HP 5973 MSD Hardware Manual Download Page 79

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Troubleshooting

1RSHDNV

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

•

Wrong tune file loaded, or tune file corrupted

•

Wrong ion polarity (there are no reagent ions visible in NCI)

•

No reagent gas flow; look for background ions and 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 74.

If MSD was recently switched from EI to CI

•

Interface tip seal 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 selected for the tune file (looking for wrong ions)

Summary of Contents for 5973 MSD

Page 1: ...H Hardware Manual HP 5973 MSD PCI NCI ...

Page 2: ...9A CI turbo pump Manual Conventions Cautions Cautions call attention to procedures which if not correctly performed or adhered to could result in damage to the instrument Warnings Warnings call attention to procedures which if not correctly performed or adhered to could result in personal injury Part Numbers In this manual Hewlett Packard part numbers are generally listed in parentheses after the ...

Page 3: ... 3 Chemical Ionization Theory Chemical ionization overview 22 Positive CI theory 24 Negative CI theory 30 Chapter 4 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 t...

Page 4: ...er 6 Troubleshooting Troubleshooting tips and tricks 69 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 ...

Page 5: ...ethane 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 Parts GC MSD interface parts 106 CI ion source parts 108 Flow control module parts 110 Ferrules 112 Miscellaneous parts 113 ...

Page 6: ...6 ...

Page 7: ...1 General Information Specifications 9 Reagent gases and regulators 10 ...

Page 8: ...ses perfluoro 5 8 dimethyl 3 6 9 trioxidodecane PFDTD as a calibrant and methane as the reagent gas Chapter 1 provides a list of the CI performance specifications and a list of reagent gases Chapter 2 presents some basics of the theory of chemical ionization and the advantages it offers Chapter 3 describes the CI hardware components and their functions Chapter 4 provides instructions for using CI ...

Page 9: ...I 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 Negative CI 500 1 RMS for 1 µl of 1 pg µl Octafluoronapthalene m z 272 0 Sensitivity SIM Positive CI 10 1 RMS for 1 µl of 100 fg µl Benzophenone m z 183 1 Negative CI 10 1 RMS for 1 µl of 1 fg µl Octafluoronapthalene m z 272 0 N O T E Installation does not include de...

Page 10: ... products that are appropriate for the purpose A gas purifier G1999 80410 is needed for use with methane and isobutane it cannot be used with ammonia A separate purifier is necessary for each gas supply Methane required Lecture bottle 0 06 m 3 56 liters UHP 99 97 Regulator 3320 Stand model J05 Swagelok female connector SS 200 7 2 Isobutane optional Lecture bottle 0 17 kg instrument 99 5 purity Reg...

Page 11: ...2 Hardware Reference Description 12 CI ion source 14 Reagent gas flow control module 16 EI CI GC MSD interface CI interface 20 ...

Page 12: ...ly optimized Special seals along the flow path of the reagent gas and very small openings in the source ensure that all the source gases stay in the source long enough for the appropriate chemical reactions to occur The CI interface has special plumbing for reagent gas The interface can be used for both EI and CI operation A spring loaded insulating seal fits onto the tip of the interface to seal ...

Page 13: ... Hardware Reference 13 ...

Page 14: ...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 CI interface tip The seal for the interface tip ensures a leak tight seal and electrical isolation between the CI interface and ion source Large slots in the drawout cylinder and ion source body provide enhanced pumpout for the ion source opt...

Page 15: ...5 CI ion focus lens CI drawout cylinder CI ion source body CI lens insulator CI drawout plate Entrance lens CI repeller CI repeller insulator CI source heater assembly CI interface tip seal CI filament Setscrew Dummy filament CI lens ...

Page 16: ... through the control panel on the front Gas A must be plumbed with Methane Gas B can be plumbed with any other reagent gas Operation of the flow module is through the control panel on the front Each button on the control pane has an LED light next to it When that button is active the light is on Gas A or Gas B opens the chosen gas select valve Only one can be open at a time Gas Off closes the gas ...

Page 17: ...n software and opens automatically during CI autotune or manual tuning allowing PFDTD to diffuse into the ion source The isolation valve prevents contamination of the flow control module by atmosphere while the MSD is vented or by PFTBA during EI operation Reagent gas select valve Mass flow controller Rear flow module cover Flow control board under Isolation valve CI calibration valve Reagent gas ...

Page 18: ...and the light for the selected gas will stop flashing and stay on When the MSD is turned off all valves are closed and all lights are off At startup all valves are closed and all lights are off except Gas Off The flow control board remembers the flow setting for each gas When either gas is selected the control board automatically sets the same flow that was used for that CI ion source Gas A Methan...

Page 19: ...Standby vented or EI mode Control panel lights LEDs Gas A green On Off On Off Off Off Gas B amber Off On Off On Off Off Purge red Off Off On On On Off Gas Off red Off Off Off Off On On Valve state Valve A Open Closed Open Closed Closed Closed Valve B Closed Open Closed Open Closed Closed MFC On setpoint On setpoint On 100 On 100 On 100 Off 0 Isolation valve Open Open Open Open Open Closed ...

Page 20: ...nds into the ionization chamber A spring loaded seal keeps reagent gases from leaking out around the tip The reagent gas is plumbed into the interface body and mixes with carrier gas and sample in the ion source This interface is also used for EI operation in CI MSDs Interface tip seal CI interface weldment CI interface cover Vacuum manifold CI interface insulator Heater sensor cable CI interface ...

Page 21: ... 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 ...

Page 22: ... energy and is much more gentle than electron ionization Since CI results in much less fragmentation CI spectra usually show high abundance of the molecular ion For this reason CI is often used to determine the molecular weights of sample compounds Methane is the most common CI reagent gas It yields certain characteristic ionization patterns Other reagent gases yield different patterns and may res...

Page 23: ...tion 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 E A Stemmler R A Hites Electron Capture Negative Ion Mass Spectra of Environmental Contaminants and Related Compounds VCH Publishers New York NY 1988 ISBN 0 89573 708 6 ...

Page 24: ...s fragmentation Because of the high background from the reagent gas ions PCI is not especially sensitive and detection limits are generally high There are four fundamental ionization processes that take place during positive chemical ionization at ion source pressures in the 0 8 2 0 Torr range These are Proton transfer Hydride abstraction Addition Charge exchange Depending on the reagent gas used ...

Page 25: ... Chemical Ionization Theory 3RVLWLYH WKHRU 25 ...

Page 26: ...es can be defined according to the reaction B H BH where the proton affinities are expressed in kcal mole Methane s proton affinity is 127 kcal mole The following tables list the proton affinities of several possible reagent gases and of several small organic compounds with various functional groups The mass spectrum generated by a proton transfer reaction depends on several criteria If the differ...

Page 27: ...ds for PCI Molecule Proton affinity kcal mole Molecule Proton affinity kcal mole Acetaldehyde 185 Methyl amine 211 Acetic acid 188 Methyl chloride 165 Acetone 202 Methyl cyanide 186 Benzene 178 Methyl sulfide 185 2 Butanol 197 Methyl cyclopropane l80 Cyclopropane 179 Nitroethane 185 Dimethyl ether 190 Nitromethane 180 Ethane 121 n Propyl acetate 207 Ethyl formate 198 Propylene 179 Formic acid 175 ...

Page 28: ...both hydride abstraction from the hydrocarbon chain and proton transfer to the ester function occur In the methane PCI spectrum of methyl stearate for example the MH peak at m z 299 is created by proton transfer and the M 1 peak at m z 297 is created by hydride abstraction Addition For many analytes proton transfer and hydride abstraction chemical ionization reactions are not thermodynamically fav...

Page 29: ...that do not react chemically with the analyte Each of these reagent gases once ionized has a recombination energy expressed as X e X or simply the recombination of the ionized reagent with an electron to form a neutral species If this energy is greater than the energy required to remove an electron from the analyte then the first reaction above is exothermic and thermodynamically allowed Charge ex...

Page 30: ...en referred to as the buffer gas When the reagent gas is bombarded with high energy electrons from the filament the following reaction occurs Reagent gas e 230eV Reagent ions e thermal If the reagent gas is methane the reaction is CH 4 e 230eV CH 4 2e thermal The thermal electrons have lower energy levels than the electrons from the filament It is these thermal electrons that react with the sample...

Page 31: ... Chemical Ionization Theory 1HJDWLYH WKHRU 31 ...

Page 32: ...e molecule and the electron is a thermal slow electron generated by the interaction between high energy electrons and the reagent gas In some cases the MX radical anion is not stable In those cases the reverse reaction can occur MX MX e The reverse reaction is sometimes called autodetachment This reverse reaction generally occurs very quickly Thus there is little time for the unstable anion to be ...

Page 33: ...s superficially similar to dissociative electron capture The ion pair formation reaction is represented by the equation MX e thermal M X e As with dissociative electron capture the sample molecule fragments Unlike dissociative electron capture however the electron is not captured by the fragments Instead the sample molecule fragments in such a way that the electrons are distributed unevenly and po...

Page 34: ...34 ...

Page 35: ...he 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 mode The following topics are covered in this chapter Venting and pumping down the CI MSD Installing the GC column in the CI interface Installing the CI ion source Installing the CI interface tip seal Switching between operating modes The following chapter provides information on setting up the software and operating the CI MSD in CI mode ...

Page 37: ...verify that the GC MSD system is performing correctly Make sure the carrier gas plumbing and GC have no air leaks EI mode Make sure the MSD vacuum system has no air leaks Make sure the reagent gas inlet line s are equipped with gas purifiers not applicable for ammonia Use extra high purity reagent gases 99 97 or better for methane and as pure as is available for other reagent gases ...

Page 38: ...re will prompt you when it is safe to switch off the power W A R N I N G I RX DUH XVLQJ K GURJHQ DV D FDUULHU JDV WKH FDUULHU JDV IORZ PXVW EH RII EHIRUH WXUQLQJ RII IRUHOLQH SXPS WR SUHYHQW K GURJHQ IURP DFFXPXODWLQJ LQ WKH 06 5HDG WKH GURJHQ DUULHU DV 6DIHW XLGH EHIRUH RSHUDWLQJ WKH 06 ZLWK K GURJHQ FDUULHU JDV C A U T I O N Be sure the GC oven and the MSD are cool before turning off carrier gas...

Page 39: ...this procedure CI analyzer cover 1 UDVS WKH IURQW RI WKH DQDO HU FRYHU DQG OLIW XS HQRXJK WR GLVHQJDJH WKH IURQW ODWFK 2 5HDFK EDFN DQG JUDVS WKH EDFN HGJH RI WKH DQDO HU FRYHU 3 3XOO IRUZDUG WR GLVHQJDJH WKH VSULQJ ODWFK It may take a firm pull to disengage the latch To replace the cover reverse the above steps Side cover 4 5HPRYH WKH DQDO HU FRYHU 5 5HPRYH WKH 7RU 7 VFUHZV WKDW KROG WKH 06 VLGH ...

Page 40: ... pump speed up to 80 The turbo pump speed should eventually reach 95 If the MSD does not pump down correctly see the manual or online help for information on troubleshooting air leaks and other vacuum problems 5 The software will prompt you to turn on the GC MSD interface heater and GC oven Click OK when you have done so 6 RDG WKH WXQH ILOH PCICH4 U LI RX DUH UXQQLQJ LQ PRGH RU ATUNE U LI RX DUH U...

Page 41: ... Purge DQG YHULI WKDW WKH Gas A DQG Purge OLJKWV DUH RQ 12 9HULI WKDW PCICH4 U LV ORDGHG DQG DFFHSW WKH WHPSHUDWXUH VHWSRLQWV 13 6HW WKH 06 LQWHUIDFH WR 14 3XUJH IRU DW OHDVW RQH KRXU 15 3UHVV WKH Purge EXWWRQ WR WXUQ RII Purge 16 6HW Gas A WR 17 HW V VWHP EDNH RXW IRU DW OHDVW KRXUV RU EHVW 1 VHQVLWLYLW EDNH RXW RYHUQLJKW 8 7 2 1 Do not turn on any heated zones until carrier gas flow is on Heatin...

Page 42: ... FROXPQ LQWR WKH DGMXVWPHQW WRRO 2 7ULP DERXW FP IURP WKH HQG RI WKH FROXPQ 3 3XOO WKH FROXPQ EDFN XQWLO WKH WLS RI WKH FROXPQ LV HYHQ ZLWK WKH HQG RI WKH WRRO RU H WHQGV OHVV WKDQ RQH PP SDVW WKH HQG The column should not extend more than 1 mm past the tip of the adjustment tool 4 8VLQJ WZR LQFK ZUHQFKHV WLJKWHQ WKH QXW Tighten only enough so that the column does not slip in the ferrule if tugged...

Page 43: ...setup 7R LQVWDOO WKH FROXPQ LQ WKH 06 LQWHUIDFH 43 Adjustment tool Interface column nut Column Interface ferrule 0 to 1 mm Vacuum manifold Column CI interface tip seal Reagent gas inlet Interface column nut ...

Page 44: ... LRQ VRXUFH 7 3ODFH WKH LRQ VRXUFH DQG LQWHUIDFH WLS VHDO LQ WKH LQ WKH LRQ VRXUFH VWRUDJH ER 8 3XPS GRZQ WKH 06 6HH SDJH C A U T I O N Always wear clean gloves while touching the analyzer or any other parts that go inside the vacuum manifold 8 7 2 1 Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components Wear a grounded anti stati...

Page 45: ...XUFH 4 QVWDOO WKH LRQ VRXUFH 6HH SDJH 5 QVWDOO WKH LQWHUIDFH WLS VHDO 6HH SDJH 6 ORVH WKH DQDO HU 7 3XPS GRZQ WKH 06 6HH SDJH 8 7 2 1 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 t...

Page 46: ...PP ILODPHQW UHSHOOHU DQG ILODPHQW ZLUHV 5 RQQHFW WKH EOXH ZLUH WR WKH HQWUDQFH OHQV SLQ DQG WKH RUDQJH ZLUH WR WKH LRQ IRFXV OHQV SLQ 6 RQQHFW WKH KHDWHU DQG VHQVRU FDEOHV 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 o...

Page 47: ...LQVWDOO WKH LRQ VRXUFH 47 CI ion source body Source heater and sensor cables CI GC MSDinterface tip CI interface tip seal CI source heater assembly Ion focus lens pin CI interface cover CI filament Entrance lens pin ...

Page 48: ...ed correctly the analyzer can be closed all the way with no resistance except the spring tension from the interface tip seal 6 RX FDQ DOLJQ WKH DQDO HU DQG LQWHUIDFH E ZLJJOLQJ WKH VLGHSODWH RQ LWV KLQJH If the analyzer still won t close contact your Hewlett Packard service representative The figure opposite shows the alignment of the interface tip seal and CI ion source C A U T I O N Electrostati...

Page 49: ... 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 To monitor high vacuum pressure 62 To use other reagent gases 64 ...

Page 50: ...ure in the CI source Checking for air leaks PCI and NCI autotunes Verify sensitivity performance Tuning macros beginning tune files and menus for CI operation are included with the updated ChemStation software The software provides instructions for setting the reagent gas flow and for performing CI autotunes Autotunes are provided for PCI with methane reagent gas and for NCI with any reagent gas N...

Page 51: ...pole temperature to 106 C for both modes Set the GC MSD interface temperature to 320 C for PCI and 280 C for NCI Start the system in PCI mode first By bringing the system up in PCI mode first you will be able to do the following Check the interface tip seal by looking at the m z 28 to 27 ratio in the methane flow adjust panel Tell if a gross air leak is present by monitoring the ions at m z19 wate...

Page 52: ...YHU EHHQ UXQ IRU WKLV WXQH ILOH WKH VRIWZDUH ZLOO SURPSW RX WKURXJK D VHULHV RI GLDORJ ER HV FFHSW WKH GHIDXOW YDOXHV XQOHVV RX KDYH D YHU JRRG UHDVRQ IRU FKDQJLQJ DQ WKLQJ The tune values have a dramatic effect on MSD performance Always start with the default values when first setting up for CI and then make adjustments for your specific application See the table below for default values for the ...

Page 53: ...50 Max electron energy eV 240 240 N Ac 240 N Ac 240 a Always set up in PCI with methane first then switch to your desired ion polarity and gas b Adjust higher or lower to get desired signal abundance Higher signal abundance also gives higher noise abun dance This is adjusted for data acquisition by setting the EMV in the method c There are no PFDTD ions formed in PCI with any reagent gas but metha...

Page 54: ...RP WKH 6HWXS PHQX The methane pretune tunes the instrument for optimum monitoring of the methane reagent ion m z 28 27 ratio 5 DPLQH WKH GLVSOD HG SURILOH VFDQ RI WKH UHDJHQW LRQV Make sure there is no visible peak at m z 32 A peak there indicates an air leak If such a peak is present find and repair the leak before proceeding Operating in the CI mode with an air leak will rapidly contaminate the ...

Page 55: ... IORZ 55 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: ... must be baked out for at least 2 hours before tuning Longer bakeout is recommended before running samples for optimal sensitivity Default starting CI tune parameters Reagent gas Methane Isobutane Ammonia EI Ion polarity Positive Negative Positive Negative Positive Negative N A Emission 150 µΑ 50 µΑ 150 µΑ 50 µΑ 150 µΑ 50 µΑ 35 µΑ Electron energy 150 eV 150eV 150eV 150eV 150eV 150eV 70 Filament 1 ...

Page 57: ... RQO 57 To perform a positive CI autotune methane only 1 RDG WKH PCICH4 U WXQH ILOH FFHSW WKH GHIDXOW VHWWLQJV 2 3HUIRUP PHWKDQH VHWXS 6HH SDJH 3 8QGHU WKH 7XQH PHQX FOLFN CI Autotune There are no tune performance criteria If autotune completes it passes ...

Page 58: ...WXQH ILOH IRU WKH UHDJHQW JDV RX DUH XVLQJ Accept the default temperature and other settings 2 I RX GRQªW DOUHDG KDYH DQ 1 WXQH ILOH IRU RXU UHDJHQW JDV FOLFN Select Reagent Gas XQGHU WKH 6HWXS PHQX DQG FOLFN RQ WKH JDV RX DUH XVLQJ 3 8QGHU WKH 7XQH PHQX FOLFN CI Autotune There are no tune performance criteria If autotune completes it passes ...

Page 59: ... Benzophenone 100 pg µl 8500 5440 1 9HULI WKDW WKH 3 8 WXQH ILOH LV ORDGHG 2 2Q WKH IORZ FRQWURO SDQHO WXUQ Purge RII DQG VHW Gas A WR IORZ 3 Q 0DQXDO 7XQH YLHZ SHUIRUP VHWXS 6HH SDJH 4 5XQ CI Autotune 6HH SDJH 5 5XQ WKH 3 VHQVLWLYLW PHWKRG 1 B3 0 XVLQJ µO RI SJ µO HQ RSKHQRQH 6 9HULI WKDW 6 1 506 ...

Page 60: ...8 WXQH ILOH DQG DFFHSW WKH WHPSHUDWXUH VHWSRLQWV 3 7XUQ Purge DQG Gas A RQ DQG OHW WKH V VWHP VWDELOL H IRU PLQXWHV 4 7XUQ Purge RII DQG VHW Gas A WR IORZ 5 Q 0DQXDO 7XQH YLHZ UXQ CI Autotune 6HH SDJH Note that there are no criteria for a passing Autotune in CI If the Autotune completes it passes 6 5XQ WKH 1 VHQVLWLYLW PHWKRG 2 1B1 0 XVLQJ µO RI SJ PO 2 1 7 9HULI WKDW 6 1 506 ...

Page 61: ...flows Gas B flows Purge with Gas A Purge with Gas B Pump out flow module Standby vented or EI mode Control panel lights LEDs Gas A green On Off On Off Off Off Gas B amber Off On Off On Off Off Purge red Off Off On On On Off Gas Off red Off Off Off Off On On Valve state Valve A Open Closed Open Closed Closed Closed Valve B Closed Open Closed Open Closed Closed MFC On setpoint On setpoint On 100 On ...

Page 62: ...nk The triode gauge tube can measure pressures between approximately 8 10 3 and 3 10 6 Torr The gauge controller is calibrated for nitrogen but all pressures listed in this manual are for helium The largest influence on operating pressure is the carrier gas column flow The following table lists typical pressures for various helium carrier gas flows These pressures are approximate and will vary fro...

Page 63: ... PCI temperatures Familiarize yourself with the measurements on your system under operating conditions and watch for changes that may indicate a vacuum or gas flow problem Source temperature 250 C Quad temperature 106 C Interface temperature 320 C Helium carrier gas flow 1ml min MFC Pressure Torr Methane Isobutane Ammonia 10 5 6 10 5 6 5 10 5 4 7 10 5 15 7 7 10 5 9 2 10 5 6 7 10 5 20 9 8 10 5 1 2 ...

Page 64: ...ent gas It radically shortens the life span of the filament N O T E Not all setup operations can be performed in all modes with all reagent gases See the following table for details Reagent gas mode Reagent ion masses Flow adj ions Ratio PFDTD Calibrant ions Methane PCI 17 29 41a a There are no PFDTD ions formed with any reagent gas but methane Tune with methane and use the same parameters for the...

Page 65: ...oton affinities ammonia chemical ionization spectra often result from the addition of NH 4 and then in some cases from the subsequent loss of water Ammonia reagent ion spectra have principal ions at m z 18 35 and 52 corresponding to NH 4 NH 4 NH 3 and NH 4 NH 3 2 To adjust your MSD for isobutane or ammonia chemical ionization use the following procedure 1 3HUIRUP D VWDQGDUG 3RVLWLYH DXWRWXQH ZLWK ...

Page 66: ... 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 Always keep the ammonia tank in an upright position Coil the ammonia supply tubing into several vertical loops by wrapping the tubing ar...

Page 67: ...s 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 Large peak at m z 19 85 Peak at m z 32 86 Tuning related symptoms overview 87 Reagent gas ion ratio is difficult to adjust or unstable 88 High electron multiplier voltage 89 Can not complete autotune 90 Pe...

Page 68: ... air and air leaks that cause no problems in PCI can destroy NCI sensitivity As with EI if the MSD tunes well and no air leak is present sample sensitivity problems should be addressed by GC injection port 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 bake out time has e...

Page 69: ...aded in memory is it the appropriate file for your mode of operation Rule 2 If complex isn t 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 and all those additional parts If you re having trouble with NCI verify that PCI still works If you re having trou...

Page 70: ...elium so these measurements are not accurate in absolute terms but are intended as a guide to typical observed readings They were taken with the following set of conditions Source temperature 250 C Quad temperature 106 C Interface temperature 320 C Helium carrier gas flow 1ml min MFC Pressure Torr Methane Isobutane Ammonia 10 5 6 10 5 6 5 10 5 4 7 10 5 15 7 7 10 5 9 2 10 5 6 7 10 5 20 9 8 10 5 1 2...

Page 71: ...ance of m z 19 to be decreasing There should not be any peak visible at m z 32 O2 This almost always indicates an air leak Special negative CI notes Since NCI is so extremely sensitive air leaks that are not detectable in EI or PCI can cause sensitivity problems in NCI To check for this kind of air leak in NCI inject OFN The base peak should be at m z 272 If the abundance of m z 238 is much greate...

Page 72: ...or one use only 4 Remember that most small air leaks visible in CI mode are located in either the carrier gas or reagent gas flow paths Leaks into the vacuum manifold are not likely to be seen in CI because of the higher pressure inside the ionization chamber 5 Half split the system By closing valves starting at the gas select valves Gas Off and Purge turned on then moving farther downstream to th...

Page 73: ...w module state diagram Result Gas A flows Gas B flows Purge with Gas A Purge with Gas B Pump out flow module Standby vented or EI mode Control panel lights LEDs Gas A green On Off On Off Off Off Gas B amber Off On Off On Off Off Purge red Off Off On On On Off Gas Off red Off Off Off Off On On Valve state Valve A Open Closed Open Closed Closed Closed Valve B Closed Open Closed Open Closed Closed MF...

Page 74: ...solute terms 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 106 C Interface temperature 320 C Helium carrier gas flow 1ml min MFC Pressure Torr Methane Isobutane Ammonia 10 5 6 10 5 6 5 10 5 4 7 10 5 15 7 7 10 5 9 2 10 5 6 7 10 5 20 9 8 10 5 1 2 10 4 8 5 10 5 25 1 2 10 4 1 4 10 4 1 0 10 4 30 1...

Page 75: ... indicates air in the system Check for and correct any leaks See the Leaks section at the beginning of this chapter Possible Cause The foreline pump is not working properly Action Replace the pump oil If that does not help it may be necessary to replace the pump Contact your local Hewlett Packard Customer Engineer Possible Cause The turbo pump is not working properly Action Check the pump speed It...

Page 76: ...at reagent ion ratios are correct See page 54 Possible Cause Air leak Action Run Methane Pre tune See page 54 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 Possible Cause Interface tip seal wasn t installed Action Check the source storage box If the seal is not in the box vent the MSD and verify that the se...

Page 77: ...butane or ammonia Possible Cause The valve on the reagent gas bottle is closed Action Check and if necessary open the valve on the reagent gas bottle Possible Cause The reagent gas supply is empty Action Check and if necessary replace the reagent gas supply Possible Cause Reagent lines kinked bent pinched or disconnected Action Inspect the reagent lines and repair any defects Check especially to m...

Page 78: ... are generally 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 or low reagent gas signal See page 81 No or low PFDTD signal See page 83 Excessive noise See page 84 Low chromatographic signal abundance See page 84 Low signal to noise ratio Large...

Page 79: ... file corrupted Wrong ion polarity there are no reagent ions visible in NCI No reagent gas flow look for background ions and 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 74 If MSD was recently switched from EI to CI Interface tip seal not installed No reagent gas flow Analyzer not sealed big air...

Page 80: ...gent gas path No reagent gas peaks in NCI Reagent gases do not ionize in NCI look for background ions instead Verify tune parameters If no background ions are visible go back to methane PCI No PFDTD calibrant peaks in NCI Look for background ions Verify tune parameters Go back to methane PCI No sample peaks in NCI Look for background ions Go back to methane PCI Large peak at m z 283 in NCI OFN spe...

Page 81: ...Cause Ion polarity is set to Negative No reagent gas ions are formed in NCI Action Switch to Positive ionization mode Possible Cause The reagent gas flow is set too low Action Increase the reagent gas flow Possible Cause Reagent gas supply tubing is blocked kinked pinched or disconnected Action Inspect and if necessary repair or replace the reagent gas supply tubing Possible Cause Wrong filament w...

Page 82: ...e filament If necessary realign the filament support arms Possible Cause The electron inlet hole is blocked Action Inspect the electron inlet hole If necessary clean the hole with the supplied 0 016 inch drill bit If the electron inlet hole is that dirty the entire ion source probably needs to be cleaned See the Maintenance chapter in this manual for more information Possible Cause Ion source wire...

Page 83: ...cm from the top of the vial Possible Cause The pressure of the methane entering the flow controller is too high Action Make sure the regulator on the methane supply is set to 10 psig 70 kPa Possible Cause The CI ion source is dirty Action Clean the ion source See the Maintenance chapter in this manual for more information Possible Cause The calibration valve was not purged after the vial was refil...

Page 84: ...an the ion source See the Maintenance chapter in this manual for more information Possible Cause Poor vacuum Action Check the pressure on the high vacuum gauge controller Possible Cause Air leak Action Run Methane Pre tune in PCI 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 Possible Cause Saturated methane i...

Page 85: ...t vented Action Bake out the system as described in the Maintenance chapter of this manual Possible Cause Moisture left over in the reagent gas supply tubing and flow module Action Purge the reagent gas supply lines for at least 60 minutes See the Maintenance chapter Possible Cause Contaminated reagent gas supply Action Replace the reagent gas supply and purge the lines and flow module Possible Ca...

Page 86: ...he Maintenance chapter of this manual Possible Cause Air leak Action Check for leaks and correct any that you find See the Leaks section at the end of this chapter for more information After all leaks have been corrected clean the ion source Possible Cause Contaminated reagent gas supply Suspect this if you have recently replaced your gas tank and you have ruled out air leaks Action Replace the re...

Page 87: ...ing 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 High electron multiplier voltage Can not complete autotune Peak widths are unstable Split peaks during autotune Incorrect m z 70 abundance in tune report ...

Page 88: ... in the system Check for and correct any leaks See the Leaks section at the beginning of this chapter Possible Cause The reagent gas supply is at the wrong pressure Action Check the regulator on the reagent gas supply It should be adjusted to 20 psi 140 kPa Possible Cause A leak in the reagent gas delivery path This is especially likely if you have set the methane flow much higher than normal and ...

Page 89: ...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 Action Replace the filament Possible Cause The analyzer is not at the proper operating temperature Action Verify the ion source and quadrupole temperatures The default source temperatur...

Page 90: ... The correct ratio should be between 1 5 and 5 0 Action If the ion ratio is incorrect adjust it See page 54 Possible Cause The CI ion source is dirty Action Clean the ion source See the Maintenance chapter in this manual for more information Possible Cause Too much air or water in the system Action See the Leaks section of this chapter for more information After eliminating these problems clean th...

Page 91: ... CI ion source is dirty Action Clean the ion source See the Maintenance chapter of this manual for more information Possible Cause Air leak Action Run Methane Pre tune in PCI 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 After eliminating all air leaks clean the ion source ...

Page 92: ...92 ...

Page 93: ...imize 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 ...

Page 94: ...cleaning The primary effect of operating the MSD in CI mode is the need for more frequent ion source cleaning In CI operation the ion source chamber is subject to more rapid contamination than in EI operation because of the higher source pressures required for CI Ammonia CI increases the need for foreline pump maintenance Ammonia when used as a reagent gas it will also change the maintenance requi...

Page 95: ...lytical performance be your guide Cleaning procedure Cleaning the CI ion source is very similar to cleaning the EI ion source Use the cleaning procedure in the chapter Maintaining the MSD of the HP 5973 MSD Hardware Manual with the following exceptions The CI ion source may not look dirty but deposits left by chemical ionization are very difficult to remove Clean the CI ion source thoroughly Use a...

Page 96: ...one hour You can continue to run samples while the pump is ballasting 4 Close the ballast valve Leaving the ballast valve open all the time will result in loss of pump oil and damage to the pump C A U T I O N Only perform this procedure if the pump is at normal operating temperature The water in the air can cause condensation of the ammonia at the ballast valve if the pump is cold Ballast control ...

Page 97: ...d metal of its oxygen and moisture traps 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 filter 5 Purge the new fi...

Page 98: ... calibrant 8500 8130 8 Replace the vial and tighten the nut 9 Reposition the MSD next to the GC 10 Reinstall the capillary column 11 Pump down the MSD See page 40 12 Purge the calibration valve See page 99 C A U T I O N Do not rinse the vial with any solvents Never expose the inside of the vial to chlorinated solvents or isopropyl alcohol or water this will result in severe loss of CI sensitivity ...

Page 99: ...n it off 2 Turn on Gas A 3 Turn on Purge 4 In Diagnostics and Vacuum Control view select Purge Cal Valve under the Vacuum menu This will open the CI calibration valve for several minutes with all analyzer voltages turned off C A U T I O N After removing the calibrant vial you must purge the calibration valve Failure to do so will result in severe contamination of the ion source and damage to the e...

Page 100: ...troller 3 Connect the power cord to the gauge controller 4 Connect the other end of the power cord to an appropriate electrical outlet 5 Pump down the MSD W A R N I N G 1HYHU FRQQHFW RU GLVFRQQHFW WKH FDEOH IURP WKH WULRGH JDXJH WXEH ZKLOH WKH 06 LV XQGHU YDFXXP 5LVN RI LPSORVLRQ DQG LQMXU GXH WR EURNHQ JODVV H LVWV W A R N I N G 1HYHU FRQQHFW RU GLVFRQQHFW WKH FDEOH IURP WKH WULRGH JDXJH WXEH ZKL...

Page 101: ... Maintenance 7R FRQQHFW WKH YDFXXP JDXJH FRQWUROOHU 101 Triode gauge tube Triode gauge cable Triode gauge cable Gauge controller Power cord ...

Page 102: ...instructions on the label 3 Connect one end of the tubing to a supply of clean dry nitrogen and turn on 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 purifier label W A R N I...

Page 103: ...8 Parts GC MSD interface parts 106 CI ion source parts 108 Flow control module parts 110 Miscellaneous parts 113 ...

Page 104: ...r the MSD can be found in the Parts chapter of the 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 Serial number of your CI flow module HP part number s of the part s needed Quantity of each part needed ...

Page 105: ... listed in this chapter check the Hewlett Packard Analytical Supplies Catalog or the on line catalogue on the worldwide web at http www dmo hp com cagcat pub HOME htm If you still cannot find it contact your Hewlett Packard service representative or your Hewlett Packard office ...

Page 106: ...y 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 0515 0380 Welded interface G1999 60401 Interface tip seal G1999 60412 Vespel blank 5181 3308 ...

Page 107: ...G1999 00405 Vacuum manifold CI interface insulation G1999 20401 Heater sensor assembly G1099 60107 CI heater clamp G1999 20410 CI interface tip seal G1999 60412 CI ionization chamber Screws for heater clamp 0515 0383 Screws to attach interface to manifold Interface O ring 0905 1405 ...

Page 108: ...terface tip seal G1999 60412 CI ion focus lens G1999 20443 CI lens insulators set G1999 20445 CI repeller G1999 20432 CI repeller insulator G1999 20433 CI source body G1999 20430 CI source heater assembly G1999 60414 Dummy filament G1999 60454 Entrance lens 05971 20126 Screw skt hd cap for mounting filaments G1999 20021 Setscrew for mounting heater and lens stack G1999 20021 Screw M3 X 4L socket h...

Page 109: ...I ion source body CI lens insulator set CI draw out plate Entrance lens 05971 20126 CI repeller G1999 20432 CI repeller insulator CI source heater assembly CI interface tip seal G1999 60412 CI filament G1099 80053 Setscrew 0515 1446 Dummy filament CI lens insulator set ...

Page 110: ...ve G1999 80402 Mass flow controller cable G1999 60464 Reagent gas select valve G1999 80401 VCR gasket 1 4 inch with retainer one use only 0100 1436 VCR gasket 1 8 inch one use only 0100 0468 CI analyzer cover G1999 60440 Front flow module cover G1999 20422 Methane isobutane gas purifier G1999 80410 Reagent gas supply tubing stainless steel 1 8 inch 7157 0210 Rear flow module cover G1999 00411 Swag...

Page 111: ... 80401 Mass flow controller 0101 1006 Rear flow module cover G1999 00411 Front flow module cover G1999 20422 CI analyzer cover G1999 60440 Calibration valve assembly G1999 60456 Reagent gas supply tubing 7157 0210 Display module G1999 65461 Isolation valve G1999 80402 ...

Page 112: ... 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 5062 3538 Injection port 0 27 mm id 90 Vespel 10 graphite for 0 10 mm id columns 5062 3518 0 37 mm id 90 Vespel 10 graphite for 0 20 mm id columns 5062 3516 0 40 mm id 90 Vespel 10 graphite for 0 25 mm id columns 5181 3323 0 47 mm id 90 Vespel 10 graphite for 0 32 mm id columns 5062 3514 0 7...

Page 113: ...00 5441 PFDTD calibrant 8500 8130 Powder alumina 8660 0791 Reagent gas line 20 ft 1 8 ID stainless steel cleaned 7157 0210 Wipes industrial 300 package 9310 4828 Swagelok fittings for gas purifier and inlet to flow module Ferrule front for 1 8 inch tubing 20 package 5180 4110 Ferrule rear for 1 8 inch tubing 20 package 5180 4116 Nut for 1 8 inch tubing 20 package 5080 8751 Nut and both front and r...

Page 114: ...114 ...

Page 115: ...verview 22 references 23 water contamination 22 ChemStation using to pump down the MSD 40 using to set up methane reagent gas flow 54 using to vent the MSD 38 CI autotune 56 Methane PCI only 57 CI calibrant vial refilling 98 CI calibration valve 17 purging 99 CI filament 14 CI interface heater clamp 20 installing a GC column 42 tip seal 14 CI interface tip seal installing 48 CI ion source cleaning...

Page 116: ...e from ammonia 96 G Gases reagent See Reagent gas Gauge controller abnormal or blank display 62 connecting 100 connecting to the triode gauge tube 100 indicated vs actual pressure 62 monitoring pressure with 62 pressure range 62 Gauge tube See Triode gauge tube GC column installing in the CI interface 42 GC MSD interface CI 20 tip seal 20 GC MSD interface See CI interface H Hardware Reference 11 H...

Page 117: ...58 buffer gas 30 dissociative electron capture 33 effect of contamination 32 electron capture 32 ion pair formation 33 ion molecule reactions 33 sensitivity 32 theory 30 thermal electrons 30 Noise declaration inside front cover P Part numbers inside front cover See also Parts Parts 103 CI interface 106 CI ion source 108 ferrules 112 flow control module 110 GC MSD interface 106 miscellaneous 113 re...

Page 118: ...ng Specifications reagent gas purity 10 sensitivity 9 Startup See also Pumpdown methane pre tune showing acceptable levels of air and water 55 setting up methane flow 54 setting up the software for CI operation 52 too much air and water 55 State diagram reagent gas flow control module 19 61 Switching from CI to EI operating mode 44 from EI to CI operating mode 45 Symptoms of malfunctions can not c...

Page 119: ... CI specific problems 68 tips and tricks 69 Turn on See Pumpdown V Vacuum gauge controller connecting 100 monitoring pressure with 62 Vacuum manifold pressure monitoring 62 Valve CI calibration 17 gas select valves 16 isolation 17 VCR fittings 16 introducing leaks by loosening 72 Vent cycle See Venting Vent program See Venting Venting 38 Vial Calibrant caution against solvent use 98 caution to pur...

Page 120: ...120 ...

Page 121: ...o do other wise by this manual WARNING Excessive fluctuations in the line voltage can create a shock hazard and can damage the instrument Make sure the sup ply voltage does not fluctuate more than 5 or 10 from the rated voltage This equip ment must be installed in a Category II environment as defined in IEC664 Thermal Safety WARNING Many parts of the MSD operate at dangerously high tempera tures M...

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