deliberately It can also be shut down accidentally by an internal or external failure Different GCs react in different ways If a 7890...

Page 25: ...down As described previously in some GCs a power failure may cause the carrier gas flow to be set to maximum As a result hydrogen may accumulate in the mass spectrometer Table 4 Hydrogen accumulation mechanisms continued Mechanism Results WARNING Once hydrogen has accumulated in a mass spectrometer extreme caution must be used when removing it Incorrect startup of a mass spectrometer filled with h...

Page 26: ...w Turn off the hydrogen at its source every time shutoff valves in an MSD are closed do not heat the capillary column without carrier gas flow Turn off the hydrogen at its source if a power failure occurs If a power failure occurs while the GC MSD system is unattended even if the system has restarted by itself 1 Immediately turn off the hydrogen at its source 2 Turn off the GC 3 Turn off the MSD a...

Page 27: ...ES 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 Information The 5977B Series MSD meets the following IEC International Electro technical Commission classifications Equipment Class I Laboratory Equipment Installation Category II Pollution Degre...

Page 28: ...nt 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 See accompanying instructions for more information Indicates a hot surface Indicates hazardous voltages Indicates earth ground terminal Indicates potential explosion hazard Indic...

Page 29: ...following measures Relocate the radio or antenna Move the device away from the radio or television Plug the device into a different electrical outlet so that the device and the radio or television are on separate electrical circuits 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 equipmen...

Page 30: ...ontact 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 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 peri...

Page 31: ...SD will already be off but for safety you should switch off the MSD and unplug the power cord It is not necessary to allow air into the analyzer chamber 2 Turn one of the fuse holders Figure 2 on page 33 counterclockwise until it pops out The fuse holders are spring loaded 3 Remove the old fuse from the fuse holder 4 Install a new fuse in the fuse holder 5 Reinstall the fuse holder WARNING Never r...

Page 32: ...g and Maintenance Manual 1 Introduction 6 Repeat steps 3 through 5 for the other fuse Always replace both fuses 7 Reconnect the MSD power cord to the electrical outlet 8 Pump down the MSD Figure 2 Primary fuses Primary fuses in holders ...

Page 33: ...Introduction 1 5977B Series MSD Troubleshooting and Maintenance Manual 33 ...

Page 34: ...34 5977B Series MSD Troubleshooting and Maintenance Manual 1 Introduction ...

Page 35: ... CI specific problems For each symptom one or more possible causes are listed In general the causes listed first are the most likely causes or the easiest to check and correct This chapter does not include corrective actions for the possible causes listed Some of the corrective actions required may be dangerous if performed incorrectly Do not attempt any corrective actions unless you are sure of t...

Page 36: ... color codes See Table 5 on page 36 for a description of the MSD state Table 5 Front panel Instrument Status LED codes Instrument status LED code Ready Solid green Acquiring data Blinking green 2 sec Not ready Solid yellow 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 ...

Page 37: ... or incorrect gas If the GC column was just replaced suspect air leaks or contaminated or bleeding column Rule 2 If complex is not working go back to simple A complex task is not only more difficult to perform but also more difficult to troubleshoot If you are having trouble detecting your sample verify that autotune is successful Rule 3 Divide and conquer This technique is known as half split tro...

Page 38: ...ply is not working correctly MSD does not turn on Nothing happens when the MSD is switched on The foreline pump does not start The cooling fan for the high vacuum pump does not turn on Disconnected MSD power cord No voltage or incorrect voltage at the electrical outlet Failed primary fuses MSD electronics are not working correctly Foreline pump is not operating The MSD is receiving power the fan i...

Page 39: ...acuum 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 This feature helps prevent the foreline pump from sucking air through the system which can damage the analyzer and pump See Pumpdown failure shutdown on page 156 You must power cycle the MSD to recover from this state ...

Page 40: ...s low If repeatability is poor No peaks If an analysis shows no chromatographic peaks only a flat baseline or minor noise run one of the automated tune programs If the MSD passes tune the problem is most likely related to the GC If the MSD does not pass tune the problem is most likely in the MSD Passes tune Incorrect sample concentration No analytes present Syringe missing from the ALS or not inst...

Page 41: ... sample path Injection is too large Incorrect GC inlet temperature Insufficient column flow GC MSD interface temperature is too low Ion source temperature is too low Peaks are fronting Column film thickness mismatched with analyte concentration column overload Initial oven temperature is too low Active sites in the sample path Injection is too large GC inlet pressure too high Insufficient column f...

Page 42: ...mn bleed Other contamination Electron multiplier voltage is too high Baseline is falling A falling baseline indicates contamination is being swept away Wait until the baseline reaches an acceptable level Common causes include 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 ...

Page 43: ...t condition in the GC that would prevent the GC from operating Retention times for all peaks drift shorter Column has been shortened Initial oven temperature was increased Column is getting old Retention times for all peaks drift longer Column flow has been reduced Initial oven temperature was decreased Active sites in the sample path Leaks in the GC inlet This could cause a fault condition in the...

Page 44: ...is too short Excessive pressure in the MSD Dirty ion source Air leak Poor filament operation Detector HED electron multiplier is not working correctly Incorrect mass filter polarity This could cause a fault condition in the GC that would prevent the GC from operating Poor repeatability Dirty syringe needle Dirty GC inlet Leaking GC inlet Injection is too large Loose column connections Variations i...

Page 45: ...wing symptoms listed under Chromatic symptoms also apply to mass spectra If sensativity is low If repeatability is poor No peaks Ion source cables not connected Bad connections to or from the detector HED power supply output cable has failed Other electronics failure Incorrect tune file inappropriate parameters Isotopes are missing or isotope ratios are incorrect Peaks are too wide or too narrow S...

Page 46: ...atory MSD has not been tuned recently or at the temperature at which it is operating Incorrect tune file inappropriate parameters No voltage to extractor lens if using an extractor ion source Peaks have precursors The tune report lists the size of the precursors for the tune masses Small precursors are not unusual If the precursors are unacceptably large for your application one of the following m...

Page 47: ...e of m z 502 should not be confused with low absolute abundances at high masses Sensitivity at high masses can be excellent even if the relative abundance of m z 502 is near 3 If your MSD produces low absolute abundances at high masses refer to the symptom High mass sensitivity is poor Tune programs other than autotune have different relative abundance targets The DFTPP and BFB target tune program...

Page 48: ...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 Wrong tune program Wrong tune file Repeller voltage is too low Not enough time for the MSD to warm up and pump down Analyzer chamber pressure is too high Column carrier gas flow is too high Poor filament operation Dirty ion source Air leak Incorrect DC polarity on the quadru...

Page 49: ...hamber pressures can only be measured if your system is equipped with the optional gauge controller Foreline pressure is too high If the pressure you observe for a given column flow has increased over time check the following Column carrier gas flow is too high Air leak usually the sideplate is not pushed in or vent valve is open Foreline pump oil level is low or oil is contaminated standard forel...

Page 50: ...g Analyzer chamber pressure is too low If the pressures you observe are below 1 10 6 Torr check for the following Column carrier gas flow is too low Column plugged or crushed by overtightened nut Empty or insufficient carrier gas supply Bent or pinched carrier gas tubing These could create a fault condition in the GC that would prevent the GC from operating Gauge controller displays 9 9 9 and then...

Page 51: ...977B Series MSD Troubleshooting and Maintenance Manual 51 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 ...

Page 52: ...ached normal operating conditions Incorrect temperature setpoint Ion source has not had enough time to reach temperature setpoint Ion source heater cartridge is not connected Ion source temperature sensor is not connected Ion source heater failed burned out or shorted to ground Ion source temperature sensor failed Source power cable is not connected to the side board MSD electronics are not workin...

Page 53: ...face will not heat up Incorrect setpoint s Setpoint entered in wrong heated zone GC MSD interface has not had enough time to reach temperature setpoint GC is off GC experienced a fault and needs to be reset GC MSD interface heater sensor cable is not connected GC MSD heater failed burned out GC MSD sensor failed GC electronics are not working correctly These will cause a GC error message GC error ...

Page 54: ...correctly Mass filter quad contacts are shorted or otherwise not working correctly Mass filter is not working correctly MSD electronics are not working correctly Difficulty with the electron multiplier supply Large peak such as the solvent peak eluted while the analyzer was on Pressure in the analyzer chamber is too high MSD electronics are not working correctly Difficulty with the fan If a coolin...

Page 55: ... You must switch the MSD off and back on to remove this error message The message will reappear if the underlying problem has not been corrected Large vacuum leak is preventing the turbo pump from reaching 80 of full speed Laboratory temperature is too high generally above 35 C Foreline pump is not working correctly Turbo pump is not working correctly Turbo pump controller is not working correctly...

Page 56: ...struments must use the IPv4 IP protocol and IPv4 IP addresses for the network interface used for the connections to the gas chromatographs and mass spectrometers If required for other applications the PC may also have the Ipv6 Protocol configured as an optional configuration for the same network interface card or a second network interface card LAN cable disconnected Incorrect IP configuration Inc...

Page 57: ...nd Vacuum Control view One of the following should be displayed as the cause Source temperature sensor is open Source temperature sensor is shorted Mass filter quad temperature sensor is open Mass filter quad temperature sensor is shorted No heater voltage heater fuse has probably failed Heater voltage is too low Temperature zone has timed out heater failed bad heater wiring or loose temperature s...

Page 58: ...System was vented on purpose no problem Fan fault has turned off the high vacuum pump power cycle the MSD to clear the fault Fuse for the high vacuum pump has failed MSD electronics are not working correctly 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 ...

Page 59: ... Manual 59 Electron multiplier voltage is too low Signal cable is not connected 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 ...

Page 60: ...18 28 32 and 44 or m z 14 and 16 Poor sensitivity Low relative abundance of m z 502 this varies with the tune program used Leaks can occur in either the GC or the MSD The most likely point for an air leak is a seal you recently opened In the GC most leaks occur in GC inlet septum GC inlet column nut Broken or cracked capillary column Leaks can occur in many more places in the MSD GC MSD interface ...

Page 61: ...SD Contamination originating in the GC typically comes from one of these sources Column or septum bleed Dirty GC inlet GC inlet liner Contaminated syringe Poor quality carrier gas Dirty carrier gas tubing Fingerprints improper handling of clean parts Contamination originating in the MSD typically comes from one of the following sources Air leak Cleaning solvents and materials Foreline pump oil sta...

Page 62: ...tuning compound 31 Methanol Cleaning solvent 43 58 Acetone Cleaning solvent 78 Benzene Cleaning solvent 91 92 Toluene or xylene Cleaning solvent 105 106 Xylene Cleaning solvent 151 153 Trichloroethane Cleaning solvent 69 Foreline pump oil or PFTBA Foreline pump oil vapor or calibration valve leak 73 147 207 221 281 295 355 429 Dimethylpolysiloxane Septum bleed or methyl silicone column bleed 149 P...

Page 63: ...lems 64 Troubleshooting Tips and Tricks 65 Air Leaks 66 Pressure Related Symptoms 70 Signal Related Symptoms 74 Tuning Related Symptoms 83 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 ...

Page 64: ... and no air leak is present sample sensitivity problems should be addressed by GC inlet maintenance first Wrong reagent gas Reagent gas not hooked up or hooked up to wrong reagent gas inlet port Wrong ions entered in tune file Wrong tune file selected Not enough bakeout time has elapsed since vent background is too high Wrong column positioning extending 2 mm past tip of interface Interface tip se...

Page 65: ...ile you have loaded in memory Is it the appropriate file for your mode of operation Rule 2 If complex is not working go back to simple A complex task is not only more difficult to perform but also more difficult to troubleshoot as well For example CI requires more parts to work correctly than EI does If you are having trouble with NCI verify that PCI still works If you are having trouble with othe...

Page 66: ...n so measurements are not accurate in absolute terms Familiarize yourself with the measurements on your system under operating conditions Watch for changes that may indicate a vacuum or gas flow problem Always look for small air leaks when setting up methane flow Run the methane pretune starting with a good PCI tune file Figure 3 on page 67 The abundance of m z 19 protonated water should be less t...

Page 67: ...z 272 If the abundance of m z 238 is much greater than that of m z 272 you have an air leak How do I find the air leak 1 See Figure 4 on page 69 and Table 7 on page 69 2 Look for the last seal that was disturbed If you just pumped down the MSD press on the sideplate to check for proper seal Poor alignment between the analyzer and the GC MSD interface seal can prevent the sideplate from sealing If ...

Page 68: ...the analyzer chamber are not likely to be seen in CI because of the higher pressure inside the ionization chamber 6 Half split the system Close valves starting at the gas select valves Gas A then Gas B then close the shutoff valve See Figure 4 on page 69 and Table 7 on page 69 Cool and vent the MSD remove the GC column and cap off the interface Using argon or other introduced gas to find air leaks...

Page 69: ...ial Shutoff valve GC MSD interface GC column CI ion source Table 7 Flow module valve state diagram Result Gas A flow Gas B flow Purge with Gas A Purge with Gas B Pump out flow module Standby vented or EI mode Gas A Open Closed Open Closed Closed Closed Gas B Closed Open Closed Open Closed Closed MFC On at setpoint On at setpoint On at 100 On at 100 On at 100 Off at 0 Shutoff valve Open Open Open O...

Page 70: ...o these measurements are not accurate in absolute terms Table 8 They are intended as a guide to typical observed readings They were taken with the following set of conditions Source temperature 250 C Quad temperature 150 C Interface temperature 280 C Helium carrier gas flow 1 mL min Table 8 Pressure measurements Pressure Torr MFC Methane Ammonia 10 5 5 10 5 5 0 10 5 15 8 0 10 5 7 0 10 5 20 1 0 10 ...

Page 71: ...ck for and correct any leaks See the Leaks section at the beginning of this chapter The foreline pump is not working properly 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 It should be ...

Page 72: ...agent ion ratios are correct Air leak Run Methane Pretune See the Operation Manual A visible peak at m z 32 indicates air in the system Check for and correct any leaks See the Leaks section at the beginning of this chapter Interface tip seal is not installed Check the source storage box If the seal is not in the box vent the MSD and verify that the seal is correctly installed ...

Page 73: ...a The valve on the reagent gas bottle is closed Check and if necessary open the valve on the reagent gas bottle The reagent gas supply is empty Check and if necessary replace the reagent gas supply Reagent lines kinked bent pinched or disconnected Inspect the reagent lines and repair any defects Check especially to ensure the reagent line is connected to the rear of the flow module Ensure the meth...

Page 74: ...ally observed during tuning but may also be observed during data acquisition Error messages in autotune due to insufficient signal may vary The following symptoms are covered in more detail in this section No peaks see page 75 No or low reagent gas signal see page 77 No or low PFDTD signal see page 79 Excessive noise see page 80 Low signal to noise ratio see page 80 Large peak at m z 19 see page 8...

Page 75: ... check pressure Wrong reagent gas selected for the tune file looking for wrong ions Large air leak Dirty ion source Poor vacuum pump problem see page 71 If the MSD was recently switched from EI to CI Isolation tip not installed No reagent gas flow Analyzer not sealed big air leak Wrong tune file loaded or tune file corrupted Ion source not assembled or connected correctly Wrong reagent gas selecte...

Page 76: ...CI No PFDTD calibrant peaks in NCI Look for background ions 17 OH 35 Cl and 235 ReO3 Verify tune parameters Go back to methane PCI No sample peaks in NCI Look for background ions 17 OH 35 Cl and 235 ReO3 Go back to methane PCI Poor quality reagent gas purity less than 99 99 Large peak at m z 238 in NCI OFN spectrum Look for background ions 17 OH 35 Cl and 235 ReO3 Find and fix your small air leak ...

Page 77: ...bing is blocked kinked pinched or disconnected Inspect and if necessary repair or replace the reagent gas supply tubing Wrong filament wires are connected to filament Ensure that the filament 1 wires are connected to the CI ion source filament and that the filament 2 wires are connected to the dummy filament Carbon has built up on the filament or the filament has sagged out of alignment Inspect th...

Page 78: ...t dirty the entire ion source probably needs to be cleaned Ion source wires are not connected or incorrectly connected Inspect the repeller Ensure the repeller lead is firmly attached to the repeller Inspect the wires to the ion focus and entrance lenses If the connections are reversed correct the problem One of the detector leads in the analyzer chamber is not connected Check and if necessary rec...

Page 79: ...ler is too high Ensure the regulator on the methane supply is set to 10 psig 70 kPa The CI ion source is dirty Clean the ion source The calibration valve was not purged after the vial was refilled Purge the calibration valve as described in To Purge the Calibration Valves on page 130 Then clean the ion source The calibrant vial was overfilled Excess PFDTD can quench the chemical ionization reactio...

Page 80: ...tune in PCI A large peak at m z 32 indicates air in the system Check for and correct any leaks See the Leaks section at the beginning of this chapter Saturated methane isobutane gas purifier Replace the gas purifier Poor quality methane purity below 99 99 Replace the methane with high purity methane If necessary clean and purge the reagent gas lines and clean the ion source Reagent gas flows too h...

Page 81: ...out sufficiently after it was last vented Bake out the system as described in the Maintenance chapter of this manual Moisture left over in the reagent gas supply tubing and flow module Purge the reagent gas supply lines for at least 60 minutes Contaminated reagent gas supply Replace the reagent gas supply and purge the lines and flow module Saturated methane isobutane gas purifier Replace the gas ...

Page 82: ...odule for at least 60 minutes See the Operation Manual Air leak Check for leaks and correct any that you find See Air Leaks on page 66 After all leaks have been corrected clean the ion source Contaminated reagent gas supply Suspect this if you have recently replaced your gas tank and you have ruled out air leaks Replace the reagent gas supply The capillary column is broken or disconnected Inspect ...

Page 83: ...toms 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 High electron multiplier voltage Cannot complete autotune Peak widths are unstable ...

Page 84: ...s supply lines and bake out the MSD See To Clean the Reagent Gas Supply Lines on page 149 Continued presence of a large peak at m z 32 may indicate an air leak After correcting the problems you may need to clean the ion source Air leak Run Methane Pretune in PCI Large peak at m z 32 indicates air in the system Check for and correct any leaks See Air Leaks on page 66 The reagent gas supply is at th...

Page 85: ...an inflection point If the curve is linear with a positive slope and no inflection point and the EMV is high the filament has stretched to the point where it does not line up with the hole in the ion source body and most electrons are not getting into the source Replace the filament The analyzer is not at the proper operating temperature Verify the ion source and quadrupole temperatures The defaul...

Page 86: ... 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 The CI ion source is dirty Clean the source Too much air or water in the system See Air Leaks on page 66 After eliminating these problems clean the ion source ...

Page 87: ...ile 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 Check for and correct any leaks See Air Leaks on page 66 After eliminating all air leaks clean the ion source ...

Page 88: ...88 3 CI Troubleshooting ...

Page 89: ...nge the Blue Oil Mist Filter on the Foreline Pump 113 To Install the Exhaust Filter on the IDP3 Dry Pump 114 To Change the Filter Cartridge on the IDP3 Dry Foreline Pump 115 To Check the DP Fluid 116 To Remove the DP 118 To Replace the DP Fluid 120 To Install the DP 123 To Remove the Foreline Gauge 125 To Install the Foreline Gauge 127 To Refill the EI Calibration Vial 128 To Purge the Calibration...

Page 90: ...90 5977B Series MSD Troubleshooting and Maintenance Manual 4 General Maintenance Maintaining the Electronics 141 To Adjust the Quad Frequency 143 To Replace the Primary Fuses 145 ...

Page 91: ...ion Table 9 Maintenance schedule Task Every week Every 6 months Every year As needed Tune the MSD X Check the foreline pump oil level X Check the calibration vial s X Replace the foreline pump oil X Replace the DP fluid X Check the dry foreline pump X Change the dry foreline pump tip seal X Change the foreline pump exhaust filter X Clean the ion source X Check the carrier gas trap s on the GC and ...

Page 92: ... potentially dangerous voltages exist on Electronic circuit boards Toroidal transformer Wires and cables between these boards Wires and cables between these boards and the connectors on the back panel of the MSD Some connectors on the back panel for example the foreline power receptacle Normally all of these parts are shielded by safety covers As long as the safety covers are in place it should be...

Page 93: ... sample is ionized by the ion source The majority of any sample passes through the ion source without being ionized It is pumped away by the vacuum system 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 WARNING Never touch these parts while your MSD is on ...

Page 94: ...touch these boards unless absolutely necessary In addition wires contacts and cables can conduct ESD to the electronics boards to which they are connected This is especially true of the mass filter quadrupole contact wires which can carry ESD to sensitive components on the side board ESD damage may not cause immediate failure but it will gradually degrade the performance and stability of your MSD ...

Page 95: ...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 CAUTION To be effective an antistatic wrist strap must fit snugly not tight A loose strap provides little or no protection Antistatic precautions are not 100 effective Handle electronic circuit boards as little as possible and then only by ...

Page 96: ...aust filters Replacing the DP fluid once a year Changing the dry foreline pump tip seal once a year Failure to perform these tasks as scheduled can result in decreased instrument performance It can also result in damage to your instrument Other procedures Tasks such as replacing a Micro Ion vacuum gauge should be performed only when needed See General Troubleshooting on page 35 Refer to the online...

Page 97: ...ch next to or behind the MSD or under the analyzer chamber at the back of the MSD Move it as needed to provide slack in the tubing and cables 5 Move the MSD away from the GC until you have access to the GC MSD interface cable See Figure 5 WARNING Ensure the GC MSD interface and GC oven have cooled before you remove the column Figure 5 Separating and connecting the MSD and GC The Agilent 7890 GC ha...

Page 98: ...nk ferrule on the end of the interface This will help keep contamination out of the MSD 7 Disconnect the GC MSD interface cable and the LVDS cable if applicable Disconnecting either cable with the GC on can cause a fault condition 8 Continue to move the MSD until you have access to the part requiring maintenance ...

Page 99: ...ow 100 C before you vent the MSD A temperature of 100 C is hot enough to burn skin always wear cloth gloves when handling analyzer parts WARNING If you are using hydrogen as a carrier gas the carrier gas flow must be closed before turning off the MSD power If the foreline pump is off hydrogen will accumulate in the MSD and an explosion may occur Before operating the MSD with hydrogen carrier gas r...

Page 100: ...slack in the tubing and cables 5 Slide the MSD backwards and then away from the GC until you have access to the GC MSD cables See Figure 6 6 Disconnect the GC MSD interface heater cables and the LVDS cable Disconnecting the interface heater cables with the GC on can cause a fault condition 7 Continue to move the MSD until you have access to the part requiring maintenance Figure 6 GC MSD interface ...

Page 101: ...ables if applicable 3 Slide the MSD to its regular position next to the GC Be careful not to damage the GC MSD interface as it passes into the GC Ensure the end of the GC MSD interface extends into the GC oven 4 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 5 Reinstall the capillary column 6 Pump down t...

Page 102: ... interface heater clamp If the thumb screw is loose when reconnecting the GC MSD it will be difficult to retighten when installing the 9000 GC MSD Tail 3 Connect the GC MSD interface heater cables and LVDS cable 4 Slide the MSD against the GC with the transfer line entering the GC side opening and the metal brackets entering their slots in the base of the GC Be careful not to damage the GC MSD int...

Page 103: ...SD Tail 9 If the MSD is equipped with a MFC attach the MFC gas lines Figure 7 GC MSD interface and bus CAUTION Do not turn on any GC heated zones until carrier gas flow is on Heating a column with no carrier gas flow will damage the column CAUTION During pumpdown do not push on the filament board safety cover while pressing on the analyzer boards This cover was not designed to withstand this type ...

Page 104: ...ce Manual 4 General Maintenance WARNING Ensure your MSD meets all the conditions listed in the Pump Down section of the 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: ... GC on page 97 2 Tighten the vent valve 3 Install the interface nut with the blank ferrule 4 Open the analyzer cover 5 Finger tighten the side plate thumbscrews See Figure 8 on page 106 6 Plug the MSD power cord in 7 Switch the MSD on for 5 minutes to establish a rough vacuum 8 Switch the MSD off 9 Close the analyzer cover 10 Disconnect the LAN remote and power cables CAUTION Do not overtighten th...

Page 106: ...t must be moved with the MSD Ensure the MSD remains upright and is never tipped on its side or inverted Figure 8 Side plate thumbscrews Front thumbscrew Rear thumbscrew CAUTION The MSD must remain upright at all times If you need to ship your MSD to another location contact your Agilent Technologies service representative for advice about packing and shipping ...

Page 107: ...age 99 2 Install a blank ferrule and interface column nut 3 Tighten the vent valve 4 Open the analyzer cover 5 Finger tighten the side plate thumbscrews See Figure 8 on page 106 6 Plug the MSD power cord in 7 Switch the MSD on for 5 minutes to establish a rough vacuum 8 Switch the MSD off 9 Close the analyzer cover 10 Disconnect the LAN remote and power cables CAUTION Do not overtighten the side p...

Page 108: ...t must be moved with the MSD Ensure the MSD remains upright and is never tipped on its side or inverted Figure 9 Side plate thumbscrews Front thumbscrew Rear thumbscrew CAUTION The MSD must remain upright at all times If you need to ship your MSD to another location contact your Agilent Technologies service representative for advice about packing and shipping ...

Page 109: ...ding oil See To Drain the Foreline Pump on page 111 and To Refill the Foreline Pump on page 112 1 Examine the oil level window Figure 10 on page 110 2 Note the two lines on the pump left of the window The oil level should be between the lines The foreline pump oil should be almost clear If the oil level is near or below the lower line add foreline pump oil See To Refill the Foreline Pump on page 1...

Page 110: ...110 5977B Series MSD Troubleshooting and Maintenance Manual 4 General Maintenance Figure 10 Pfeiffer Duo 2 5 foreline pump Fill cap Oil level line Drain plug Oil mist filter ...

Page 111: ... 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 3 Remove the fill cap See Figure 10 on page 110 4 Place a container under the drain plug 5 Remove the drain plug Allow the pump oil to drain out The oil drains faster if it is still warm If necessary you can place a book or other object under the pump motor to ...

Page 112: ...s worn or damaged replace it 3 Remove the propping object from under the pump motor 4 Add foreline pump oil until the oil level in the window is near but not above the upper line The foreline pump requires approximately 0 28 L of oil 5 Wait a few minutes for the oil to settle If the oil level drops add oil to bring the oil level near the upper line 6 Reinstall the fill cap 7 If necessary slide the...

Page 113: ...he Foreline Pump Materials needed Blue mist filter G1099 80039 Procedure 1 Disconnect the foreline pump exhaust hose from the filter 2 Unscrew the filter from the top of pump 3 Screw the replacement filter on to the pump and replace the exhaust hose Figure 11 Foreline Pump with oil mist filter Oil mist filter Pump exhaust ...

Page 114: ...xhaust Filter on the IDP3 Dry Pump Materials needed Exhaust filter G3170 80041 Procedure 1 Disconnect the foreline pump exhaust hose from the adapter 2 Unscrew the adapter from the pump 3 Screw the filter on to the pump Figure 12 IDP3 pump with exhaust filter Exhaust filter Exhaust hose Hose adapter ...

Page 115: ...the IDP3 Dry Foreline Pump Materials needed Exhaust filter cartridge G3170 80041 Procedure 1 Unscrew the cap from the exhaust filter See Figure 12 on page 114 2 Pull the filter cartridge out of the filter cap 3 Replace the filter cartridge 4 Align the cap onto the filter and the cap counter clockwise to lock in place ...

Page 116: ...he DP is on and is at its normal operating temperature Use the COLD marks if the pump is off and has had time to cool If the fluid level is below the bottom of the appropriate range replace the DP fluid Do not just add fluid The pump fluid should be clear or almost clear Dark or cloudy pump fluid indicates an air leak or excessive heat If the pump fluid appears dark or cloudy replace it Then check...

Page 117: ...General Maintenance 4 5977B Series MSD Troubleshooting and Maintenance Manual 117 Figure 13 DP Fan Fluid level window sight glass ...

Page 118: ...D from the GC See To Separate the MSD from the 7890 GC on page 97 3 Disconnect high vacuum power HIVAC POWER cable from the back panel of the MSD This is the thick black cable that emerges near the bottom of the pump 4 Disconnect the DP temperature sensor wires from the wiring harness 5 Support the DP with one hand WARNING Treat the DP fluid as hazardous as it may contain traces of toxic chemicals...

Page 119: ...O ring on clean aluminum foil shiny side down to keep your lab bench and the O ring clean 9 Remove the DP through the side of the MSD You may have to tilt the pump slightly to remove it 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 Figur...

Page 120: ...mbly from the top of the DP 2 Cover the top of the DP with aluminum foil shiny side up 3 Heat the DP at 60 C for 15 minutes For 7820A or 7890 GC s you can use the GC oven 4 Pour the old DP fluid out the top of the pump Even after heating the pump fluid pours very slowly 5 Check the color of the pump fluid WARNING The pump and pump fluid will be hot Wear protective gloves when you remove the pump f...

Page 121: ...e baked onto the internal parts stack of the pump If so you may have to remove the DP stack and clean its parts and the interior of the pump with methylene chloride Be very careful when reinstalling the stack Misalignment of stack components can seriously reduce DP performance 6 Clean the DP flange on the analyzer chamber 7 Preheat the new DP fluid following the instructions on the bottle Figure 1...

Page 122: ... 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 DP fluid Pour the fluid between the center stack and the side wall Watch the sight glass while pouring Do not overfill 9 Reinstall the DP See To Install the DP on page 123 ...

Page 123: ...2 Slide the DP into the MSD You may have to tilt the pump slightly to get it into the MSD Do not tilt it past 45 degrees 3 Install the O ring assembly on the DP See Figure 16 on page 124 4 Lift the DP into its normal position 5 Install the KF50 clamp 6 Reconnect the DP temperature sensor wires to the wiring harness 7 Reconnect the high vacuum power cable to the HIVAC POWER connector on the back pa...

Page 124: ...124 5977B Series MSD Troubleshooting and Maintenance Manual 4 General Maintenance Figure 16 Installing the DP Foreline gauge assembly KF50 clamp O ring assembly DP DP outlet ...

Page 125: ...See To Separate the MSD from the 7890 GC on page 97 3 Unplug the foreline gauge cable from the foreline gauge 4 Disconnect the foreline gauge assembly from the DP outlet 5 Loosen the hose clamp 6 Pull the foreline gauge assembly out of the foreline hose See Figure 17 on page 126 WARNING The foreline pump and DP may still be hot CAUTION Ensure the MSD is vented to atmosphere before breaking the sea...

Page 126: ...126 5977B Series MSD Troubleshooting and Maintenance Manual 4 General Maintenance Figure 17 Foreline gauge assembly Foreline gauge ...

Page 127: ...oreline hose 2 Tighten the hose clamp 3 Connect the foreline gauge assembly to the DP outlet 4 Connect the foreline gauge cable to the foreline gauge 5 Reconnect the MSD to the GC See To Reconnect the MSD to the 7890 GC on page 101 6 If necessary slide the foreline pump back under the analyzer chamber The foreline pump may be located on the floor on the lab bench next to or behind the MSD or under...

Page 128: ...gauge 4 Remove the analyzer window cover 5 Loosen the calibration vial collar See Figure 18 Do not remove the collar 6 Pull the calibration vial out You may feel some resistance due to residual vacuum 7 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 8 Push the calibration vial into the valve a...

Page 129: ...llar clockwise to tighten it The collar should be snug but not overly tight Do not use a tool to tighten the collar It does not require that much force 11 Reinstall the analyzer window cover 12 Purge the EI calibration valve See To Purge the Calibration Valves on page 130 CAUTION Failure to purge the calibration valve will result in damage to the filaments and detector ...

Page 130: ...ve for several minutes with all analyzer voltages turned off CI calibration valve After adding new PFDTD to the calibrant vial you must purge the air out of the vial and valve 1 If the vacuum gauge controller is on turn it off 2 Verify that PCICH4 U is loaded 3 In Tune and Vacuum Control view select Purge Calibrant Valve under the Vacuum menu This will open the CI calibration valve for several min...

Page 131: ...ct it 3 Loosen the collar and remove the calibration vial See Figure 18 on page 128 Just loosen the collar do not remove it 4 Remove the two screws holding the valve assembly to the top of the analyzer chamber Do not lose the O ring under it CAUTION Removing the valve with the vial installed can result in liquid calibrant getting into the restrictor of the valve Liquid in the restrictor will preve...

Page 132: ...and Vent Valve Assembly on page 131 and Figure 18 on page 128 2 Ensure the valve O ring is in place If it is worn or damaged replace it 3 Install the calibration and vent valve assembly and tighten the screws that hold it in place 4 Reconnect the calibration valve cable to the connector next to the fan 5 Remove the vial from the new calibration valve See To Refill the EI Calibration Vial on page 1...

Page 133: ...he four fan screws and the safety grill Remove the fan Keep the screws 5 Install the new fan with the flow arrow on the side pointing toward the pump The wires should be at the upper left close to the connector 6 Add the safety grill and the four screws Tighten the screws firmly 7 Connect the fan wiring to the fan connector on the MSD frame 8 Reinstall the MSD covers 9 Pump down the MSD WARNING Do...

Page 134: ...134 5977B Series MSD Troubleshooting and Maintenance Manual 4 General Maintenance Figure 19 Replacing the pump fan DP shown Fan wiring Fan wiring connector ...

Page 135: ...the back of the ion vacuum gauge 3 Unscrew the red plastic thumbnut on the gauge clamp 4 Remove the long screw from the clamp 5 While supporting the gauge body remove the clamp from the mounting flange 6 Remove the gauge 7 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 ...

Page 136: ...1 Place the KF16 O ring in the groove on the analyzer chamber flange Replace it if it is worn or damaged 2 Hold the gauge flange against the chamber flange with the O ring Push the clamp over both flanges 3 Insert the long screw add the thumbnut and tighten 4 Attach the communication cable to the back of the gauge and connect the other end to the back of the MS ...

Page 137: ...on the side plate Procedure 1 Vent the MSD 2 Open the analyzer chamber 3 Use a clean lint free cloth or glove to spread a thin coat of high vacuum grease only on the exposed surface of the O ring See Figure 20 on page 138 4 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 5 Close the analyzer chamber 6 Pump down the MSD CAUTIO...

Page 138: ...138 5977B Series MSD Troubleshooting and Maintenance Manual 4 General Maintenance Figure 20 Side plate O ring Side plate O ring ...

Page 139: ... procedure Procedure 1 Vent the MSD 2 Completely remove the vent valve knob See Figure 21 on page 140 3 Inspect the O ring If the O ring appears damaged replace it 4 Use a clean lint free cloth or glove to spread a thin coat of high vacuum grease on the exposed surface of the O ring 5 Use a clean lint free cloth or glove to wipe away excess grease If the O ring looks shiny there is too much grease...

Page 140: ...nance 6 Reinstall the vent valve knob 7 Pump down the MSD Figure 21 Vent valve O ring Vent valve knob CAUTION Be very careful when reinstalling the vent valve knob It is possible to cross thread the knob and damage the threads in the valve body Ensure the O ring stays in place ...

Page 141: ...by electrostatic discharge ESD Do not handle or touch these boards unless absolutely necessary In addition wires contacts and cables can conduct ESD to the printed circuit boards to which they are connected This is especially true of the mass filter quadrupole contact wires which can carry ESD to sensitive components on the side board ESD damage may not cause immediate failure but it will graduall...

Page 142: ...blies that have been removed from the MSD This includes the analyzer More information is available More information about the functions of electronic components section is found later in this manual See Chapter 8 Electronics on page 211 Most of the procedures in this chapter are illustrated with video clips CAUTION To be effective an antistatic wrist strap must fit snugly not tight A loose strap p...

Page 143: ...ing screw can significantly affect coil adjustment 4 In the Tune and Vacuum Control view select Optimize Quadrupole Frequency from the Execute menu 5 Enter an m z value of 100 6 Slowly turn the quad frequency adjustment screws to minimize the voltage displayed See Figure 22 on page 144 Turn the adjustment screws alternately Turn each screw only a little bit at a time Keep the screws at equal exten...

Page 144: ...l Maintenance 8 Repeat steps 4 through 7 for m z 650 9 Exit the Set Optimize Quadrupole Frequency program 10 Select MS OFF from the Execute menu 11 Close the analyzer cover 12 Tune the MSD Figure 22 Adjusting the quad frequency RF cover Quad frequency adjustment screws ...

Page 145: ... MSD will already be off but for safety you should switch off the MSD and unplug the power cord It is not necessary to allow air into the analyzer chamber 2 Turn one of the fuse holders counterclockwise until it pops out See Figure 23 on page 146 The fuse holders are spring loaded 3 Remove the old fuse from the fuse holder 4 Install a new fuse in the fuse holder 5 Reinstall the fuse holder WARNING...

Page 146: ...nance Manual 4 General Maintenance 6 Repeat steps 2 through 5 for the other fuse Always replace both fuses 7 Reconnect the MSD power cord to the electrical outlet 8 Pump down the MSD Figure 23 Primary fuses turbo model shown Primary fuses in holders ...

Page 147: ...5 CI Maintenance To Replace the Methane Isobutane Gas Purifier 148 To Clean the Reagent Gas Supply Lines 149 To Refill the CI Calibrant Vial 150 This chapter describes maintenance procedures and requirements that are unique to 5977B Series MSDs equipped with the Chemical Ionization hardware ...

Page 148: ... the reduced metal of the oxygen and moisture traps Procedure 1 To install the methane isobutane gas purifier follow the instructions on the label for installation and replacement intervals 2 Disconnect the fittings on the old filter 3 Remove the ferrules from the tubing at the outlet of the gas purifier Using the tubing cutter cut off the end of the tubing with the ferrules 4 Install the new filt...

Page 149: ...following the instructions on the label 3 Connect one end of the tubing to a supply of clean dry nitrogen and turn on the gas flow 4 Use the heat gun to warm the tubing starting at the supply end and working your way to the free end 5 Repeat for any other pieces of tubing that need to be cleaned 6 Reconnect the tubing to the gas supply gas purifier and MSD Follow the instructions on the gas purifi...

Page 150: ...e vial no higher than the bottom of the internal tube with fresh PFDTD calibrant 8500 8510 8 Replace the vial and tighten the collar 9 Reposition the MSD next to the GC See To Reconnect the MSD to the 7890 GC on page 101 10 Reinstall the capillary column 11 Pump down the MSD 12 Purge the calibration valve See To Purge the Calibration Valves on page 130 CAUTION Do not rinse the vial with any solven...

Page 151: ...CI Maintenance 5 5977B Series MSD Troubleshooting and Maintenance Manual 151 Figure 24 CI calibration valve and vial Calibration valve Calibration vial Collar ...

Page 152: ...152 5977B Series MSD Troubleshooting and Maintenance Manual 5 CI Maintenance ...

Page 153: ...s 156 Foreline Pump 157 High Vacuum Pump 161 Analyzer Chamber 162 Side Plate 163 Vacuum Seals 166 Face seals 166 KF NW seals 166 Compression seals 167 High voltage feedthrough seal 167 Foreline Gauge 168 Diffusion Pump and Fan 169 Turbo Pump and Fan 175 Calibration Valves and Vent Valve 176 Micro Ion Vacuum Gauge 179 This chapter describes components of the MSD vacuum system ...

Page 154: ...ed for operation The 5977B Series MSD uses one of two kinds of high vacuum pumps a diffusion pump or a turbomolecular turbo pump The pump type determines the maximum column flow supported by the MSD The 5977B HES Series MSD model G7079B uses a turbomolecular turbo pump for high vacuum It has a maximum column flow rate of 4 0 mL min Most vacuum system operation is automated Operator interaction is ...

Page 155: ...e plate analyzer door and front and rear end plates Vacuum seals Calibration valve s and vent valve Vacuum control electronics Vacuum gauges and gauge control electronics Each of these is discussed in more detail in this chapter Figure 25 Example vacuum system components MSD with turbo pump shown High vacuum High vacuum Analyzer GC MSD Ion vacuum gauge if present CI flow control Vent valve cooling...

Page 156: ...ress until the sound from the foreline pump becomes quieter Pumpdown failure shutdown The system will shut down both the high vacuum and the foreline pump if the system fails to pump down correctly Two conditions that trigger shutdown are Diffusion pump MSDs shutdown occurs if the foreline pressure is above 300 mTorr after 7 minutes Turbo pump MSDs speed below 80 after 7 minutes This is usually be...

Page 157: ...d to the high vacuum pump by a 130 cm hose called the foreline hose There are four different types of foreline pumps the Pfeiffer DUO Figure 26 the MVP 070 3 Figure 27 on page 158 the MVP 070 3C not shown and the IDP3 Figure 28 on page 158 The dry foreline pumps are not supported with diffusion pump base MSDs Figure 26 Pfeiffer DUO foreline pump Hose to vacuum pump Ballast control Fill cap Exhaust...

Page 158: ...uum System Figure 27 MVP 070 3 dry foreline pump Figure 28 IDP3 dry foreline pump CAUTION Agilent does not recommend using hydrogen as a carrier gas on systems equipped with an IDP3 rough pump Exhaust outlet Power switch Hose to vacuum pump Power cord Exhaust filter ...

Page 159: ...stall an 11 mm id hose to remove the exhaust from your lab A window sight glass in the front of the standard foreline pump shows the level of the foreline pump oil 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 WARNING The oil trap supplied with the s...

Page 160: ... rags paper towels and similar absorbents in the oil pan could ignite and damage the pump and other parts of the MSD WARNING Combustible materials or flammable nonflammable wicking material placed 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 ...

Page 161: ...on pump uses baffling to prevent vapor from migrating into the analyzer chamber Foreline pressure is monitored by the foreline gauge 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 gau...

Page 162: ...m gauge calibration valve vent valve GC MSD interface and high vacuum pump Diffusion pump version The diffusion pump attaches with a KF50 seal to a baffle adapter that is clamped to the bottom of the manifold A vapor baffle helps prevent migration of pump fluid vapor into the manifold Cooling fins on the bottom of the manifold keep the baffle cool so the vapor will condense on it Turbo pump versio...

Page 163: ...hs are built into the side plate Wires connect the feedthroughs to analyzer components The electronic side board is mounted on the atmospheric side of the side plate Thumbscrews are located at each end of the side plate CAUTION Fasten both side plate thumbscrews for shipping or storage only For normal operation both thumbscrews should be loose For operation with hydrogen carrier gas or with flamma...

Page 164: ...ooting and Maintenance Manual 6 Vacuum System Figure 30 Side plate feedthroughs HES version High voltage HED Detector focus Ion source and heater Mass Filter quadrupole Signal detector output EM voltage PE1 PE2 and Ext feedthroughs ...

Page 165: ...shooting and Maintenance Manual 165 Figure 31 Side plate feedthroughs non HES version High voltage HED Detector focus Ion source and heater Mass filter quadrupole Screws for radiator mounting brackets Signal detector output EM voltage 2 of 4 ...

Page 166: ...The side plate swings into place against the side plate O ring and must be held in place when the MSD is turned on for pump down to ensure a good seal The front and rear end plates are screwed onto the manifold and should not need to be removed The GC MSD interface fastens to the manifold with three screws The calibration valve assembly is fastened onto the front end plate by two screws The vent v...

Page 167: ...e the collar Tightening the collar presses the ferrule compressing the O ring around the part The calibration vials use compression seals High voltage feedthrough seal The high voltage HED feedthrough seal is an O ring that is compressed against the side plate by a threaded collar Figure 32 Vacuum seals Side plate O ring seal KF seal with internal centering ring KF seal with external centering rin...

Page 168: ...fusion 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 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 w...

Page 169: ...ter clamped to the bottom of the analyzer chamber The diffusion pump has a cylindrical body surrounded by fins to help dissipate heat Its inlet is open to the interior of the analyzer chamber through the adapter and baffle 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 See Figure 33 on page 169 and Figure 34 on page 1...

Page 170: ...es strikes the gas molecules that are present This forces the gas molecules down toward the outlet near the bottom of the pump Another nozzle in the stack points directly at the outlet and forces the gas molecules out 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 Figure 34 Diffusion pump parts Foreline ga...

Page 171: ...ses above 400 mTorr the diffusion pump heater will turn off The AC board allows the analyzer electronics to turn on when the diffusion pump is hot The diffusion pump typically maintains an indicated pressure below 1 0 10 4 Torr for GC helium carrier gas flows up to 2 mL min High vacuum manifold pressure can only be measured if your MSD is equipped with the optional gauge controller The small size ...

Page 172: ...e fluid Otherwise replace the fluid once a year Function Keeps analyzer turned off until the pump is hot enough to for adequate vacuum Prevents analyzer damage Shuts off diffusion pump and analyzer if the pump overheats Prevents damage to the pump and analyzer Message The high vacuum pump is not ready Difficulty with the high vacuum pump What it means Normal during pumpdown Always indicates a prob...

Page 173: ...roubleshooting and Maintenance Manual 173 Figure 35 The diffusion pump Inlet Cooling fins Too cold sensor Too hot sensor Diffusion pump outlet Cold fluid level marker Diffusion pump heater cable Hot fluid level marker Fluid level window ...

Page 174: ...rating 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 Maintaining the Vacuum System on page 96 The troubleshooting sections of the MSD Data Acquisition online help ...

Page 175: ...rrent to the pump and monitors pump motor speed and temperature A cooling fan is located between the turbo pump and the front panel of the MSD The fan draws air from outside the MSD and blows it over the pump The turbo pump automatically turns on when the MSD power is switched on The system allows the analyzer to be turned on when the turbo pump is greater than 80 speed but the pump normally opera...

Page 176: ...calibrant for each vacuum system Perfluorotributylamine PFTBA is the most commonly used tuning compound for EI operation PFTBA is required for automatic tuning of the MSD Other compounds can be used for manual tuning CI calibration valve The CI tuning compound is perfluoro 5 8 dimethyl 3 6 9 trioxidodecane PFDTD The CI calibration valve is part of the reagent gas flow control module It is controll...

Page 177: ...oubleshooting and Maintenance Manual 177 Figure 36 Calibration valves EI calibration valve EI calibration vial Vent valve knob CI calibration valve CI calibration vial EI calibration above analyzer window CI calibration right side of MSD ...

Page 178: ...178 5977B Series MSD Troubleshooting and Maintenance Manual 6 Vacuum System Figure 37 Vent valve Vent valve knob O ring Air passage Valve closed Valve open Valve open too far ...

Page 179: ...amber pressure in daily operation and in troubleshooting The gauge is calibrated for nitrogen N2 The carrier gas is usually helium which does not ionize as readily as nitrogen Therefore the indicated pressure for helium is approximately six times lower than the absolute pressure For example a reading of 2 0 10 5 Torr versus an absolute pressure of 1 2 10 4 Torr In a CI MSD the indicated pressure r...

Page 180: ...180 5977B Series MSD Troubleshooting and Maintenance Manual 6 Vacuum System ...

Page 181: ...nts 199 Other Source Elements 201 Magnet 201 Repeller 201 Drawout plate and cylinder 201 Ion focus 202 Entrance lens 202 Quadrupole Mass Filter 203 AMU gain 204 AMU offset 204 219 width 204 DC polarity 205 Mass axis gain 205 Mass axis offset 205 Quadrupole maintenance 205 Detector 206 Detector ion focus 206 High energy dynode 206 EM horn 206 Analyzer Heaters and Radiators 208 ...

Page 182: ...ss filter The mass filter allows selected ions to pass through the filter and strike the detector The detector generates a signal current proportional to the number of ions striking it The analyzer is attached to the vacuum side of the side plate The side plate is hinged for easy access The ion source and the mass filter are independently heated Each is mounted inside a radiator for correct heat d...

Page 183: ...r 7 5977B Series MSD Troubleshooting and Maintenance Manual 183 Figure 38 The analyzer with an HES Feedthrough board Mass filter heater assembly Detector Ion source inside radiator Mass filter inside radiator ...

Page 184: ...ing and Maintenance Manual 7 Analyzer Figure 39 The analyzer with an XTR source Detector Mass filter contact cable Mass filter heater assembly Feedthrough board Mass filter contact Ion source inside radiator Mass filter inside radiator ...

Page 185: ...pushes the positive ions into the lens stack where they pass through several electrostatic lenses These lenses concentrate the ions into a tight beam which is directed into the mass filter Ion source body The ion source body See Figure 40 on page 186 and Figure 41 on page 187 is a cylinder It holds the other parts of the ion source including the lens stack With the repeller and in the SST Inert io...

Page 186: ...6 5977B Series MSD Troubleshooting and Maintenance Manual 7 Analyzer Figure 40 SST Inert ion source structure Entrance lens Filament Drawout cylinder Drawout plate Repeller Ion focus lens Lens insulation ...

Page 187: ...lyzer 7 5977B Series MSD Troubleshooting and Maintenance Manual 187 Figure 41 Extractor ion source structure Entrance lens Filament Extractor lens Ceramic insulator Repeller Ion focus lens Lens insulation ...

Page 188: ...ge 188 Item number Item description Part number SSL Part number Inert 1 Gold plated set screw G1999 20022 G1999 20022 2 Gold plated screw G3870 20021 G3870 20021 3 Interface socket G1099 20136 G1099 20136 4 Source body G1099 20130 G2589 20043 5 Drawout cylinder G1072 20008 G1072 20008 1 2 8 15 15 15 15 14 14 14 2 2 16 16 16 8 12 12 12 10 2 8 8 7 17 18 3 8 8 7 12 13 4 6 5 11 9 ...

Page 189: ...6 11 Ion focus lens 05971 20143 05971 20143 12 Repeller insulator G1099 20133 G1099 20133 13 Repeller G3870 60172 G3870 60173 14 Flat washer 3050 0627 3050 0627 15 Belleville spring washer 3050 1301 3050 1301 16 Repeller nut 0535 0071 0535 0071 17 Source heater block assembly G3870 60180 G3870 60179 18 Repeller block insert G3870 20135 G3870 20135 Table 12 Parts list for the standard or inert EI i...

Page 190: ...actor ion source Table 13 Parts list for extractor ion source Figure 43 on page 190 Item number Item description Part number 1 Setscrews G3870 20446 2 Screws G3870 20021 3 Source body G3870 20440 4 Extractor lens G3870 20444 5 Extractor lens insulator G3870 20445 6 Filaments G7005 60061 ...

Page 191: ...2 8 Lens insulator G3870 20530 9 Entrance lens G3170 20126 10 Ion focus lens 05971 20143 11 Repeller insulator G3870 20133 12 Repeller G3870 60171 13 Flat washer 3050 0891 14 Belleville spring washer 3050 1301 15 Repeller nut 0535 0071 16 Source heater block assembly G3870 60177 17 Insulator G1099 20133 Table 13 Parts list for extractor ion source Figure 43 on page 190 continued Item number Item d...

Page 192: ... The positive voltage on the repeller pushes the positive ions into the lens stack where they pass through several electrostatic lenses These lenses concentrate the ions into a tight beam directed into the mass filter Ion source body The ion source body is a cylinder It holds the other parts of the ion source including the lens stack The repeller source mount and filament block form the ionization...

Page 193: ...12 14 8 12 Table 14 Parts list for HES EI ion source Figure 44 on page 193 Item number Item description Part number 1 Source finger grip G7002 20008 2 Filament block G7005 60061 3 Extractor lens 5 with 3 mm opening G7002 20061 4 Ceramic insulator for extractor G7002 20064 5 Entrance lens 1 G7002 20065 6 Ion focus lens 2 G7002 20068 ...

Page 194: ...ractor lens 1 4 G7002 20104 12 M2 x 6 mm gold plated screw G7002 20083 13 Locking ring lens insulator G7002 20126 14 High efficiency dual filament G7002 60001 15 Ring heater sensor assembly G7002 60043 16 Source mount 1 5 mm G7002 60053 17 Repeller assembly G7002 67057 The number in parenthesis is the number engraved on the lens Table 14 Parts list for HES EI ion source Figure 44 on page 193 conti...

Page 195: ...es in the ion source electron entrance and ion exit are very small 0 5 mm making it possible to pressurize the ionization chamber Both the source body and the plate are at repeller potential electrically isolated from the radiator and the interface tip The seal for the interface tip Figure 46 on page 196 ensures a leak tight seal and electrical isolation between the CI interface and ion source Ion...

Page 196: ...196 5977B Series MSD Troubleshooting and Maintenance Manual 7 Analyzer Figure 46 Interface tip seal Interface tip seal ...

Page 197: ... Table 15 Parts list for the CI ion source Figure 47 on page 197 Item number Item description Part number 1 Setscrew G1999 20022 2 Filament screw G1999 20021 3 CI interface tip seal G3870 20542 4 CI repeller insulator G1999 20433 5 CI lens insulator G3170 20540 6 CI drawout cylinder G1999 20444 ...

Page 198: ...rance lens G3170 20126 10 CI ion source body G3170 20430 11 CI ion focus lens G1999 20443 12 CI repeller G1999 20432 13 CI filament G7005 60072 14 Dummy filament G1999 60454 Not labeled Curved washer 3050 9082 Not labeled Flat washer 3050 1374 Table 15 Parts list for the CI ion source Figure 47 on page 197 continued Item number Item description Part number ...

Page 199: ... a general instrument shutdown Three parameters affect the filaments filament selection Filament filament emission Emission current and electron energy EIEnrgy Filament selection The filament selection parameter Filament selects which filament in the ion source is active In the CI ion source it is always Filament 1 Sometimes one EI filament will give better performance than the other does To selec...

Page 200: ...ecially after any maintenance was performed If you are controlling your MSD from the Manual Tune screen always select MSOff before changing any of the filament parameters When setting up data acquisition parameters set the solvent delay so that the analyzer will not turn on while the solvent peak is eluting When the software prompts Override solvent delay at the beginning of a run always select NO...

Page 201: ...age can be varied from 0 to 42 8 VDC Some tune programs use a fixed repeller voltage Others ramp the repeller voltage to find the optimum setting Setting repeller voltage too low results in poor sensitivity and poor high mass response Setting repeller voltage too high results in precursors poor mass filtering and poor low mass resolution Drawout plate and cylinder The drawout plate forms another w...

Page 202: ...nt results in poor high mass response Entrance lens The entrance lens is at the entrance to the quadrupole mass filter This lens minimizes the fringing fields of the quadrupole which discriminate against high mass ions Entrance lens offset The entrance lens offset EntOff controls the fixed voltage applied to the entrance lens It can be varied from 0 to 64 VDC 20 V is typical Increasing the entranc...

Page 203: ...ected adjacent segments are electrically isolated One pair has positive voltages applied the other has negative voltages applied A combined direct current DC and radio frequency RF signal is applied to the two pairs of segments The magnitude of the RF voltage determines the m z of the ions that pass through the mass filter and reach the detector The ratio of DC to RF determines the resolution widt...

Page 204: ...ge to RF frequency on the mass filter Higher offset yields narrower peaks AMU offset generally affects peak widths equally at all masses 219 width m z 219 is a prominent ion near the middle of the mass range of PFTBA The width parameter Wid219 makes small corrections to the m z 219 peak width Amu gain and amu offset must be readjusted after the 219 width is changed If you are tuning with a compoun...

Page 205: ...ffset MassOffs also controls the mass assignment A higher offset yields higher mass assignment Mass offset generally affects peaks equally at all masses Quadrupole maintenance The mass filter requires no periodic maintenance It should not be removed from the radiator If absolutely necessary that is if the only alternative is replacement the quadrupole can be cleaned Cleaning must be performed by A...

Page 206: ...t is located off axis from the center of the quadrupole mass filter to minimize signals due to photons hot neutrals and electrons coming from the ion source When the ion beam hits the HED electrons are emitted These electrons are attracted to the more positive EM horn Do not touch the insulator EM horn The EM horn carries a voltage of up to 3 000 V at its opening and 0 V at the other end The elect...

Page 207: ... other probable cause it may need to be replaced Check your tune charts for gradual degradation which indicates wearing out Select the Tune Plot icon from the Program menu of your desktop to see the tune plots Sudden changes usually indicate a different type of problem See Also Troubleshooting in the online help for more information about symptoms that may indicate EM problems Figure 49 The detect...

Page 208: ... set and monitored from the MSD Data Acquisition software In selecting the temperatures to use consider the following Higher temperatures help keep the analyzer clean longer Higher ion source temperatures result in more fragmentation and therefore lower high mass sensitivity After pumpdown it takes at least 2 hours for the analyzer to reach thermal equilibrium Data acquired sooner may not be repro...

Page 209: ... 7 5977B Series MSD Troubleshooting and Maintenance Manual 209 Figure 50 Heaters and radiators with an XTR source Mass filter radiator Mass filter heater assembly Ion source radiator Ion source heater assembly ...

Page 210: ...es MSD Troubleshooting and Maintenance Manual 7 Analyzer Figure 51 Heaters and radiators with an HES Mass filter radiator Mass filter heater assembly Ion source radiator Ion source heater sensor wires gray and purple ...

Page 211: ...plies 220 Back Panel and Connectors 221 Interfacing to External Devices 224 The following assemblies make up the MSD electronics Most of this material is not essential for day to day operation of the MSD It may be of interest to persons responsible for servicing the MSD WARNING Dangerous voltages are present under the safety covers Do not remove safety covers Refer servicing to your Agilent Techno...

Page 212: ...alyzer vacuum or turbo pump speed View foreline pump vacuum Vent or pumpdown the MSD View the firmware version and serial number of the MSD Enable LVDS on the MSD Reboot the MSD Enable BOOTP on the MSD Power switch The power switch is part of the electronics module and is located on the lower left of the front of the MSD It is used to turn the MSD and foreline pump on and off Front Panel LED The f...

Page 213: ... Instrument Status LED codes Instrument status LED code Ready Solid green Acquiring data Blinking green Not ready Solid yellow 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 ...

Page 214: ...tage is proportional to the mass selected Generates the DC component of the voltage applied to the quadrupole mass filter The magnitude of this voltage is proportional to the RF voltage Passes voltages generated on the main board and the detector focus voltage from the HED power supply to elements in the ion source and the detector Generates and adjusts filament emission current and electron energ...

Page 215: ...ceives and decodes digital instructions from the LAN MS control card Sends digital information to the LAN MS control card Generates voltages for the ion source lenses Generates control signals for filament selection filament emission current and electron energy Generates control signals for quadrupole RF drive quad frequency adjustment DC polarity selection and all detector voltages Performs analo...

Page 216: ...tor signal current Lens driver board for HES The lens driver board provides the lens voltages for the extractor post extractor 1 and post extractor 2 lenses AC board The AC board is mounted on the opposite side of the electronics panel from the LAN MSD control card The AC board is also sometimes called the power distribution vacuum control board It performs these functions Provides input voltage t...

Page 217: ...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 Any discrepancy is applied as an error signal to adjust the power If the power distribution board senses a malfunction in the diffusion pump power regulator it shuts off power to the diffusion pump See Figure 52 Turbo pu...

Page 218: ...AC board will shut down both the high vacuum and the foreline pump if the system fails to pump down correctly Other conditions that trigger shutdown are turbo pump speed below 80 after 7 minutes or foreline pressure above 300 mTorr after 7 minutes This is usually because of a large air leak either the sideplate has not sealed correctly or the vent valve is still open This feature helps prevent the...

Page 219: ...MS control card include Instrument controller Data processor Main processor Serial communication processor Network communication controller Remote start processor Random access memory RAM Status LEDs Local Control panel firmware Mini display module LEDs on the LAN MS control card are visible on the rear panel The upper two LEDs indicate network communication The two bottom LEDs are the power On di...

Page 220: ... HED in the detector for the EI MSD The EI PCI NCI MSD requires a bipolar power supply that can also provide 10 000 V for NCI operation The HED power supply also provides 600 VDC for the detector focus lens Due to the high impedance of this circuit measuring the detector focus voltage with a handheld voltmeter will give a typical reading of 90 to 100 V where the polarity matches that of the HED vo...

Page 221: ...r connector carries power for the diffusion pump heater or the turbo controller from the AC board Primary fuses The primary fuses limit current into the MSD in case of a short circuit in the foreline pump The primary fuses are on the AC board Power cord receptacle The AC power cord brings in all electrical power for the MSD The power cord can be detached from the MSD FORELINE PUMP The foreline pum...

Page 222: ...s to the CI flow module if it is installed on the MSD It handles data communication between the GC and the MSD LAN The LAN cable from the data system is connected to this LAN connector This cable carries all data communication between the PC and the MSD LAN MSD control card LEDs The two upper LEDs indicate network communication The two bottom LEDs are the power and the heartbeat indicator GC COMM ...

Page 223: ...ing and Maintenance Manual 223 Figure 53 Back panel connections Remote start Primary fuses Power cord LAN High vacuum control High vacuum power Foreline pump RS 232 Serial B power cord RS 232 Serial A GC communication High vacuum gauge connector ...

Page 224: ...ts the GC and the MSD Remote start signals It is often necessary to communicate with external devices for example a purge and trap during a run Typically these communications are requests to send a system ready signal They also include Receive a start run signal from an external device Program the timing of events during a run System ready When interfacing to an external device it is often desirab...

Page 225: ...ame high can be detected between the ready and ground pins on the remote start connector on the MSD Start run input The best way to generate a start run signal is to use the remote start connector on the GC Since remote start cables are made for most common devices this is often the simplest way A general purpose remote start cable 05890 61080 that terminates in spade lugs is also available Ensure...

Page 226: ...226 5977B Series MSD Troubleshooting and Maintenance Manual 8 Electronics ...

Page 227: ... pump and related parts 236 Turbo pump and related parts 237 Analyzer 238 CI ion source 244 EI ion source 241 The HES Ion Source 246 EI GC MSD Interface 247 CI MSD Interface 249 Consumables and Maintenance Supplies 251 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 r...

Page 228: ...as new parts Rebuilt assemblies can be identified by their part numbers The first two digits of the second part of the part number are 69 or 89 such as xxxxx 69xxx or xxxxx 89xxx Rebuilt assemblies are available on an exchange only basis When you return the original part to Agilent Technologies after you receive the rebuilt assembly you will receive a credit If you cannot find a part you need If y...

Page 229: ...lectronics 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 ...

Page 230: ...e 56 on page 233 and Figure 57 on page 235 diffusion pump and related components Table 22 on page 236 and Figure 58 on page 236 and turbo pump vacuum system components Table 23 on page 237 and Figure 59 on page 237 O rings and seals Table 18 O rings and seals Description Part number Calibration valve O ring 1 4 inch 5180 4182 KF10 16 seal foreline pump inlet Micro Ion vacuum gauge KC16AV KF10 16 s...

Page 231: ...se assembly hose and internal spring 05971 60119 Hose Clamp used with 05971 60119 Hose clamps are interchangeable but give an optimum fit if they are matched 1400 3241 Foreline pump inlet seal KF10 16 KC116AV KF10 16 Clamp foreline inlet Micro Ion vacuum gauge KC160000AB Oil drip tray G3170 00012 Drain plug for foreline pump 0100 2452 O ring for foreline pump drain plug 0905 1619 Fill plug 0100 24...

Page 232: ...232 5977B Series MSD Troubleshooting and Maintenance Manual 9 Parts Figure 55 Pfeiffer DUO pump ...

Page 233: ...eline pump and related parts Table 20 Dry foreline pump and related parts Figure 56 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 ...

Page 234: ...d with 05971 60119 Hose clamps are interchangeable but give an optimum fit if they are matched 1400 3241 Dry foreline pump G3870 60600 Replace tip seal set non ammonia IDP3TS Solid tip seal kit inert G3870 67000 KF10 16 Clamp foreline inlet Micro Ion vacuum gauge 0100 1397 KF16 Hose adapter G1099 20531 Vibration Isolation kit IDP3VIBISOKIT Exhaust hose G3170 60100 Exhaust adapter G3170 80029 Barbe...

Page 235: ... 9 5977B Series MSD Troubleshooting and Maintenance Manual 235 Figure 57 IDP3 Dry foreline pump CAUTION Agilent does not recommend using hydrogen as a carrier gas on systems equipped with an IDP3 rough pump ...

Page 236: ... components Figure 58 Item Description Part number 1 Diffusion pump 120 V G1099 80500 220 240 V G1099 80501 2 Fan for high vacuum pump G7005 60564 3 Foreline gauge assembly G1099 60545 KF50 clamp 0100 1395 Figure 58 Diffusion pump removed from analyzer chamber connection and related parts Diffusion pump Foreline gauge assembly High vacuum fan ...

Page 237: ... 23 Turbo pump MSD vacuum system components Figure 59 Description 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 Figure 59 Turbo pump and related parts Turbo Pump Ion gauge assembly ...

Page 238: ... Analyzer screws are listed in the tables that follow Table 24 Analyzer chamber and related parts Description Part number Calibration bulb G3170 80002 Vent valve knob G7077 20554 Figure 60 Analyzer chamber and related parts Calibration bulb Vent valve knob Table 25 Analyzer parts Description Part number TAD assembly Detector HED bracket G7002 80105 Detector Electron multiplier horn G7002 80103 EI ...

Page 239: ...EI 350 extractor ion source G3870 67720 HES ion source G7002 67055 CI ion source G7077 67404 Tip Seal G3870 20542 Table 25 Analyzer parts continued Description Part number Figure 61 Analyzer parts non HES version Ion source Electron multiplier horn under clips Detector ...

Page 240: ...Troubleshooting and Maintenance Manual 9 Parts Figure 62 Analyzer parts HES version Detector Electron multiplier horn under clips Ion source Table 26 Analyzer screws Description Part number Ion source thumbscrew G1099 20138 ...

Page 241: ...Parts 9 5977B Series MSD Troubleshooting and Maintenance Manual 241 EI ion source ...

Page 242: ... 20440 4 Extractor lens G3870 20444 5 Extractor lens insulator G3870 20445 6 Filaments G7005 60061 7 Spring washer 3050 1301 7 Flat washer 3050 0982 8 Lens insulator G3870 20530 9 Entrance lens G3170 20126 10 Ion focus lens 05971 20143 11 Repeller insulator G3870 20133 12 Repeller G3870 60171 13 Flat washer 3050 0891 14 Belleville spring washer 3050 1301 15 Repeller nut 0535 0071 16 Source heater ...

Page 243: ...Parts 9 5977B Series MSD Troubleshooting and Maintenance Manual 243 Figure 63 Extractor EI ion source ...

Page 244: ... interface tip seal G3870 20542 4 CI repeller insulator G1999 20433 5 CI lens insulator G3170 20540 6 CI drawout cylinder G1999 20444 7 CI drawout plate G1999 20446 8 CI ion source heater block assembly G3870 60415 9 Entrance lens G3170 20126 10 CI ion source body G3170 20430 11 CI ion focus lens G1999 20443 12 CI repeller G1999 20432 13 CI filament G7005 60072 14 Dummy filament G1999 60454 15 Cur...

Page 245: ...Parts 9 5977B Series MSD Troubleshooting and Maintenance Manual 245 Figure 64 The CI ion source 15 16 ...

Page 246: ...02 20061 4 Ceramic insulator for extractor G7002 20064 5 Entrance lens 1 G7002 20065 6 Ion focus lens 2 G7002 20068 7 Lens insulator holder G7002 20074 8 M2 x 0 4 screw x 12 mm long gold plated screw G7002 20083 9 Source body G7002 20084 10 Post extractor lens 2 3 G7002 20090 11 Post extractor lens 1 4 G7002 20104 12 M2 x 6 mm gold plated screw G7002 20083 13 Locking ring lens insulator G7002 2012...

Page 247: ...d to the EI GC MSD interface Figure 66 on page 248 illustrates the parts Figure 65 HES ion source 1 2 8 16 17 15 9 4 3 11 10 6 5 7 13 12 14 8 12 Table 30 EI GC MSD interface Item Description Part number Not shown EI Transferline Assembly G7077 67300 1 Transferline tip cap threaded G3870 20547 2 1 16 Ferrule no hole qty 10 5181 3308 ...

Page 248: ...48 5 Transfer tip G3870 20542 6 Column nut 05988 20066 7 M3 screw G1999 20022 8 M4 X 0 7 16MM LG 0515 0383 9 Heater clamp G7077 20210 10 Transfer line spring G1999 20023 11 Welded interface assembly G3870 60301 12 Heater sensor assembly G1099 60109 Table 30 EI GC MSD interface Item Description Part number Figure 66 EI GC MSD interface ...

Page 249: ...erline Assembly untested G7077 67400 1 Transferline tip cap threaded G3870 20547 2 1 16 Ferrule no hole qty 10 5181 3308 3 M3 set screw 0515 0236 4 Transferline tip base threaded G3870 20548 5 Transfer tip G3870 20542 6 Column nut 05988 20066 7 M3x3L screw set gold plated G1999 20022 8 M4 X 0 7 16MM LG screws for heater clamp 0515 0383 9 Heater clamp G7077 20410 10 Transfer line spring G1999 20023...

Page 250: ...250 5977B Series MSD Troubleshooting and Maintenance Manual 9 Parts Figure 67 CI GC MSD interface ...

Page 251: ...rt number Abrasive paper 30 µm 5061 5896 Alumina powder 100 g 3937 6201 Cloths clean qty 300 05980 60051 Cloths cleaning qty 300 9310 4828 Cotton swabs qty 100 5080 5400 Diffusion pump fluid 2 required 6040 0809 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 ...

Page 252: ... 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 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...

Page 253: ...508 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 3538 For the GC MSD interface using a self tightening column nut 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 0 and 0 25 mm id columns 5062 3508 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 Fi...

Page 254: ...ghtening column nuts Description Part number 0 27 mm id 90 10 for 0 10 mm id columns 5062 3518 0 37 mm id 90 10 for 0 20 mm id columns 5062 3516 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 Figure 69 GC inlet with self tightening column nut GC inlet with self tightening nut ...

Page 255: ...phthalene OFN 1 pg µL 5188 5348 Octafluoronaphthalene OFN 100 fg µL 5188 5347 OFN 10 fg µL 5190 0585 PFHT 100 pg µL 5188 5357 PFTBA 10 g 8500 0656 PFTBA sample kit 05971 60571 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 G19...

Page 256: ...256 5977B Series MSD Troubleshooting and Maintenance Manual 9 Parts ...

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Page 258: ... G3870 90003 G7077 90028 Agilent Technologies Inc Printed in USA September 2016 Agilent Technologies ...

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