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HP 5973 MSD Hardware Manual

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HP 5973 MSD
PCI / NCI
Hardware Manual

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Summary of Contents for HP 5973 MSD

  • Page 1 ® HP 5973 MSD PCI / NCI Hardware Manual...
  • Page 2 G1999-90001 source which is not equipped Identification personal injury. with a protective earth contact Each HP 5973 MSD is identi- First edition, 2/98 creates a shock hazard for the Part Numbers fied by a unique 10-character Printed in USA...

  • Page 3: Table Of Contents

    Table of Contents Chapter 1 General Information Specifications, 9 Reagent gases and regulators, 10 Chapter 2 Hardware Reference CI ion source, 14 Reagent gas flow control module, 16 EI/CI GC/MSD interface (CI interface), 20 Chapter 3 Chemical Ionization Theory Chemical ionization overview, 22 Positive CI theory, 24 Negative CI theory, 30 Chapter 4...
  • Page 4 Contents Chapter 5 CI operation CI operation, 51 To set up the software for CI operation, 52 To set up methane reagent gas flow, 54 To perform CI autotune, 56 To perform a positive CI autotune (methane only), 57 To perform a negative CI autotune (any reagent gas), 58 To verify positive CI performance, 59 To verify negative CI performance, 60 To operate the reagent gas flow control module, 61...
  • Page 5 Contents Chapter 7 Maintenance To clean the CI ion source, 95 To minimize foreline pump damage from ammonia, 96 To replace the methane/isobutane gas purifier, 97 To refill the CI calibrant vial, 98 To purge the CI calibration valve, 99 To connect the vacuum gauge controller, 100 To clean the reagent gas supply lines (tubing), 102 Chapter 8...

  • Page 7: General Information

    Specifications, 9 Reagent gases and regulators, 10 General Information...
  • Page 8 General information This manual contains information pertaining to the operation, and maintenance of the HP 5973 CI MSD. It is intended to be used in addition to the HP 5973 MSD Hardware Manual. The CI hardware consists of a chemical ionization source, GC/MSD interface, a reagent gas mass flow controller, and associated electronics.

  • Page 9: Specifications

    Specifications This section lists the principal performance specifications for the HP G1999A (HP 5973 MSD with factory-installed CI.) These specifications are subject to change without notice. These specifications do not apply to CI upgrades; see the upgrade installation documents. Sensitivity, Scan Positive CI: 75:1 RMS for 1 µl of 100 pg/µl Benzophenone (m/z = 183.1)

  • Page 10: Reagent Gases And Regulators

    The following reagent gases and hardware may be required for operation of CI with the HP 5973 MSD (depending on your choice of reagent). Use the highest purity gases available. Do not use gases of less than the listed purity. The hardware items listed below are available from Matheson and Swagelok.
  • Page 11 Description, 12 CI ion source, 14 Reagent gas flow control module, 16 EI/CI GC/MSD interface (CI interface), 20 Hardware Reference...
  • Page 12 Description The chemical ionization (CI) hardware allows the HP 5973 MSD to operate in the positive and negative CI modes (PCI and NCI) and produce high-quality, classical CI spectra, which include molecular adduct ions. A variety of reagent gases (including methane, isobutane, and ammonia) can be used.

  • Page 13: Hardware Reference

     Hardware Reference...

  • Page 14: Ci Ion Source

     Hardware Reference &, LRQ VRXUFH CI ion source The CI ion source is similar to the EI source, but only has one part in common with the EI source — the entrance lens. The single CI filament has a straight wire and a reflector.
  • Page 15  Hardware Reference &, LRQ VRXUFH CI ion source body Setscrew CI repeller CI repeller insulator CI filament CI source heater assembly Dummy filament CI lens insulator CI ion focus lens CI drawout cylinder CI drawout plate CI lens Entrance lens CI interface tip seal...

  • Page 16: Reagent Gas Flow Control Module

     Hardware Reference 5HDJHQW JDV IORZ FRQWURO PRGXOH Reagent gas flow control module The CI reagent gas flow control module regulates the flow of reagent gas into the EI/CI GC/MSD interface. The flow control module consists of a mass flow controller (MFC), gas select valves, CI calibration valve, isolation valve, control panel, control and display electronics, and plumbing.
  • Page 17  Hardware Reference 5HDJHQW JDV IORZ FRQWURO PRGXOH • The flow control display shows the gas flow as a percentage of the total possible flow (5 ml/min for methane). • The flow control knob adjusts the gas flow. If the selected flow rate can not be achieved or maintained, the numbers in the flow control display will flash.
  • Page 18  Hardware Reference 5HDJHQW JDV IORZ FRQWURO PRGXOH CI ion source Green Gas A light (Methane) supply Isolation Gas select valve valve A Mass Flow Controller Gas select valve B Gas B EI/CI Calibration (Other gas) GC/MSD valve supply interface Amber light Restrictor...
  • Page 19  Hardware Reference 5HDJHQW JDV IORZ FRQWURO PRGXOH gas last time. Flow control module state diagram: Result Gas A flows Gas B flows Purge Purge Pump out Standby, vented, with Gas A with Gas B flow module or EI mode Control panel lights (LEDs) Gas A (green) Gas B (amber) Off...

  • Page 20: Ei/Ci Gc/Msd Interface (Ci Interface)

     Hardware Reference (,&, *&06' LQWHUIDFH &, LQWHUIDFH EI/CI GC/MSD interface (CI interface) The CI interface mounts onto the side of the vacuum manifold, with one end in the GC oven and the other in the MSD. Reagent gas is plumbed into the interface. The tip of the interface assembly extends into the ionization chamber.

  • Page 21: Chemical Ionization Theory

    Chemical ionization overview, 22 References on chemical ionization, 23 Positive CI theory, 24 Proton transfer, 26 Hydride abstraction, 28 Addition, 28 Charge exchange, 29 Negative CI theory, 30 Electron capture, 32 Dissociative electron capture, 33 Ion pair formation, 33 Ion-molecule reactions, 33 Chemical Ionization Theory...

  • Page 22: Chemical Ionization Overview

     Chemical Ionization Theory &KHPLFDO LRQL]DWLRQ RYHUYLHZ Chemical ionization overview Chemical ionization (CI) is a technique for creating ions used in mass spectrometric analyses. There are significant differences between CI and electron ionization (EI). This section describes the most common chemical ionization mechanisms. In EI, relatively high-energy electrons (70 eV) collide with molecules of the sample that is to be analyzed.

  • Page 23: References On Chemical Ionization

     Chemical Ionization Theory &KHPLFDO LRQL]DWLRQ RYHUYLHZ References on chemical ionization A. G. Harrison, Chemical Ionization Mass Spectrometry, 2nd Edition, CRC Press, INC. Boca Raton, FL (1992) ISBN 0-8493-4254-6. W. B. Knighton, L. J. Sears, E. P. Grimsrud, “High Pressure Electron Capture Mass Spectrometry”, Mass Spectrometry Reviews (1996), 14, 327-343.

  • Page 24: Positive Ci Theory

     Chemical Ionization Theory 3RVLWLYH &, WKHRU\ Positive CI theory Positive CI occurs with the same analyzer voltage polarities as EI. For PCI, the reagent gas is ionized by collision with emitted electrons. The reagent gas ions react chemically with sample molecules (as proton donors) to form sample ions. PCI ion formation is more “gentle”...
  • Page 25  Chemical Ionization Theory 3RVLWLYH &, WKHRU\...

  • Page 26: Proton Transfer

     Chemical Ionization Theory 3RVLWLYH &, WKHRU\ Proton transfer Proton transfer can be expressed as + M → MH where the reagent gas B has undergone ionization resulting in protonation. If the proton affinity of the analyte (sample) M is greater than that of the reagent gas, then the protonated reagent gas will transfer its proton to the analyte, forming a positively charged analyte ion.
  • Page 27  Chemical Ionization Theory 3RVLWLYH &, WKHRU\ Reagent gas proton affinities Species Proton affinity Reactant ion formed kcal/mole ( m/z 3) ( m/z 17) ( m/z 29) ( m/z 19) ( m/z 35) ( m/z 33) ( m/z 57) ( m/z 18) Proton affinities of selected organic compounds for PCI Molecule Proton affinity...

  • Page 28: Hydride Abstraction

     Chemical Ionization Theory 3RVLWLYH &, WKHRU\ Hydride abstraction In the formation of reagent ions, various reactant ions can be formed that have high – hydride-ion (H ) affinities. If the hydride-ion affinity of a reactant ion is higher than –...

  • Page 29: Charge Exchange

     Chemical Ionization Theory 3RVLWLYH &, WKHRU\ Charge exchange Charge-exchange ionization can be described by the reaction: · · + M → M where X is the ionized reagent gas, and M is the analyte of interest. Examples of reagent gases used for charge exchange ionization include the noble gases (helium, neon, argon, krypton, xenon, and radon,) nitrogen, carbon dioxide, carbon monoxide, hydrogen, and other gases that do not react “chemically”...

  • Page 30: Negative Ci Theory

     Chemical Ionization Theory 1HJDWLYH &, WKHRU\ Negative CI theory Negative chemical ionization (NCI) is performed with analyzer voltage polarities reversed to select negative ions. There are several chemical mechanisms for negative chemical ionization. Not all mechanisms provide the dramatic increases in sensitivity often associated with negative chemical ionization.
  • Page 31  Chemical Ionization Theory 1HJDWLYH &, WKHRU\...

  • Page 32: Electron Capture

     Chemical Ionization Theory 1HJDWLYH &, WKHRU\ Electron capture Electron capture, is the primary mechanism of interest in negative CI. Electron capture (often referred to as high-pressure electron capture mass spectrometry, or HPECMS) provides the high sensitivity for which NCI is known. For some samples, and under ideal conditions, electron capture can provide sensitivity as much as 10 to 1000 times higher than positive ionization.

  • Page 33: Dissociative Electron Capture

     Chemical Ionization Theory 1HJDWLYH &, WKHRU\ Dissociative electron capture Dissociative electron capture is also known as dissociative resonance capture. It is a process similar to electron capture. The difference is that during the reaction, the sample molecule fragments or dissociates. The result is typically an anion and a neutral radical.

  • Page 35: Ci Setup

    CI setup, 37 To vent the CI MSD, 38 To remove the CI MSD covers, 39 To pump down the MSD, 40 To install the GC column in the EI/CI GC/MSD interface, 42 To switch from CI to EI operating mode, 44 To switch from EI to CI operating mode, 45 To install the CI ion source, 46 To install the CI interface tip seal, 48...
  • Page 36  CI setup CI hardware setup This chapter provides information and instructions about setting up the HP 5973 CI MSD hardware for operation in CI mode. The following topics are covered in this chapter • Venting and pumping down the CI MSD •...

  • Page 37: Ci Setup

     CI setup &, VHWXS CI setup In setting up your CI MD for operation in CI mode requires special care to avoid contamination and air leaks. General guidelines • Before venting in EI mode, verify that the GC/MSD system is performing correctly.

  • Page 38: To Vent The Ci Msd

    7R YHQW WKH &, 06' To vent the CI MSD Software changes This procedure is the same as in the HP 5973 MSD Hardware Manual except for the following details. See the MSD reference Collection CD-ROM for a video of this procedure.

  • Page 39: To Remove The Ci Msd Covers

     CI setup 7R UHPRYH WKH &, 06' FRYHUV To remove the CI MSD covers Materials needed: Screwdriver, Torx T-15 (8710-1622) Screwdriver, Torx T-10 (8710-1623) The analyzer cover is removed for venting and for many maintenance procedures. The side cover is removed to access the electronics module. See the MSD reference Collection CD-ROM for a video of this procedure.

  • Page 40: To Pump Down The Msd

     CI setup 7R SXPS GRZQ WKH 06' To pump down the MSD Software changes The software is revised periodically. If the steps in this procedure do not match your MSD ChemStation software, refer to the manuals and online help supplied with the software for more information.
  • Page 41  CI setup 7R SXPS GRZQ WKH 06' & $ 8 7 , 2 1 Do not turn on any heated zones until carrier gas flow is on. Heating a column with no carrier gas flow will damage the column. 8 Reinstall the MSD analyzer cover.

  • Page 42: To Install The Gc Column In The Ei/Ci Gc/Msd Interface

     CI setup 7R LQVWDOO WKH *& FROXPQ LQ WKH (,&, *&06' LQWHUIDFH To install the GC column in the EI/CI GC/MSD interface Materials needed: Adjustment tool (G1099-20030) Ferrules 0.27-mm id, for 0.10-mm id columns (5062-3518) 0.37-mm id, for 0.20-mm id columns (5062-3516) 0.40-mm id, for 0.25-mm id columns (5181-3323) 0.47-mm id, for 0.32-mm id columns (5062-3514) 0.74-mm id, for 0.53-mm id columns (5062-3512)
  • Page 43  CI setup 7R LQVWDOO WKH *& FROXPQ LQ WKH (,&, *&06' LQWHUIDFH Column Interface column nut Adjustment tool 0 to 1 mm Interface ferrule Column Vacuum manifold CI interface tip seal Reagent gas inlet Interface column nut...

  • Page 44: To Switch From Ci To Ei Operating Mode

    Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components. Wear a grounded anti-static wrist strap (see page 98 of the HP 5973 MSD Hardware Manual) and take other anti-static precautions EHIRUH you open the vacuum manifold.

  • Page 45: To Switch From Ei To Ci Operating Mode

    Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components. Wear a grounded anti-static wrist strap (see page 98 of the HP 5973 MSD Hardware Manual) and take other anti-static precautions EHIRUH you open the vacuum manifold.

  • Page 46: To Install The Ci Ion Source

     CI setup 7R LQVWDOO WKH &, LRQ VRXUFH To install the CI ion source C A U T I O N Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components. Wear a grounded anti-static wrist strap and take other anti-static precautions EHIRUH you open the vacuum manifold.
  • Page 47  CI setup 7R LQVWDOO WKH &, LRQ VRXUFH CI ion source body CI filament CI source heater assembly CI interface tip seal CI GC/MSD interface CI interface cover Source heater and sensor cables Ion focus lens pin Entrance lens pin...

  • Page 48: To Install The Ci Interface Tip Seal

     CI setup 7R LQVWDOO WKH &, LQWHUIDFH WLS VHDO To install the CI interface tip seal Materials needed: Interface tip seal (G1099-60412) The interface tip seal must be in place for CI operation. It is necessary to achieve adequate ion source pressure for CI. C A U T I O N Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components.
  • Page 49 CI operation, 51 To set up the software for CI operation, 52 To set up methane reagent gas flow, 54 To perform CI autotune, 56 To perform a positive CI autotune (methane only), 57 To perform a negative CI autotune (any reagent gas), 58 To verify positive CI performance, 59 To verify negative CI performance, 60 To operate the reagent gas flow control module, 61...
  • Page 50 CI Operation This chapter provides information and instructions about operating an HP 5973 CI MSD in CI mode. Most of the material is related to methane chemical ionization but one section discusses the use of other reagent gases. The following topics are covered in this chapter •...

  • Page 51: Ci Operation

     CI operation &, RSHUDWLRQ CI operation Operating your MSD in the CI mode is slightly more complicated than operating in the EI mode. After tuning, gas flow, source temperature, and electron energy may need to be optimized for your specific analyte. General guidelines •...

  • Page 52: Ci Operation

     CI operation 7R VHW XS WKH VRIWZDUH IRU &, RSHUDWLRQ To set up the software for CI operation 1 6ZLWFK WR WKH 0DQXDO 7XQH YLHZ 2 6HOHFW IURP WKH PHQX Load Tune Values File 3 6HOHFW WKH WXQH ILOH PCICH4.U.
  • Page 53  CI operation 7R VHW XS WKH VRIWZDUH IRU &, RSHUDWLRQ Default Tune Control Limits (used by CI autotune only. These limits should not be confused with the parameters set in Edit MS Parameters, or with those appearing on the tune report.) Reagent gas Methane Isobutane...

  • Page 54: To Set Up Methane Reagent Gas Flow

     CI operation 7R VHW XS PHWKDQH UHDJHQW JDV IORZ To set up methane reagent gas flow The reagent gas flow must be adjusted for maximum stability before tuning the CI system. Do the initial setup with methane in positive ion mode (PCI). No flow adjustment procedure is available for NCI, as no negative reagent ions are formed.
  • Page 55  CI operation 7R VHW XS PHWKDQH UHDJHQW JDV IORZ Methane pre-tune after more than a day of baking out. Note the low abundance of m/z 19 and absence of any visible peak at m/z 32. Your MSD will probably show more water, but the abundance of m/z 19 should still be less than that of m/z 17.

  • Page 56: To Perform Ci Autotune

     CI operation 7R SHUIRUP &, DXWRWXQH To perform CI autotune After the reagent gas flow is adjusted, the lenses and electronics of the MSD should be tuned. Perfluoro-5,8-dimethyl-3,6,9-trioxidodecane (PFDTD) is used as the calibrant. Instead of flooding the entire vacuum chamber, the PFDTD is introduced directly into the ionization chamber through the GC/MSD interface by means of the gas flow control module.

  • Page 57: To Perform A Positive Ci Autotune (Methane Only)

     CI operation 7R SHUIRUP D SRVLWLYH &, DXWRWXQH PHWKDQH RQO\ To perform a positive CI autotune (methane only) 1 /RDG WKH WXQH ILOH $FFHSW WKH GHIDXOW VHWWLQJV PCICH4.U 2 3HUIRUP PHWKDQH VHWXS 6HH SDJH  3 8QGHU WKH 7XQH PHQX FOLFN CI Autotune There are no tune performance criteria.

  • Page 58: To Perform A Negative Ci Autotune (Any Reagent Gas)

     CI operation 7R SHUIRUP D QHJDWLYH &, DXWRWXQH DQ\ UHDJHQW JDV To perform a negative CI autotune (any reagent gas) 1 /RDG RU DQ H[LVWLQJ WXQH ILOH IRU WKH UHDJHQW JDV \RX DUH XVLQJ  NCICH4.U Accept the default temperature and other settings. 2 ,I \RX GRQªW DOUHDG\ KDYH DQ 1&, WXQH ILOH IRU \RXU UHDJHQW JDV FOLFN XQGHU WKH 6HWXS PHQX DQG FOLFN RQ WKH JDV \RX DUH XVLQJ Select Reagent Gas...

  • Page 59: To Verify Positive Ci Performance

     CI operation 7R YHULI\ SRVLWLYH &, SHUIRUPDQFH To verify positive CI performance Materials needed: Benzophenone, 100 pg/µl (8500-5440) 1 9HULI\ WKDW WKH 3&,&+8 WXQH ILOH LV ORDGHG 2 2Q WKH IORZ FRQWURO SDQHO WXUQ RII DQG VHW WR  IORZ Purge Gas A...

  • Page 60: To Verify Negative Ci Performance

     CI operation 7R YHULI\ QHJDWLYH &, SHUIRUPDQFH To verify negative CI performance Materials needed: OFN, 1 pg/µl (8500-5441) 1 9HULI\ WKDW WKH 06' SHUIRUPV FRUUHFWO\ LQ (, PRGH 2 /RDG WKH 1&,&+8 WXQH ILOH DQG DFFHSW WKH WHPSHUDWXUH VHWSRLQWV 3 7XUQ RQ DQG OHW WKH V\VWHP VWDELOL]H IRU  PLQXWHV Purge...

  • Page 61: To Operate The Reagent Gas Flow Control Module

    7R RSHUDWH WKH UHDJHQW JDV IORZ FRQWURO PRGXOH To operate the reagent gas flow control module For a video demonstration of the gas flow control module, see the HP 5973 MSD Reference Collection CD-ROM. Flow control module state diagram: Result...

  • Page 62: To Monitor High Vacuum Pressure

    7R PRQLWRU KLJK YDFXXP SUHVVXUH To monitor high vacuum pressure Materials needed: Gauge controller (HP 59864B) Triode gauge cable (8120-6573) : $ 5 1 , 1 * 1HYHU FRQQHFW RU GLVFRQQHFW WKH FDEOH IURP WKH WULRGH JDXJH WXEH ZKLOH WKH 06' LV XQGHU...
  • Page 63 7R PRQLWRU KLJK YDFXXP SUHVVXUH Typical pressure readings Use the HP 59823B high-vacuum gauge controller. Note that the mass flow controller is calibrated for methane, and the high vacuum gauge controller is calibrated for helium, so these measurements are not accurate, but are intended as a guide to typical observed readings.

  • Page 64: To Use Other Reagent Gases

    To use other reagent gases This section describes the use of isobutane or ammonia as the reagent gas. You should be familiar with operating the CI-equipped HP 5973 MSD with methane reagent gas before attempting to use other reagent gases.
  • Page 65  CI operation 7R XVH RWKHU UHDJHQW JDVHV Isobutane CI Isobutane (C ) is commonly used for chemical ionization when less fragmentation is desired in the chemical ionization spectrum. This is because the proton affinity of isobutane is higher than that of methane; hence, less energy is transferred in the ionization reaction.
  • Page 66  CI operation 7R XVH RWKHU UHDJHQW JDVHV C A U T I O N Use of ammonia affects the maintenance requirements of the MSD. See the maintenance chapter for more information. C A U T I O N The pressure of the ammonia supply must be less than 5 psig. Higher pressures can result in ammonia condensing from a gas to a liquid.

  • Page 67: Troubleshooting

    Common CI-specific problems, 68 Air leaks, 70 Pressure-related symptoms (overview), 74 Poor vacuum without reagent gas flow, 75 High pressure with reagent gas flow, 76 Pressure does not change when reagent flow is changed, 77 Signal-related symptoms (overview), 78 No peaks, 79 No or low reagent gas signal, 81 No or low PFDTD signal, but reagent ions are normal, 83 Excessive noise or low signal-to-noise ratio, 84...

  • Page 68: Common Ci-Specific Problems

    Troubleshooting This chapter outlines the troubleshooting of HP 5973 MSDs equipped with PCI/NCI. Most of the troubleshooting information in the HP 5973 MSD Hardware Manual (G1099-90001) also applies to MSDs equipped with the CI accessory. Common CI-specific problems Because of the added complexity of the parts required for CI, there are many potential problems added.

  • Page 69: Troubleshooting Tips And Tricks

     Troubleshooting 7URXEOHVKRRWLQJ WLSV DQG WULFNV Troubleshooting tips and tricks The following are general rules for troubleshooting, with specific CI examples. Rule 1: “Look for what has been changed.” Many problems are introduced accidentally by human actions. Every time any system is disturbed, there is a chance of introducing a new problem. •...

  • Page 70: Air Leaks

     Troubleshooting $LU OHDNV Air leaks How do I know if I have an air leak? Large air leaks can be detected by vacuum symptoms: loud gurgling noise from the foreline pump, inability of the turbo pump to reach 95% speed, or, in the case of smaller leaks, high pressure readings on the high vacuum gauge controller.
  • Page 71  Troubleshooting $LU OHDNV Always look for small air leaks when setting up methane flow. Run the methane pre-tune. The abundance of m/z 19 (protonated water) should be less than that of m/z 17. If the MSD was just pumped down, look for the abundance of m/z 19 to be decreasing.
  • Page 72  Troubleshooting $LU OHDNV How do I find the air leak? 1 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.
  • Page 73  Troubleshooting $LU OHDNV Schematic of CI flow control module CI ion source Green Gas A light (Methane) supply Isolation Gas select valve valve A Mass Flow Controller Gas select valve B Gas B EI/CI Calibration (Other gas) GC/MSD valve supply interface Amber...

  • Page 74: Pressure-Related Symptoms (Overview)

     Troubleshooting 3UHVVXUHUHODWHG V\PSWRPV RYHUYLHZ Pressure-related symptoms (overview) The following symptoms are all related to high vacuum pressure. Each symptom is discussed in more detail in the following pages. The mass flow controller is calibrated for methane, and the high vacuum gauge controller is calibrated for helium, so these measurements are not accurate in absolute terms, They are intended as a guide to typical observed readings.

  • Page 75: Poor Vacuum Without Reagent Gas Flow

     Troubleshooting 3RRU YDFXXP ZLWKRXW UHDJHQW JDV IORZ Poor vacuum without reagent gas flow Possible Cause Excess water in the background. Action Scan from 10 – 40 amu. A large peak at m/z 19 (> m/z 17) indicates water in the background.

  • Page 76: High Pressure With Reagent Gas Flow

     Troubleshooting +LJK SUHVVXUH ZLWK UHDJHQW JDV IORZ High pressure with reagent gas flow Possible Cause The reagent gas flow rate is too high. Action On the flow controller, turn down reagent gas flow as appropriate. Verify that reagent ion ratios are correct. See page 54. Possible Cause Air leak.

  • Page 77: Pressure Does Not Change When Reagent Flow Is Changed

     Troubleshooting 3UHVVXUH GRHV QRW FKDQJH ZKHQ UHDJHQW IORZ LV FKDQJHG Pressure does not change when reagent flow is changed Possible Cause The reagent gas regulator is closed. Action Check and, if necessary, open the reagent gas regulator. Possible Cause The reagent gas regulator is set to the wrong pressure.

  • Page 78: Signal-Related Symptoms (Overview)

     Troubleshooting 6LJQDOUHODWHG V\PSWRPV RYHUYLHZ Signal-related symptoms (overview) This section describes symptoms related to the signal. The symptom may be too much signal, too little signal, a noisy signal, or an incorrect signal. Signal-related symptoms are generally observed during tuning but may also be observed during data acquisition.

  • Page 79: No Peaks

     Troubleshooting 1R SHDNV No peaks When troubleshooting “no peaks” it is important to specify what mode of operation is being used, and what kind of peaks are not being seen. Always start with methane PCI and verify presence of reagent ions. No reagent gas peaks in PCI If MSD has been working well and nothing seems to have been changed •...
  • Page 80  Troubleshooting 1R SHDNV No PFDTD peaks in PCI • Incorrect reagent gas. There are no PCI PFDTD peaks created with isobutane or ammonia. Switch to methane. • Analyzer not sealed (big air leak) • No calibrant in vial • Defective calibration valve •...

  • Page 81: No Or Low Reagent Gas Signal

     Troubleshooting 1R RU ORZ UHDJHQW JDV VLJQDO No or low reagent gas signal Possible Cause If you have just installed the CI ion source, and have an air leak or large amounts of water in the system, and have run one or more autotunes, the ion source is probably dirty now.
  • Page 82  Troubleshooting 1R RU ORZ UHDJHQW JDV VLJQDO Possible Cause Too much air or water in the system. Action Run the methane pre-tune. Peaks at m/z 32 and 19 usually indicate air and water, respectively. Bake out and purge the instrument until the peak at m/z 32 is smaller than that at m/z 31 and the peak at m/z 19 is reduced to a very low level.

  • Page 83: No Or Low Pfdtd Signal, But Reagent Ions Are Normal

     Troubleshooting 1R RU ORZ 3)'7' VLJQDO EXW UHDJHQW LRQV DUH QRUPDO No or low PFDTD signal, but reagent ions are normal Possible Cause You are flowing any reagent gas but methane in PCI. Action Switch to methane. Possible Cause Wrong or corrupted tune file loaded.

  • Page 84: Excessive Noise Or Low Signal-To-Noise Ratio

    Excessive noise or low signal-to-noise ratio Possible Cause The GC injection port needs maintenance. Action Refer to the HP 6890 GC manual. Possible Cause The CI ion source is dirty. Action Clean the ion source. See the Maintenance chapter in this manual for more information.

  • Page 85: Large Peak At M/Z 19

     Troubleshooting /DUJH SHDN DW P]  Large peak at m/z 19 If the abundance of the peak at m/z 19 is more than twice the abundance of the peak at m/z 17, then there is probably too much water in the system. Possible Cause The system was not baked out sufficiently after it was last vented.

  • Page 86: Peak At M/Z 32

     Troubleshooting 3HDN DW P]  Peak at m/z 32 A visible peak at m/z 32 in methane pre-tune often indicates air in the system. Possible Cause Residual air from recent venting — check for water indicated by a large peak at m/z 19.

  • Page 87: Tuning-Related Symptoms (Overview)

     Troubleshooting 7XQLQJUHODWHG V\PSWRPV RYHUYLHZ Tuning-related symptoms (overview) This section describes symptoms related to tuning. Most symptoms involve difficulties with tuning or with the results of tuning. The following symptoms are covered in this section: • CI ion ratio is difficult to adjust or unstable •...

  • Page 88: Reagent Gas Ion Ratio Is Difficult To Adjust Or Unstable

     Troubleshooting 5HDJHQW JDV LRQ UDWLR LV GLIILFXOW WR DGMXVW RU XQVWDEOH Reagent gas ion ratio is difficult to adjust or unstable Possible Cause Residual air and water in the MSD or in the reagent gas supply lines. Action Run the methane pre-tune. Air will appear as a peak at m/z 32 and excessive water as a peak at m/z 19 >...

  • Page 89: High Electron Multiplier Voltage

     Troubleshooting +LJK HOHFWURQ PXOWLSOLHU YROWDJH High electron multiplier voltage The electron multiplier voltage can range from a few hundred volts to 3000 V. If the CI autotune program consistently sets the electron multiplier voltage at or near 3000 V, but can still find peaks and complete the tune, it may indicate a problem. Possible Cause The filament is worn out.

  • Page 90: Can Not Complete Autotune

     Troubleshooting &DQ QRW FRPSOHWH DXWRWXQH Can not complete autotune Possible Cause Wrong or corrupted tune file. Action Check the tune parameters. Possible Cause The m/z 28/27 ion ratio (for methane) is incorrect. The correct ratio should be between 1.5 and 5.0. Action If the ion ratio is incorrect, adjust it.

  • Page 91: Peak Widths Are Unstable

     Troubleshooting 3HDN ZLGWKV DUH XQVWDEOH Peak widths are unstable Possible Cause Wrong or corrupted tune file. Action Check the tune parameters. Possible Cause The CI ion source is dirty. Action Clean the ion source. See the Maintenance chapter of this manual for more information.
  • Page 93 To clean the CI ion source, 95 To minimize foreline pump damage from ammonia, 96 To replace the methane/isobutane gas purifier, 97 To refill the CI calibrant vial, 98 To purge the CI calibration valve, 99 To connect the vacuum gauge controller, 100 To clean the reagent gas supply lines (tubing), 102 Maintenance...
  • Page 94 MSDs equipped with the CI unless it is superseded by information in this chapter. Be sure to read Before starting in the chapter Maintaining the MSD of the HP 5973 MSD Hardware Manual (G1099-90001) before using any of the procedures or information in this chapter.

  • Page 95: Maintenance

    • Do not use halogenated solvents, and use hexane for the final rinse. 1 2 7 ( The HP 5973 MSD Reference Collection CD-ROM illustrates using a small drill bit to clean the small holes in the ion source body and drawout plate. This is not recommended. Use the tip of a clean, round toothpick instead.

  • Page 96: To Minimize Foreline Pump Damage From Ammonia

     Maintenance 7R PLQLPL]H IRUHOLQH SXPS GDPDJH IURP DPPRQLD To minimize foreline pump damage from ammonia Gas ballasting for an hour every day removes most, of the ammonia from the pump oil. This will greatly increase the life of the pump. C A U T I O N Only perform this procedure if the pump is at normal operating temperature.

  • Page 97: To Replace The Methane/Isobutane Gas Purifier

     Maintenance 7R UHSODFH WKH PHWKDQHLVREXWDQH JDV SXULILHU To replace the methane/isobutane gas purifier Materials needed: Methane/isobutane gas purifier (G1999-80410) Front ferrule for 1/8-inch tubing (5180-4110) Rear ferrule for 1/8-inch tubing (5180-4116) Tubing cutter (8710-1709) The methane/isobutane gas purifier needs to be replaced after four tanks of reagent gas.

  • Page 98: To Refill The Ci Calibrant Vial

     Maintenance 7R UHILOO WKH &, FDOLEUDQW YLDO To refill the CI calibrant vial Materials needed: PFDTD calibrant (8500-8130) 1 Set the reagent gas flow to Gas Off 2 Vent the MSD 3 Remove the capillary column from the GC/MSD interface 4 Pull the MSD away from the GC 5 Loosen the nut holding the vial in place 6 Remove the calibrant vial...

  • Page 99: To Purge The Ci Calibration Valve

     Maintenance 7R SXUJH WKH &, FDOLEUDWLRQ YDOYH To purge the 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 Turn on Gas A.

  • Page 100: To Connect The Vacuum Gauge Controller

    C A U T I O N use an HP 59864 (older model) triode gauge controller with the HP 5973 CI MSD. 1 Connect the triode gauge cable to the triode gauge tube. 2 Connect the other end of the triode gauge cable to the gauge controller.
  • Page 101  Maintenance 7R FRQQHFW WKH YDFXXP JDXJH FRQWUROOHU Triode gauge tube Triode gauge cable Gauge controller Triode gauge cable Power cord...

  • Page 102: To Clean The Reagent Gas Supply Lines (Tubing)

     Maintenance 7R FOHDQ WKH UHDJHQW JDV VXSSO\ OLQHV WXELQJ To clean the reagent gas supply lines (tubing) Materials needed: Clean, dry nitrogen Heat gun Tubing cutter (8710-1709) If the reagent gas lines become contaminated, they can be cleaned. 1 Disconnect the reagent gas tubing from the gas supply, the gas purifier, and the MSD.

  • Page 103: Parts

    GC/MSD interface parts, 106 CI ion source parts, 108 Flow control module parts, 110 Miscellaneous parts, 113 Parts...
  • Page 104 HP 5973 MSD Hardware Manual. To order parts To obtain parts for the HP 5973 MSD, address the order or inquiry to your local Hewlett-Packard office. Supply them with the following information: • Model and serial number of your MSD •...
  • Page 105 If you need a part that is not listed in this chapter, check the Hewlett- Packard Analytical Supplies Catalog or the on-line catalogue on the worldwide web at . If you still cannot <http://www.dmo.hp.com/cagcat/pub/HOME.htm> find it, contact your Hewlett-Packard service representative or your Hewlett-Packard office.

  • Page 106: Gc/Msd Interface Parts

     Parts *&06' LQWHUIDFH SDUWV GC/MSD interface parts Description HP part number CI/EI GC/MSD interface assembly G1999-60400 Heater clamp G1999-20410 Heater/sensor assembly G1099-60107 Interface cover G1999-00405 Interface insulation (two pieces) G1999-20401 Screws for heater clamp 0515-0383 Screws to attach interface to manifold...
  • Page 107  Parts *&06' LQWHUIDFH SDUWV CI interface cover G1999-00405 CI interface insulation G1999-20401 CI heater clamp G1999-20410 CI welded interface G1999-60401 Interface O-ring 0905-1405 CI ionization chamber CI interface tip seal G1999-60412 Vacuum manifold Heater/sensor assembly G1099-60107 Screws to attach interface to manifold Screws for heater clamp 0515-0383...

  • Page 108: Ci Ion Source Parts

     Parts &, LRQ VRXUFH SDUWV CI ion source parts Description HP part number Box for ion source shipping and storage G1999-65001 CI ion source (tested) G1999-65402 CI drawout cylinder G1999-20444 CI drawout plate G1999-20446 CI filament G1099-80053 CI heater block...
  • Page 109  Parts &, LRQ VRXUFH SDUWV CI ion source body Setscrew 0515-1446 CI repeller G1999-20432 CI repeller insulator CI filament G1099-80053 CI source heater assembly Dummy filament CI lens insulator (set) CI ion focus lens CI draw-out cylinder CI draw-out plate CI lens insulator (set)

  • Page 110: Flow Control Module Parts

     Parts )ORZ FRQWURO PRGXOH SDUWV Flow control module parts Description HP part number CI flow control module (complete) G1999-65450 Calibration valve assembly G1999-60456 PFDTD calibrant 8500-8130 Sample vial 05980-20018 Sample vial O-ring, 1/4-inch Viton 0905-1217 Solenoid valve and cable...
  • Page 111  Parts )ORZ FRQWURO PRGXOH SDUWV Rear flow module cover G1999-00411 CI analyzer cover G1999-60440 Front flow module cover G1999-20422 Display module G1999-65461 Isolation valve G1999-80402 Calibration valve assembly G1999-60456 Mass flow controller 0101-1006 Reagent gas select valve G1999-80401 Reagent gas supply tubing 7157-0210...

  • Page 112: Ferrules

     Parts )HUUXOHV Ferrules Description HP part number Blank, graphite-vespel 5181-3308 GC/MSD interface 0.3-mm id, 85% Vespel 15% graphite, for 0.10-mm id columns 5062-3507 0.4-mm id, 85% Vespel 15% graphite, for 0.20-mm id and 5062-3508 0.25-mm id columns 0.5-mm id, 85% Vespel 15% graphite, for 0.32-mm id columns 5062-3506 0.8-mm id, 85% Vespel 15% graphite, for 0.53-mm id columns...

  • Page 113: Miscellaneous Parts

     Parts 0LVFHOODQHRXV SDUWV Miscellaneous parts Description HP part number Benzophenone, 100 pg/µl 8500-5440 Bipolar HED power supply G1099-80018 Cotton swabs (100) 5880-5400 Foreline pump secondary containment tray G1099-00015 Gloves, clean large 8650-0030 small 8650-0029 Methane/isobutane gas purifier G1999-80410 OFN, 1 pg/µl...
  • Page 115 Index ChemStation using to pump down the MSD, 40 Adduct ion, 28 using to set up methane reagent gas flow, 54 Alignment, analyzer and CI interface, checking, 48 using to vent the MSD, 38 Ammonia CI autotune, 56 increased maintenance required, 94 Methane PCI only, 57 maintenance caution, 22 CI calibrant vial...
  • Page 116 Index CI spectra classical, 12 Gases, reagent. See Reagent gas endosulfan methane NCI, 31 Gauge controller methyl stearate methane and ammonia PCI, 25 abnormal or blank display, 62 Control panel, reagent gas flow control module, 16 connecting, 100 Covers connecting to the triode gauge tube, 100 reinstalling, 39 indicated vs.
  • Page 117 Index Maintenance, 93 Part numbers, inside front cover CI ion source cleaning, 95 See also Parts cleaning reagent gas supply tubing, 102 Parts, 103 connecting the vacuum gauge controller, 100 CI interface, 106 foreline pump, 96 CI ion source, 108 increased need for ion source cleaning, 94 ferrules, 112 methane/isobutane gas purifier, 97...
  • Page 118 Index methane pre-tune showing acceptable levels of air and water, 55 Reagent gas setting up methane flow, 54 ammonia, using, 65 setting up the software for CI operation, 52 carbon dioxide, using for NCI buffer gas, 66 too much air and water, 55 CI theory overview, 22 State diagram, reagent gas flow control module, cleaning supply tubing, 102...
  • Page 119 Index Thermal electrons, in NCI, 30 Warnings, inside front cover Triode gauge tube Water connecting a gauge controller to, 100 contamination of CI systems by, 22 ignition of hydrogen by, 62 detecting in CI, 55, 85 implosion hazard, 62 monitoring high vacuum pressure, 62 turning on, 62 Troubleshooting, 67 See also Symptoms of malfunctions...
  • Page 121 GC oven. Study the Hydro- ing of fuse holders creates a gen Carrier Gas Safety Guide shock hazard for the operator (HP Part No. 5955-5398) before and can damage the instru- operating the MSD with hydro- ment. Replace fuses only with gen carrier gas.
  • Page 122 ®       Copyright © 1998 Manual Part Number Hewlett-Packard G1999-90001 Printed in USA 2/98...

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