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5973N MSD Hardware Manual

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1. 7 e gt ZS terf ket nterface socke ss on source body SSS aa EE O ring ORAS SS 0905 1405 many fA X 7 AE YT I I A Analyzer chamber aaa Screw a 0515 0380 gaan K Heater sensor assembly G1099 60107 nterface cover G1099 00005 nsulation G1099 20301 309 Table 21 12 Parts Consumables and maintenance supplies Consumables and maintenance supplies This section lists parts available for cleaning and maintaining your MSD Maintenance supplies Description Abrasive paper 30 um Alumina powder Cloths clean package of 300 Cloths cleaning package of 300 Cotton swabs package of 100 Diffusion pump fluid 2 required Foreline pump oil Inland 45 1 liter Gloves clean large small Grease Apiezon L high vacuum Paint touch up Glacier Gray One year maintenance kit Part number 9061 5896 8660 0791 05980 60051 9310 4828 5080 5400 6040 0809 6040 0834 8650 0030 8650 0029 6040 0289 6010 1497 9183 0296 360 12 Parts Consumables and maintenance supplies Table 22 Tools Description Part number Column installation tool G1099 20030 Tool kit G1099 60566 Ball drivers 1 5 mm 8710 1570 2 0 mm 8710 1804 2 5 mm 8710 1681 Hex nut driver 5 5 mm 8710 1220
2. See also A video demonstration of this procedure is on the 5973N MSD Maintenance CD ROM 201 Materials needed CAUTION CAUTION To lubricate the vent valve O ring Cloths clean 05980 60051 Gloves clean lint free large 8650 0030 small 8650 0029 Grease Apiezon L high vacuum 6040 0289 O ring vent valve 0905 1217 replace if the old O ring is worn or damaged The vent valve O ring needs a thin coat of lubrication to ensure a good vacuum seal and smooth operation If the vent valve O ring does not turn smoothly or does not seal correctly lubricate it using this procedure Vacuum seals other than the side plate O ring and vent valve O ring do not need to be lubricated Lubricating other seals can interfere with their correct function Vent the MSD See page 54 Completely remove the vent valve knob Inspect the O ring If the O ring appears damaged replace it 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 Excess grease can trap air and dirt Grease on surfaces of the O ring other than the exposed surface can trap air resulting in air spikes during operation 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 202 6 Maintaining the MSD To lubricate the vent valve O ring Front end plate
3. CAUTION To adjust the RF coils Screwdriver flat blade large 8730 0002 Make sure the MSD is at thermal equilibrium It takes at least 2 hours after all heated zones have reached their setpoints for the MSD to reach thermal equilibrium Remove the analyzer cover See page 52 Do not remove the side board cover the RF cover or any other covers Dangerous voltages are present under these covers Make sure the RF cover is secure and no screws are missing A loose RF cover or missing screw can significantly affect coil adjustment In the Diagnostics Vacuum Control view select Set RFPA from the Diagnostics menu Enter an amu value of 100 Slowly turn the RF coil adjustment screws to minimize the voltage displayed Turn the adjustment screws alternately Turn each screw only a little bit at a time Keep the screws at equal extension The minimum voltage is typically between 70 and 100 mV Do not use a coin to adjust the RF coils If you drop it it could fall into the electronics fan and cause significant damage When the voltage is minimized click the Stop button 240 6 Maintaining the MSD To adjust the RF coils RF coil adjustment screw RF coil adjustment screw 8 Repeat steps 4 through 7 for 650 amu The minimum voltage is typically between 500 and 650 mV 9 Exit the Set RFPA program 10 Select MS OFF from the Diagnostics menu 11 Reinstall the analyzer cover 12 Tune the
4. 153 Table 6 6 Maintaining the MSD Spare parts and supplies Description Abrasive paper Alumina abrasive powder Aluminum foil clean Beakers glass 50 ml and 500 ml Cloths clean lint free quantity 20 Container for catching old foreline pump oil 500 ml Cotton swabs quantity 100 Diffusion pump fluid Electron multiplier horn Filament assembly Foreline exhaust oil trap Foreline pump oil 1 liter Gloves chemical resistant resistant to oils and solvents clean lint free large clean lint free small Grease Apiezon L high vacuum Heater sensor assemblies GC MSD interface ion source mass filter Octafluoronaphthalene 1 pg u Perfluorotributylamine PFTBA certified 1 gram PFIBA sample kit Solvents reagent grade acetone methanol methylene chloride Triode gauge tube Ultrasonic bath Part number 9061 5896 8660 0791 05980 60051 9080 5400 6040 0809 05971 80103 05972 80053 61099 80037 6040 0834 8650 0030 8650 0029 6040 0289 61099 60107 G1099 60177 G1099 60172 8500 5441 8500 0656 05971 60571 0960 0897 154 WARNING 6 Maintaining the MSD Many parts of the MSD carry high voltages that are potentially dangerous Whenever the MSD is plugged in even if the power switch is off potentially dangerous voltage 120 V ac or 200 240 V ac exists on e The wiring and fuses between where the power cord enters the instrument and the power switch When the power switc
5. 3 Operating the CI MSD To use other reagent gases Ammonia CI Ammonia NH3 is commonly used for chemical ionization when less fragmenta tion is desired in the chemical ionization spectrum This is because the proton affinity of ammonia is higher than that of methane hence less energy is trans ferred in the ionization reaction Because many compounds of interest have insuf ficient proton affinities ammonia chemical ionization spectra often result from the addition of NH4 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 corre sponding to NH4 NH4 NH3 and NH4 NH3 9 To adjust your MSD for isobutane or ammonia chemical ionization use the follow ing procedure Perform a standard Positive CI autotune with methane and PFDTD Under the Setup menu click Select Reagent Gas and select Isobutane or Ammonia This will change the menus to use the selected gas and select appropriate default tune parameters Select a new tune file name or load an existing PCI tune file for the specific gas If you use an existing tune file be sure to save it with a new name if you don t want to over write the existing values Accept the default temperature and other set tings Turn Gas B on After the amber light stops flashing and the Purge light goes off set the gas flow to 20 Click Isobutane or Ammonia Flow Adjust on the Setup menu There is n
6. Vent valve O ring Vent valve knob 6 Reinstall the vent valve knob CAUTION Be very careful when reinstalling the vent valve knob It is very easy to cross thread the knob and damage the threads in the front end plate Be sure the O ring stays in place 7 Pump down the MSD See page 60 203 CAUTION WARNING Maintaining the analyzer The analyzer requires no periodic maintenance None of the analyzer components requires periodic maintenance Some tasks however must be performed when MSD behavior indicates they are necessary These tasks include e Cleaning the ion source e Replacing filaments e Replacing the electron multiplier horn Troubleshooting the MSD on page 93 provides information about symp toms that indicate the need for analyzer maintenance The troubleshooting material in the online help in the MSD ChemStation software provides more extensive information Care must be taken during analyzer maintenance to keep components clean Analyzer maintenance involves opening the analyzer chamber and removing parts from the analyzer During analyzer maintenance procedures care must be take to avoid contaminating the analyzer or interior of the analyzer chamber Clean gloves should be worn during all analyzer maintenance procedures After cleaning parts must be thoroughly baked out before they are reinstalled After cleaning analyze
7. Mounting screw HED ceramic don t touch HED high energy dynode High voltage HED wire Electron multiplier horn EMV electron multiplier voltage wire Detector focus wire HED feedthrough Rear side plate humbscrew 313 10 Analyzer Analyzer heaters and radiators CAUTION Analyzer heaters and radiators The ion source and mass filter are housed in cylindrical aluminum tubes called radiators The radiators control the distribution of heat in the analyzer They also provide electrical shielding for analyzer components The source heater and tem perature sensor are mounted in the source heater block The mass filter quad heater and temperature sensor are mounted on the mass filter radiator Analyzer temperatures can be set and monitored from the MSD ChemStation In selecting the temperatures to use consider the following e Higher temperatures help keep the analyzer clean longer e 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 equilib rium Data acquired sooner may not be reproducible Recommended settings for EI operation e Jon source 230 C e Quadrupole 150 C Do not exceed 200 C on the quadrupole or 250 C on the ion source The GC MSD interface ion source and mass filter quad heated zones
8. Under the Tune menu click Cl Autotune Avoid tuning unless absolutely necessary this will minimize PFDTD background noise and help prevent ion source contamination There are no tune performance criteria If autotune completes it passes If the tune sets the electron multiplier voltage EMVolts at or above 2600V however you may not be able to acquire data successfully if your method sets EMVolts to 400 or higher 82 NCI Methane Tune Instrument GC MS Instrument 1 Tue Sep 23 10 53 30 1997 3 Operating the Cl MSD To perform a negative Cl autotune any reagent gas C HPCHEM 1 5973 NCITUNE U Flow 40 Gas A Mass 185 10 Mass 351 00 Mass 449 00 Ab 513077 Ab 260962 Ab 12776 Ion Pol NEG MassGain 403 Pw50 0 62 Pw50 0 57 Pw50 0 61 o MassOffs 10 Emission 49 4 AmuGain 1433 EleEnergy123 7 AmuOffs 130 Filament 1 Wid219 0 032 DC Pol POS Repeller 3 99 IonFocus 149 0 HED ON EntLens 7 5 EMVolts 1765 EntOffs 19 58 Samples 8 PFDTD OPEN Averages 3 StepSize 0 10 zones MS Source 150 TurboSpd 100 MS Quad 106 a JA LAS T i ae A 182 187 348 353 446 451 Scan 175 00 700 00 Samples 8 Thresh 100 183 peaks Base 185 00 Abundance 434048 100 80 J 60 40 4 204 0 44 tt a qa 200 300 400 500 600 Mass Abund Rel Abund Iso Mass Iso Abund Iso Ratio 185 00 434048 100 00 186 00 14115 3 25 351 00 226560 52 20 352 00 13892 6 13 449 00 11096 2 56 450 00 11
9. e Distributes ac line power to the ac dc power supply the foreline pump and the turbo pump controller e Turns the calibration valve on or off as directed to by the main board e Provides the voltage for the calibration valve e Provides logic interface to turbo controller e Controls the diffusion pump Controls the foreline gauge Turns on the diffusion pump once the foreline pressure is low enough as directed by the main board Regulates the ac power to the diffusion pump heater Turns off the diffusion pump if the foreline pressure is too high or if the diffusion pump is too hot e Passes the foreline pressure signal from the foreline gauge or turbo pump speed and other vacuum status information to the main board e Turns off the foreline pump in case of a problem with pumpdown Turbo pump control The ac board sends control signals to and receives turbo pump status information from the turbo pump controller The turbo pump controller provides power to the turbomolecular pump and regulates pump speed If the pump fails to reach 80 speed within 7 minutes after beginning pumpdown or if the speed drops below 50 during operation the controller shuts off the turbo pump and the ac board shuts off the foreline pump Your MSD is equipped with one of two types of turbo controller e Integrated power supply and controller e Power supply and separate EXDC mini controller 326 11 Electronics AC board
10. e GC MSD interface e Analyzer parts e Vacuum pumps Never touch these parts while your MSD is on After the MSD is turned off give these parts enough time to cool before handling them The GC MSD interface heater is powered by the Thermal Aux 2 heated zone on the GC The interface heater can be on and at a dangerously high temperature even though the MSD is off The GC MSD interface is well insulated Even after it is turned off it cools very slowly The GC injection ports and GC oven also operate at very high temperatures Use the same caution around these parts See the documentation supplied with your GC for more information 156 WARNING WARNING 6 Maintaining the MSD Chemical residue is another potential danger Only a small portion of your 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 It will also contain tiny droplets of foreline pump oil An oil trap is supplied with the foreline pump This trap stops only pump oil droplets It does not trap any other chemicals If you are using toxic solvents or analyzing toxic chemicals do not use the oil trap Instead install a hose to take the exhaust from the foreline pump outdoors or into a fume hood vented to the outdoors Be sure to comply with
11. 229 Materials needed 6 Maintaining the MSD To replace the electron multiplier horn To replace the electron multiplier horn Electron multiplier horn 05971 80103 Gloves clean lint free large 8650 0030 small 8650 0029 Vent the MSD See page 54 Open the analyzer chamber See page 56 Open the retaining clip Pinch the two arms of the clip together and swing the clip down Remove the electron multiplier horn Install the new electron multiplier horn Close the retaining clip The signal pin on the horn should rest on the outside of the loop in the contact strip Do not put the signal pin on the inside of the loop in the contact strip Incor rect installation will result in poor sensitivity or no signal Close the analyzer chamber See page 58 Pump down the MSD See page 60 230 6 Maintaining the MSD To replace the electron multiplier horn Contact strip Retaining clip Electron multiplier horn Signal pin Signal pin 231 Maintaining the GC MSD interface The GC MSD interface requires no periodic maintenance Rarely the heater cartridge in the GC MSD interface fails In those cases it is necessary to replace the heater and sensor This section contains proce dures for removing the heater and sensor and installing new ones More information is available If you need more informatio
12. Action Check the tune parameters Possible Cause The Cl ion source is dirty Action Clean the ion source See the Maintenance chapter of this manual for more infor mation Possible Cause Air leak Action Run Methane Pretune 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 149 150 Before starting 152 Maintaining the vacuum system 159 Maintaining the analyzer 204 Maintaining the GC MSD interface 232 Maintaining the electronics 238 Maintaining the MSD How to perform common maintenance procedures for the MSD Many of these procedures are demonstrated on the MSD Maintenance CD ROM Table 4 Before starting You can perform much of the maintenance required by your MSD For your safety read all of the information in this introduction before performing any maintenance tasks Some parts of the MSD require regularly scheduled maintenance Common maintenance tasks are listed in Table 4 Performing these tasks when scheduled can reduce operating problems prolong system life and reduce overall operating costs Keep a record of system performance tune reports and maintenance operations performed This makes it easier to identify variations from nor mal operation and to take corrective action Maintenance schedule Task Every Every
13. Connect the fan wiring to the fan connector on the MSD frame Reinstall the MSD covers Pump down the MSD See page 60 194 Fan wiring disconnect from back side of fan also 6 Maintaining the MSD To replace the fan for the high vacuum pump Fan Safety grill 195 Materials needed 6 Maintaining the MSD To remove the triode gauge tube WARNING To remove the triode gauge tube Gloves clean lint free large 8650 0030 small 8650 0029 Vent the MSD See page 54 Disconnect the cable from the triode gauge tube Never connect or disconnect the cable from the triode gauge tube while the MSD is under vacuum The stress could cause the tube to implode Loosen the triode gauge collar by turning it counterclockwise Do not remove the collar Pull the triode gauge tube out of the collar Remove the baffle from the open end of the triode gauge tube Wear clean gloves when handling the baffle If you set the baffle down make sure it is on a clean surface 196 Baffle Triode gauge tube Triode gauge cable 6 Maintaining the MSD To remove the triode gauge tube Triode gauge collar if A a Hl Af f f n f n i I i l 197 Materials needed
14. KF50 clamp O ring assembly Diffusion pump Diffusion pump outlet 178 Materials needed 6 Maintaining the MSD To reconnect the MSD to the GC To reconnect the MSD to the GC Wrench open end 1 4 inch x 5 16 inch 8710 0510 Position the MSD so the end of the GC MSD interface is near the GC Reconnect the GC MSD interface cable 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 Make sure the end of the GC MSD interface extends into the GC oven 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 the analyzer chamber at the back of the MSD Reinstall the capillary column See page 28 Pump down the MSD See page 60 Turn on the GC Re establish appropriate temperature setpoints for the GC MSD interface and GC oven 179 6 Maintaining the MSD To reconnect the MSD to the GC REE 180 Materials needed 6 Maintaining the MSD To remove the El calibration vial To remove the EI calibration vial None Stop any tuning or data acquisition Turn off the analyzer There are several ways to turn off the analyzer e Inthe Diagnostics Vacuum Control view select MS OFF from
15. Possible Cause Saturated methane isobutane gas purifier Action Replace the gas purifier 143 5 Cl Troubleshooting Tuning related symptoms overview Tuning related symptoms overview This section describes symptoms related to tuning Most symptoms involve diffi culties with tuning or with the results of tuning The following symptoms are cov ered in this section e Clion ratio is difficult to adjust or unstable e High electron multiplier voltage e Can not complete autotune e Peak widths are unstable 144 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting Reagent gas ion ratio is difficult to adjust or unstable Reagent gas ion ratio is difficult to adjust or unstable The interface tip seal is incorrectly placed damaged or missing Inspect the interface tip seal If necessary remove and reinstall it to insure a good seal with the Cl ion source Replace it if it is damaged Install it if it is missing Residual air and water in the MSD or in the reagent gas supply lines Run the methane pretune Air will appear as a peak at m z 32 and excessive water as a peak at m z 19 gt m z 17 If either of conditions is present purge the reagent gas supply lines and bake out the MSD See page 256 Continued presence of a large peak at m z 32 may indicate an air leak After correcting the problems you may
16. Too hot switch Too cold switch Foreline gauge High vacuum cooling fan diffusion pump position 264 8 Vacuum System Turbo pump MSD vacuum system Turbo pump MSD vacuum system The 5973N MSD can have one of two turbo pumps The performance turbo pump can accept up to 4 ml min carrier gas flow while the standard turbo pump can accept up to 2 4 ml min carrier gas flow The turbo pump has a screen to keep debris out of the pump but no baffle is necessary Pump speed is controlled by the turbo controller there is no foreline gauge Calibration valve specific to type of turbo pump Turbo pump analyzer chamber ap i LA p T m D imi ile H cll 4 Turbo pump controller Performance turbo pump or Standard turbo pump High vacuum cooling fan turbo pump position 265 8 Vacuum System Diffusion pump analyzer chamber Diffusion pump analyzer chamber The analyzer chamber is the chamber in which the analyzer operates The mani fold is extruded and machined from an aluminum alloy Large openings in the side front and rear of the analyzer chamber are closed by plates O rings provide the seals between the plates and the manifold Ports in th
17. 72 3 Operating the Cl MSD To set up the software for Cl operation To set up the software for CI operation Switch to the Manual Tune view Select Load Tune Values from the File menu Select the tune file PCICH4 U If CI autotune has never been run for this tune file the software will prompt you through a series of dialog boxes Accept the default values unless you have a very good reason for changing anything 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 Tune Control Limits box 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 Ammonia lon polarity Positive Negative Positive Negative Positive Negative Abundance target 1x108 1x108 N A 1x108 N A 1x108 Peakwidth target 0 6 0 6 N AS 0 6 N AS 0 6 Maximum repeller 4 4 N AS 4 N AS 4 Maximum emission current 240 50 N A 50 N A 50 Max electron energy eV 240 240 N AS 240 N AS 240 a Always set up in PCI with methane first then switch to your desired ion polarity and reagent gas b Adjust higher or lower to get desired signal abundance Higher signal abundance also gives higher noise abundance This is adjusted for data acq
18. Hardware Manual nee an Agilent Technologies Innovating the HP Way 5973Network Mass Selective Detector Copyright 1999 Agilent Technologies All Rights Reserved Reproduction adaptation or translation without prior written permission is prohibited except as allowed under the copyright laws Document History Publication number G2589 90001 First edition 11 99 Printed in USA Warranty The information contained in this document is subject to change without notice Agilent Technologies makes no warranty of any kind with regard to this material including but not limited to the implied warranties of merchantability and fitness for a particular purpose Agilent Technologies shall not be liable for errors contained herein or for incidental or consequential damages in connection with the furnishing performance or use of this material Agilent Technologies assumes no responsibility for the use or reliability of its software on equipment that is not furnished by Agilent Technologies Noise Declaration Deutsch LpA lt lt 70 dB am Arbeitsplatz normaler Betrieb nach EN 27779 1991 English LpA lt lt 70 dB operator position normal operation per ISO 7779 1988 Instrument Identification Each 5973N Mass Selective Detector MSD is identified bya unique 10 character serial number This serial number is located on a label on the lower left side near the front of the instrument see pag
19. Reinstall the analyzer cover Select Purge Cal Valve from the Vacuum menu in the Diagnostics Vacuum Control view Failure to purge the calibration valve will result in damage to the filaments and detector 183 6 Maintaining the MSD To refill and reinstall the El calibration vial Calibration valve Collar Calibration vial 184 6 Maintaining the MSD To purge the calibration valves CAUTION Special Procedure for CI MSD To purge the calibration valves After removing a calibrant vial you must purge the calibration valve Failure to do so will result in damage to the filaments and the electron multiplier EI calibration valve After adding new PFTBA to the calibrant vial you must purge the air out of the vial and valve If the vacuum gauge controller is on turn it off 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 CI calibration valve After adding new PFDTD to the calibrant vial you must purge the air out of the vial and valve If the vacuum gauge controller is on turn it off Turn on Gas A Turn on Purge Verify that PCICH4 U is loaded 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
20. After the software prompts you to turn on the interface heater and GC oven perform the following steps Check vacuum gauge controller to verify that the pressure is decreasing Press Gas A and Purge and verify that the Gas A and Purge lights are on Verify that PCICH4 U is loaded and accept the temperature setpoints Always start up and verify system performance in PCI mode before switching to NCI Set the GC MSD interface to 320 C Purge for at least one hour Press the Purge button to turn off Purge Set Gas A to 20 Let system bake out and purge for at least two hours If you will be running NCI best sensitivity bake the MSD out overnight 62 Materials needed 2 Operating the MSD To connect the gauge controller WARNING CAUTION CAUTION To connect the gauge controller Gauge controller 59864B Power cord Triode gauge cable 8120 6573 The high vacuum gauge controller is required for operating the MSD in CI mode Never connect or disconnect the cable from the triode gauge tube while the MSD is under vacuum Risk of implosion and injury due to broken glass exists Be sure to orient the cable and the gauge tube as illustrated Excessive force on the pins can break the tube Do not stress the cable Connect the triode gauge cable to the triode gauge tube Connect the other end of the triode gauge cable to the gauge controller Connect the power cord to the gauge controller Co
21. C and 350 C A setpoint below ambient temperature turns off the interface heater Never exceed the maximum temperature for your column Click Apply to download setpoints or click 0K to download setpoints and close the window To make the new settings part of the method select Save from the Method menu Make sure that the carrier gas is turned on and the column has been purged of air before heating the GC MSD interface or the GC oven 44 2 Operating the MSD To set the GC MSD interface temperature from the PC Instrument Edit Aux 6890 45 Materials needed 2 Operating the MSD To monitor high vacuum pressure WARNING WARNING To monitor high vacuum pressure Gauge controller 59864B Triode ionization gauge cable 8120 6573 Never connect or disconnect the cable from the triode gauge tube while the MSD is under vacuum Risk of implosion and injury due to broken glass exists If you are using hydrogen as a carrier gas do not turn on the triode gauge tube if there is any possibility that hydrogen has accumulated in the analyzer chamber The triode gauge filament can ignite hydrogen Read the Hydrogen Carrier Gas Safety Guide 5955 5398 before operating the MSD with hydrogen carrier gas Connect the gauge controller to the ionization gauge tube page 63 Start up and pump down the MSD page 60 Switch on the power switch on the back of the gauge controller Press and release the G
22. Nut for 1 8 inch tubing 20 package Nut and both front and rear ferrules 20 sets package Tubing cutter for stainless steel tubing Tubing cutter replacement blades Part number 8500 5440 G1099 80018 61099 00015 61999 80410 8500 8130 7157 0210 9310 4828 5180 4110 5180 4116 5080 8751 5080 8751 8710 1709 8710 1710 365 Table 26 12 Parts CI Parts Cl Flow control module parts Description Cl flow control module complete Calibration valve assembly PFDTD calibrant Sample vial Sample vial O ring 1 4 inch Viton Solenoid valve and cable Cl main power harness cable Display module Flow control knob Flow control PCA Mass flow controller Isolation valve Mass flow controller cable Reagent gas select valve VCR gasket 1 4 inch with retainer one use only VCR gasket 1 8 inch one use only Cl analyzer cover Front flow module cover Methane isobutane gas purifier Reagent gas supply tubing stainless steel 1 8 inch Rear flow module cover Swagelok fittings for gas purifier and inlet to flow module Ferrule front for 1 8 inch tubing 20 package Ferrule rear for 1 8 inch tubing 20 package Nut for 1 8 inch tubing 20 package Nut and both front and rear ferrules 20 sets package Part number 61999 65450 61999 60456 8500 8130 05980 20018 0905 1217 G1999 80405 G1999 60462 G1999 65461 0370 3401 61999 65005 0101 1006 61999 80402 61999 60464 61999 80401 0100 1436 0100 0468 61999 60440 61999 20422 G
23. Pliers long nose 1 5 inch nose 8710 1094 Screwdrivers flat blade large 8730 0002 ORX T 10 8710 1623 ORX T 15 8710 1622 ORX T 20 8710 1615 Shipping kits 5973N MSD 62589 60043 6890 Series GC 61530 60860 Tweezers non magnetic Wrenches open end 1 4 inch x 5 16 inch 10 mm Wrist strap anti static small medium large 8710 0907 8710 0510 8710 2353 9300 0969 9300 1257 9300 0970 361 Table 23 12 Parts Consumables and maintenance supplies Ferrules Description 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 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 74 mm id 90 Vespel 10 graphite for 0 53 mm id columns 5062 3512 362 Table 24 12 Parts Consumables and maintenance supplies Miscellaneous parts and samples Description Part number Diffusion pump fluid 2 required 6040 0809 Electron multiplier horn 05971 80103 Filament assembly El 0
24. Pump down the MSD See page 60 Always replace both fuses 243 244 To set up your MSD for CI operation 247 To install the Cl ion source 248 To install the CI interface tip seal 250 To clean the CI ion source 252 To minimize foreline pump damage from ammonia 254 To replace the methane isobutane gas purifier 255 To clean the reagent gas supply lines tubing 256 To refill the CI calibrant vial 257 CI Maintenance 245 WARNING CI Maintenance This chapter describes maintenance procedures and requirements that are unique to 5973N MSDs equipped with the Chemical Ionization hardware Maintenance videos on the multimedia manual in the 5973N User Preparation Kit Most of these maintenance procedures are demonstrated on the multimedia MSD Reference Collection CD ROM Please view these videos CI increases the need for ion source 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 Always perform any maintenance procedures using hazardous solvents under a fume hood Be sure to operate the MSD in a well vented room Ammonia CI increases the need for foreline pump maintenance Ammonia when used as a reagent gas it will also change the maintenance requirements slightly Ammonia causes the fo
25. control closed fully clockwise at all times except when ballasting the pump A window sight glass in the front of the 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 To check and add foreline pump oil see page 160 272 Foreline hose from high vacuum pump Ballast control Oil fill cap Exhaust outlet use 11 mm id hose Oil drip tray Drain plug 8 Vacuum System Foreline pump Oil level window sight glass 273 See Also 8 Vacuum System Foreline gauge Foreline gauge The foreline gauge monitors the pressure vacuum at the exit of the diffusion pump The primary function of the foreline gauge is diffusion pump control When the foreline pump has reduced the pressure in the analyzer chamber to below 300 mTorr 0 3 Torr the diffusion pump is automatically switched on If the fore line pressure rises above 400 mTorr 0 4 Torr the ac board switches off the diffu sion pump heater and the analyzer electronics The foreline pressure can be monitored from your data system The turbo pump MSD does not require a foreline gauge Instead the motor speed is monitored To view MSD temperature and vacuum status page 38 Gauge contr
26. lon source Drawout plate and cylinder The drawout plate forms another wall of the ionization chamber The ion beam passes through the hole in the drawout plate and into the drawout cylinder The drawout cylinder is slotted The slots correspond to slots in the source body These slots allow carrier gas and un ionized sample molecules or fragments to be pulled away by the vacuum system The drawout plate and drawout cylinder are both at ground potential Ion focus The voltage on the ion focus lens can be varied from 0 to 127 V dc A typical volt age is between 70 and 90 V dc In general e Increasing the ion focus voltage improves sensitivity at lower masses e Decreasing the ion focus voltage improves sensitivity at higher masses e Incorrect ion focus adjustment results in poor high mass response Entrance lens The entrance lens is located at the entrance to the quadrupole mass filter This lens minimizes the fringing fields of the quadrupole which discriminate against high mass ions There is a permanent 4 4 volt voltage added to the entrance lens The total voltage applied to the entrance lens is the sum of the entrance lens offset and entrance lens gain and the 4 4 volt permanent offset Entrance lens voltage 4 4 V dc offset gain x mass 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 V dc 20 V is typical Increasing
27. one of the following may be responsible e Repeller voltage is too high e Peaks are too wide e Incorrect dc polarity on the quadrupole mass filter e Dirty quadrupole mass filter Peak widths are inconsistent e MSD has not had enough time to reach thermal equilibrium e Large variations in the temperature of the laboratory e Incorrect tuning e Calibration vial is empty or almost empty e Calibration valve is not working correctly e Dirty ion source e Electron multiplier is nearing the end of it useful lifetime e Ground loop problems 104 4 Troubleshooting the MSD Mass spectral symptoms Relative abundance of m z 502 is less than 3 Autotune should give an m z 502 relative abundance greater than 3 The rela tive abundance of m z 502 can however vary a great deal depending on column flow ion source temperature and other variables As long as relative abundance is above 3 the stability of the relative abundance is more important than the absolute value If you observe significant changes in the relative abundance of m z 502 for a fixed set of operating parameters there may be a problem The charts in the MSD ChemStation software are useful for identifying changes Select View Tunes from the Qualify menu in the Instrument Control view Low relative abundance 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
28. setting 42 Autotune 50 CI 78 CI negativemode 82 CI positive mode 80 column flow and temperatures for 50 relative abundances of m z 502 produced by different autotunes 105 report generated by 50 viewing tune history 50 Auxiliary heated zones 36 387 Index B Back panel and connectors 332 Background air and water checking for at CI startup 77 checking for at startup 76 effect on NCI sensitivity 384 effect on PCI 376 troubleshooting in CI 124 Background air and water in CI 77 Background chemical minimizing by avoiding unnecessary tuning 80 82 294 Background high 103 119 Ballast control on foreline pump 272 Ballast foreline pump 254 Baseline chromatographic falling 100 high 100 rising 100 wandering 101 BFB tune 50 Bleed See Column bleed or Septum bleed C Cables part numbers for external 339 part numbers for internal 340 Calibrant CI calibrant ions not visible 138 Calibrant vial 283 Calibrant vial CI refilling 257 Calibrant vial CI refilling Calibration valve 283 O ring 270 Calibration valve CI 283 294 Calibration valve EI reinstalling 192 removing 190 Calibration vial EI refilling and reinstalling 183 removing 181 Carrier gas contaminated 119 flow 36 purity requirement 21 34 See also Column flow Cautions inside front cover Charge exchange PCI 381 Checklist pre operation 34 Chemical background effect on NCI 382 Chemical ionization
29. starts and spins down stops quickly This simplifies pumpdown and venting From initial power on the system can pump down to operating pressure in 5 to 10 minutes Gauge controller page 287 To pump down the MSD page 60 To vent the MSD page 54 Turbo pump control see 326 Table 2 Typical MSD pressure readings for various carrier gas flow rates page 47 280 8 Vacuum System Standard turbo pump Standard turbo pump Turbo pump inlet with screen Turbo outlet port Connector turbo controller 281 8 Vacuum System Performance turbo pump Performance turbo pump Turbo pump inlet with screen Interstage port blanked off Turbo outlet port Connector turbo controller 282 8 Vacuum System Calibration valves and vent valve Calibration valves and vent valve Calibration valves A calibration valve is an electromechanical valve with a vial to hold the tuning compound When a calibration valve is opened tuning compound in the vial dif fuses into the ion source EI MSDs have only one calibration valve while CI MSDs have another calibration valve for the CI tuning compound The valves are con trolled by the MSD ChemStation EI calibration valve The EI calibration valve is held onto the front end plate of the analyzer chamber by two screws A small O ring provides a face seal The diffusion pump and the standard turbo pump MSDs have a calibra
30. switch off the triode gauge controller Before venting a CI MSD press the Gas Off button turns off the reagent gas flow and closes the isolation valve On a Cl MSD the Gas Off light must be on when the MSD is venting Select Vent from the from the Vacuum menu in the software Follow the instructions presented Set the GC MSD interface heater and the GC oven temperatures to ambient 25 C If you are using hydrogen as a carrier gas the carrier gas flow must be off before turning off the MSD power If the foreline pump is off hydrogen will accumulate in the MSD and an explosion may occur Read the Hydrogen Carrier Gas Safety Guide 5955 5398 before operating the MSD with hydrogen carrier gas Be sure the GC oven and the GC MSD interface are cool before turning off carrier gas flow When prompted turn off the MSD power switch Unplug the MSD power cord When the MSD is vented do not put the ChemStation into Top view Doing so will turn on the interface heater Remove the analyzer cover page 52 54 2 Operating the MSD To vent the MSD C sl lt we eae P _ NO 8 Turn the vent valve knob counterclockwise only 3 4 turns or until you hear the hissing sound of air flowing into the analyzer chamber Do not turn the knob too far or the O ring may fall out of its groove Be sure to reti
31. 2 82 IonFocus 120 5 HED ON EntLens 11 0 EMVolts 918 EntOffs 18 57 Samples 8 PFDTD OPEN Averages 3 StepSize 0 10 Zones MS Source 250 TurboSpd 100 MS Quad 150 LAN MA y a E mi T T 38 43 265 270 596 ane 601 Scan 35 00 700 00 Samples 8 Thresh 100 Step 0 10 200 peaks Base 267 00 Abundance 659968 100 80 4 60 5 40 20 100 200 300 400 500 600 Mass Abund Rel Abund Iso Mass Iso Abund Iso Ratio 41 10 285952 100 00 42 00 11676 4 08 267 00 659968 230 80 268 00 35528 5 38 599 00 630784 220 59 600 00 75248 11 93 CI Reagent Ions 17 29 Ratio 0 48 19 29 Ratio 0 07 32 29 Ratio 0 00 28 27 Ratio 2 9 28 29 Ratio 0 08 41 29 Ratio 0 30 29 Abundance 948608 counts 81 3 Operating the Cl MSD To perform a negative Cl autotune any reagent gas CAUTION CAUTION To perform a negative CI autotune any reagent gas Always verify MSD performance in El before switching to Cl operation See page 51 Always set up the Cl MSD in PCI first even if you are going to run NCI Load NCICH4 U or an existing tune file for the reagent gas you are using If you use an existing tune file be sure to save it with a new name if you don t want to over write the existing values Accept the default temperature and other settings If you don t already have an NCI tune file for your reagent gas use Select Reagent Gas under the Setup menu
32. 283 CI calibration 283 294 gas select valves 293 isolation 294 purge 293 vent 283 vent proper operation of 55 VCR fittings 293 causing leaks by loosening 126 Vent cycle See Venting Vent cycle See Venting Vent program See Venting Vent valve 283 lubricating the O ring 202 Venting ChemStation control of 34 damage to MSD from incorrect 36 if ChemStation is not working 68 normal 54 preparing the MSD for 55 proper use of the vent valve 55 Top view turns on interface heater 55 Vial calibrant 283 See also Calibrant vial Vial calibrant caution against solvent use 257 Vial Calibrant CI caution to purge calibration valve after refilling 257 Voltages dangerous 155 401 Index W Warnings inside front cover Warranty claims inside back cover Warranty inside back cover Water contamination of CI systems by 374 detecting in CI 77 141 Wid219 parameter 309 Wiring dangerous voltages on 155 402 Warranty Agilent Technologies warrants its Analytical products against defects in materials and workmanship for the warranty period During the warranty period Agilent Technologies will at its option repair or replace products which prove o be defective Products that are installed by Agilent Technologies are warranted rom the installation date all others from the date of delivery f Buyer schedules or delays installation more than 30 days after delivery then warranty peri
33. 50 uA 50 uA 35 uA Electron energy 50 eV 150eV 50eV 150eV 50eV 150eV 70 Filament 1 l 1or2 Repeller 3V 3V 3V 3V 3V 3V 30 V on focus 30 V 130 V 30 V 130 V 30 V 130 V 90 V Entrance lens offset 20V 20 20V 20 20V 20 25 EMVolts 200 1200 200 1200 200 1200 1200 Gas Off Off Off Off Off Off Off On Gas select valve A A B B B B None Suggested flow 20 40 20 40 20 40 N A Source temp 250 C 150 C 250 C 150 C 250 C 150 C 230 C Quad temp 150 C 150 C 150 C 150 C 150 C 150 C 150 C nterface temp 320 C 280 C 320 C 280 C 320 C 280 C 280 C Autotune Yes Yes No Yes No Yes Yes Suggested starting parameters for El PCI MSDs Reagent gas Methane Isobutane Ammonia El on polarity positive only Emission 50 uA 50 WA 150 pA 35 pA Electron energy 50 eV 50eV 150eV 70 Filament 1 1or2 Repeller 3V 3V 3V 30 V on focus 30 V 30 V 130 V 90 V Entrance lens offset 20V 20V 20V 25 EMVolts 200 200 1200 1200 Gas Off Off Off Off On Gas select valve A B B None Suggested flow 10 10 10 N A Source temp 250 C 250 C 250 C 230 C Quad temp 150 C 150 C 150 C 150 C Interface temp 320 C 320 C 320 C 280 C Autotune Yes No No Yes 79 3 Operating the CI MSD To perform a positive CI autotune methane only CAUTION CAUTION To perform a positive CI autotune methane only Always verify MSD performance in El before switching to CI operation See page 51 Always set up the CI MSD in PCI first even if
34. 8 Vacuum System Diffusion pump and fan Gauge controller page 287 Table 2 Typical MSD pressure readings for various carrier gas flow rates page 47 The small size of the diffusion pump allows it to heat up and cool down quickly This simplifies pumpdown and venting From initial power on the system can pump down to operating pressure in approximately 15 minutes If the power fails the diffusion pump fluid stops boiling before the analyzer chamber pressure begins to rise significantly This helps prevent back diffusion of pump fluid into the ana lyzer chamber Your data system has pumpdown and venting programs to guide you through these procedures Follow their instructions carefully To pump down the MSD page 60 Diffusion pump control page 328 To vent the MSD page 54 Diffusion pump operational readiness is monitored by two thermal switches Diffusion pump thermal switches Thermal Switch Normal state Changes at Function Message What it means What to do Too Cold Normally open 170 C rising 140 C falling Keeps analyzer turned off until the pump is hot enough to for adequate vacuum Prevents analyzer damage The high vacuum pump is not ready Normal during pumpdown Wait for pump to heat up Too Hot Normally closed 365 C rising Shuts off diffusion pump and analyzer if the pump overheats Prevents damage to the pump and analyzer Difficulty with the high vacuum pump Always indica
35. 8650 0030 small 8650 0029 Hex ball driver 1 5 mm 8710 1570 Hex ball driver 2 0 mm 8710 1804 Hex nut driver 5 5 mm 8710 1220 Vent the MSD See page 54 Open the analyzer chamber See page 56 Remove the ion source from the source radiator See page 206 Remove the filaments Remove the repeller assembly The repeller assembly includes the source heater assembly repeller and related parts Remove the repeller nut washer repeller insulators and repeller You do not need to remove the heater and temperature sensor from the heater block The new source heater assembly includes all three parts already assembled 222 6 Maintaining the MSD To remove the heater and sensor from the ion source Source body Repeller Repeller insulator Filament Repeller insulator Washer Repeller nut Filament Source heater assembly 223 Materials needed 6 Maintaining the MSD To reinstall the heater and sensor in the ion source CAUTION To reinstall the heater and sensor in the ion source Gloves clean lint free large 8650 0030 small 8650 0029 Hex ball driver 1 5 mm 8710 1570 Hex ball driver 2 0 mm 8710 1804 Hex nut driver 5 5 mm 8710 1220 Source heater assembly G1099 60177 Unpack the new source heater assembly The heater temperature sensor and heater block are already assembled Reinstall the repeller repeller insulator
36. Cl filament G1099 80053 Cl source heater assembly G1999 60414 Dummy filament FD G1999 20454 y F o lens insulator set 999 20445 ion focus lens 999 20443 999 20444 draw out plate 999 20446 C G C G Cl draw out cylinder G C G Cl lens insulator set 61999 20445 Entrance lens 05971 20126 Cl interface tip seal G1999 60412 12 Parts CI Parts 369 Table 28 12 Parts CI Parts EI Cl GC MSD interface parts Description CI El GC MSD interface assembly Heater clamp Heater sensor assembly Interface cover Interface insulation two pieces Screws for heater clamp Screws to attach interface to manifold Welded interface Interface tip seal Vespel blank Part number G1999 65400 1999 20410 1099 60107 1999 00405 1999 20401 0515 0383 0515 0380 61999 60401 61999 60412 9181 3308 G G G G 370 12 Parts Heater sensor assembly Cl Parts Cl interface cover G1999 00405 Cl interface insulation y G1999 20401 lt L CI heater clamp G1999 20410 f CI welded interface N G1999 60401 A Interface O ring A 0905 1405 D i Z SENEE E ore Cl ionization chamber Fan ma SS g Kya iy My
37. Edit Parameters screen always select MSOff before changing any of the filament parameters e When setting up data acquisition parameters set the solvent delay so that the analyzer will not turn on while the solvent peak is eluting e When the software prompts Override solvent delay at the beginning of a run always select NO e Higher emission current will reduce filament life e Higher electron energy will reduce filament life e Leaving the filament on for short times lt 1 minute during data acquisition will reduce filament life Magnet The field created by the magnet directs the electrons emitted by the filament into and across the ionization chamber The magnet assembly is a permanent magnet with a charge of 350 gauss in the center of the field Repeller The repeller forms one wall of the ionization chamber A positive charge on the repeller pushes positively charged ions out of the source through a series of lenses The repeller voltage is also known as the ion energy although the ions only receive about 20 of the repeller energy The repeller voltage can be varied from 0 to 42 8 V dc Some tune programs use a fixed repeller voltage Others ramp the repeller voltage to find the optimum setting e Setting repeller voltage too low results in poor sensitivity and poor high mass response e Setting repeller voltage too high results in precursors poor mass filtering and poor low mass resolution 303 10 Analyzer
38. G1099 60427 G1099 60130 61099 60410 G1099 60416 61099 60428 61099 60438 61099 60435 1 Nota user replaceable part Refer service to your Agilent Technologies service representative 340 Source power cable G1099 60428 Side board control cable G1099 60410 HED power supply output cable G1099 60431 Remote start cable G1530 60930 LAN cable shielded 8121 0008 Signal cable G1099 60416 AC board control cable G1099 6 0422 HED con G1099 6 trol cable 0430 Low voltage PS input cable G1099 60426 Low voltage PS output cable G1099 60427 12 Parts Electronics 341 Table 11 12 Parts Electronics Printed circuit boards Description ac board fan for electronics module HED power supply bipolar HED power supply El PCI NCI MSDs only LAN MS control card 30 pin SIMM 2 required 72 pin SIMM 1 required low voltage ac dc power supply main board signal amplifier board toroid transformer Control panel assembly Side board Part number 62589 69005 3160 1038 G1099 80017 G1099 80018 05990 69420 1818 4271 1818 5709 0950 3067 G1099 69010 61
39. MSD See page 50 241 Materials needed 6 Maintaining the MSD To replace the primary fuses WARNING WARNING To replace the primary fuses Fuse T8 A 250 V 2110 0969 2 required Screwdriver flat blade 8730 0002 The most likely cause of failure of the primary fuses is a problem with the foreline pump If the primary fuses in your MSD fail check the foreline pump Vent the MSD and unplug the power cord from the electrical outlet If one of the primary fuses has failed the 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 Never replace the primary fuses while the MSD is connected to a power source If you are using hydrogen as a GC carrier gas a power failure may allow it to accumulate in the analyzer chamber In that case further precautions are required See the Hydrogen Carrier Gas Safety Guide 5995 5398 Turn one of the fuse holders counterclockwise until it pops out The fuse holders are spring loaded Remove the old fuse from the fuse holder Install a new fuse in the fuse holder Reinstall the fuse holder 242 6 Maintaining the MSD To replace the primary fuses p Primary fuses in holders A 0 Repeat steps 3 6 for the other fuse Always replace both fuses Reconnect the MSD power cord to the electrical outlet
40. PCI produces ions with almost any sample molecule Other reagent gases such as isobutane or ammonia are more selective and cause even less fragmentation Because of the high back ground 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 e Proton transfer e Hydride abstraction e Addition e Charge exchange Depending on the reagent gas used one or more of these four processes can be used to explain the ionization products observed in the resulting mass spectra EI methane PCI and ammonia PCI spectra of methyl stearate are shown opposite The simple fragmentation pattern large abundance of the MH ion and the pres ence of the two adduct ions are characteristic of positive chemical ionization using methane as a reagent gas The presence of air or water in the system especially in the presence of PFDTD calibrant quickly contaminates the ion source 376 Appendix A Chemical lonization Theory Positive Cl theory Methyl stearate MW 298 El methane PCI and ammonia PCI Abundance Scan 1443 9 799 min FAMESO3 D 255 199 97 129 267 111 157 474 185 213 397 241 sali zal a al t t TT l 268 o 150 200 250 300 Scan 1405 9 723 min FAMES04 D 10 299 methane PCI M 29 az MM 31
41. Possible Cause Action 5 Cl Troubleshooting Excessive noise or low signal to noise ratio Excessive noise or low signal to noise ratio The GC injection port needs maintenance Refer to the 6890 Plus GC manual The Cl ion source is dirty Clean the ion source See the Maintenance chapter in this manual for more infor mation Poor vacuum Check the pressure on the high vacuum gauge controller 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 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 high Gin EI PCI MSDs Verify that the reagent gas setup is correct 140 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting Large peak at m z 19 Large peak at m z 19 If the abundance of the peak at m z 19 is more than half abundance of the peak at m z 17 then there is probably too much water in the system The system was not baked out sufficiently after it was last vented Bake out the system as described in the Maintenance chapter of this manual Moisture left over in the reagent gas supply tu
42. The foreline pump reduces the pressure in the analyzer chamber so the high vac uum pump can operate It also pumps away the gas load from the high vacuum pump The foreline pump is connected to the high vacuum pump by a 130 cm hose called the foreline hose The foreline pump is a two stage rotary vane pump The foreline pump turns on when the MSD power is turned on The foreline pump has a built in anti suckback valve to help prevent backstreaming in the event of a power failure The foreline pump can be placed under the analyzer chamber at the rear of the MSD with the exhaust outlet to the rear or on the floor below the MSD An oil trap not shown is available that can be used to filter pump oil out of the foreline pump exhaust This trap stops only pump oil Do not use the trap if you are analyzing toxic chemicals or using toxic solvents or if you have a CI MSD Instead install an 11 mm id hose to remove the exhaust from your lab The foreline pump exhaust contains traces of solvents analytes and foreline pump oil The supplied oil trap stops only pump oil It does not trap or filter out toxic chemicals If you are using toxic solvents or analyzing toxic chemicals remove the oil trap and install a hose to take the foreline pump exhaust outside or to a fume hood Do not place the foreline pump near any equipment that is sensitive to vibration The ballast control knob controls the amount of air allowed into the pump Keep the ballast
43. TurboSpd Quad 150 Emission 0 0 to 315 2 34 6 JR 39 Software changes 2 Operating the MSD To set monitors for MSD temperature and vacuum status To set monitors for MSD temperature and vacuum status Monitors display the current value of a single instrument parameter They can be added to the standard instrument control window Monitors can be set to change color if the actual parameter value varies beyond a user determined limit from the parameter setpoint This procedure describes how to add monitors to your instru ment control view 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 Select MS Monitors from the Instrument menu In the Edit MS Monitors box under Type select Zone Under Parameter select MS Source and click Add Under Parameter select MS Quad and click Add Under Parameter select Foreline or TurboSpd and click Add Click OK The new monitors will be stacked on top of each other in the lower right corner of the Instrument Control window They must be moved for you to see them all Click and drag each monitor to the desired position See the accompanying illustration for an example of arranging the monitors To make the new settings part of the method select Save from the Method menu 40 2 Operating the MSD To set mo
44. chamber The foreline pump may be located on the floor on the lab bench next to or behind the MSD or under the analyzer chamber at the back of the MSD Pump down the MSD See page 60 164 Fill cap Upper line Oil level window Drain plug 6 Maintaining the MSD To refill the foreline pump 165 Materials needed 6 Maintaining the MSD To replace the oil trap WARNING WARNING WARNING WARNING CAUTION To replace the oil trap Gloves oil and solvent resistant Oil trap foreline exhaust G1099 80037 If you are using an oil trap on the exhaust port of the foreline pump you should replace the trap whenever the white filter element turns brown The trap can be replaced without turning off the MSD Do not breathe the pump exhaust it may contain pump oil vapor Do not replace the trap while samples are being analyzed Do notuse the trap with a CI MSD or if you are using toxic solvents or analyzing toxic chemicals The trap stops only foreline pump oil It does not trap or filter out toxic chemicals Install a hose to take the foreline pump exhaust outside or to a fume hood Remove the clamp that holds the oil trap to the trap adapter Do not touch the foreline pump it may be hot Remove the oil trap Make sure the O ring assembly stays on the adapter Install a new oil trap Reinstall the clamp that holds the
45. clear Dark or cloudy pump fluid indi cates an air leak or excessive heat If the pump fluid appears dark or cloudy replace it Then check for an air leak The diffusion pump fluid should be replaced at least once a year or more often if the pump fluid level is low or if the fluid is dark or cloudy Keep your hair away from the cooling fan if the MSD is turned on 168 6 Maintaining the MSD o check the diffusion pump fluid ZS ON JS N AENA oy A M SX S LFV4 Fluid level window sight glass 6 Maintaining the MSD To replace the turbo pump To replace the turbo pump The turbo pumps are not customer replaceable parts The procedure is demon strated on the 5973N Maintenance CD ROM and is for use by Agilent Technolo gies service personnel only 170 Materials needed See also 6 Maintaining the MSD To separate the MSD from the GC WARNING To separate the MSD from the GC Wrench open end 1 4 inch x 5 16 inch 8710 0510 A video demonstration of this procedure is on the 5973N MSD Maintenance CD ROM Vent the MSD See page 54 Turn off the GC Remove the capillary column from the GC MSD interface Make sure the GC MSD interface and GC oven have cooled before you remove the column If necessary slide the foreline pump out from under the analyzer chamber The foreline pump may be located on the floo
46. conditioned capillary column is installed in the GC inlet and in the GC MSD interface e The GC is on but the heated zones for the GC MSD interface the injection port and the oven are off e Carrier gas of at least 99 999 purity is plumbed to the GC with the recommended traps e If hydrogen is used as carrier gas carrier gas flow must be off and the front sideplate thumbscrew must be loosely fastened e The foreline pump exhaust is properly vented 34 WARNING WARNING 2 Operating the MSD The exhaust from the foreline pump contains solvents and the chemicals you are analyzing It also contains traces of pump oil The supplied oil trap stops only pump oil It does not trap or filter out toxic chemicals If you are using toxic solvents or analyzing toxic chemicals remove the oil trap Install a hose 11 mm id to take the foreline pump exhaust outside or to a fume exhaust hood If you are using hydrogen as a carrier gas do not start carrier gas flow until the MSD has been pumped down If the vacuum pumps are off hydrogen will accumulate in the MSD and an explosion may occur Read the Hydrogen Carrier Gas Safety Guide 5955 5398 before operating the MSD with hydrogen carrier gas The data system or control panel help you pump down the MSD Pumpdown is mostly automated Once you close the vent valve and turn on the main power switch while pressing on the sideplate the MSD pumps down by itself The data
47. conditions listed in the introduction to this chapter page 34 before starting up and pumping down the MSD Failure to do so can result in personal injury If you are using hydrogen as a carrier gas do not start carrier gas flow until the MSD has been pumped down If the vacuum pumps are off hydrogen will accumulate in the MSD and an explosion may occur Read the Hydrogen Carrier Gas Safety Guide 5955 5398 before operating the MSD with hydrogen carrier gas Plug in the MSD power cord Select Diagnostics Vacuum Control from the View menu Select Pump Down from the Vacuum menu When prompted switch on the MSD Press lightly on the side board to ensure a correct seal Press on the metal box on the side board The rough pump will make a gurgling noise This noise should stop within a minute If the noise continues there is a large air leak in your system probably at the side plate seal the interface column nut or the vent valve Once communication with the PC has been established click OK 60 CAUTION CAUTION 2 Operating the MSD To pump down the MSD Pump Down PUMP DOWN IN PROGRESS Turbo pump status Pump on Not up to speed MS Source 27 deg C Turbo pump speed 70 percent MS Temp setpoints will remain OFF until pump ready Within 10 to 15 minutes the diffusion pump should be hot or the turbo pump speed up to 80 The turbo pump speed should eventually reach 95 If these condition
48. end Hand tighten the nut Make sure the position of the column does not change as you tighten the nut Tighten the nut 1 4 to 1 2 turn Check the tightness after one or two heat cycles 29 Materials needed Note 1 Installing GC Columns To install a capillary column using the installation tool To install a capillary column using the installation tool Column cutter 65181 8836 Column installation tool not supplied with the MSD G1099 20030 Ferrules 0 3 mm id for 0 10 mm id columns 5062 3507 0 4 mm id for 0 20 and 0 25 mm id columns 5062 3508 0 5 mm id for 0 32 mm id columns 5062 3506 0 8 mm id for 0 53 mm id columns 5062 3538 Gloves clean large 8650 0030 small 8650 0029 Interface column nut 05988 20066 Septum may be old used inlet septum Wrenches open end 1 4 inch x 5 16 inch 8710 0510 2 required The column installation tool is not recommended for applications requiring optimal sensitivity performance See To install a capillary column without the installation tool page 28 Vent the MSD See page 54 Slide a septum interface column nut and conditioned ferrule onto the free end of the column The tapered end of the ferrule should point toward the nut Insert the column into the column installation tool Slide the column through until the end extends past the end of the tool Cut 1 cm off the end of the column page 22 Position the column so that 1 to 2 mm extends p
49. flow 20 Methane PCI 17 29 41 41 267 599 28 27 1 5 5 0 Methane NCI 17 35 235 185 351 449 N A lsobutane PCI 39 43 57 N A 57 43 5 0 30 0 Isobutane NCI 17 35 235 185 351 449 N A Ammonia PCI 18 35 52 N A 35 18 0 1 1 0 Ammonia NCI 17 35 235 185 351 517 N A 3 Operating the CI MSD To use other reagent gases Flow adj ions Ratio EI PCI MSD Standard turbo pump Recommended flow 10 28 27 0 5 3 0 No negative CI capability 57 43 1 0 5 0 No negative CI capability 35 18 0 02 0 2 No negative Cl capability a There are no PFDTD ions formed with any reagent gas but methane Tune with methane and use the same parameters for the other gas b There are no negative reagent gas ions formed To pretune in negative mode use background ions 17 OH 35 CI and 235 ReOz These ions can not be used for reagent gas flow adjustment Set flow to 40 for NCI and adjust as necessary to get acceptable results for your application Isobutane CI Isobutane C4H10 is commonly used for chemical ionization when less fragmen tation 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 trans ferred in the ionization reaction Addition and proton transfer are the ionization mechanisms most often associated with isobutane The sample itself influences which mechanism dominates 89 CAUTION
50. following material The analyzer has four basic components The analyzer consists of the following components e Jon source e Mass filter e Detector e Heaters and radiators 298 Detector HED electron multiplier Detector end mounting bracket ass filter contact cable ass filter inside radiator ass filter heater assembly on source inside radiator Side board Feedthrough board Side plate Source end mounting bracket Mass filter contact cable 10 Analyzer 299 10 Analyzer lon source Ion source The ion source operates by electron ionization EI The sample enters the ion source from the GC MSD interface Electrons emitted by a filament enter the ion ization chamber guided by a magnetic field The high energy electrons interact with the sample molecules ionizing and fragmenting them 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 which is directed into the mass filter Ion source body The ion source body is a cylinder Its cylindrical geometry ensures proper align ment of the lens stack It holds the other parts of the ion source With the repeller and the drawout plate it forms the ionization chamber The ionization chamber is the space where the ions are formed Slots in the sourc
51. heater block 0515 0319 Screws for radiator mounting brackets and for side board 0515 0430 Source radiator screws 0515 1052 ass filter contact 4 required ass filter cable kit G1099 60130 ass filter heater assembly on source inside radiator G1099 69106 Source heater assembly G1099 60177 Magnet assembly 05971 60160 Repeller G1099 20132 Feedthrough board G1099 60425 303 Table 18 12 Parts Analyzer El lon source parts Description lon source complete drawout cylinder drawout plate entrance lens filament interface socket ion focus lens lens insulator pair repeller assembly complete screws for filaments and holding repeller assembly on source setscrew for lens stack source body Part number G1099 69106 G1072 20008 05971 20134 05971 20126 05972 60053 G1099 20136 05971 20143 05971 20130 G1099 60170 0515 1046 0515 1446 G1099 20130 354 Source body G1099 20130 Setscrew 0515 1446 Filament 05972 60053 GC MSD interface socket G1099 20136 Repeller assembly G1099 60170 Screws 0515 1046 Screws 0515 1046 Lens insulator set 05971 20130 Entrance lens 05971 20126 on focus lens 05971 20143 Drawout cylinder G1072 20008 Drawout plate 05971 20134 12 Parts Analyzer 305 Table 19 12 Parts Analyzer Repeller
52. interact The analyzer heaters may not be able to accurately control temperatures if the set point for one zone is much lower than that of an adjacent zone 314 Detector end mounting bracket Mass filter radiator Mass filter heater assembly lon source radiator Side plate Feedthrough board Source heater assembly Source end mounting bracket 10 Analyzer Analyzer heaters and radiators 315 316 11 Control panel and power switch 320 Side board 322 Electronics module 323 Main board 324 Signal amplifier board 325 AC board 326 Turbo pump control 326 Diffusion pump control 328 Pumpdown failure shutdown 328 LAN MSD control card 330 Power supplies 331 Toroid transformer 331 Back panel and connectors 332 Interfacing to external devices 334 Electronics This chapter describes the MSD electronics Electronics The following assemblies make up the MSD electronics e Control panel and power switch e Electronics module e Main board e Signal amplifier board e LAN MS control card e AC board e Turbo pump controller e Low voltage ac dc power supply e High voltage HED power supply e Toroid transformer assembly e Back panel connectors e Side board Each is discussed in this chapter Except for the Back panel and connec tors Status display and power switch and Interfacing to other devices sections most of this material is
53. ions are formed in NCI Switch to Positive ionization mode The reagent gas flow is set too low Increase the reagent gas flow Reagent gas supply tubing 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 Make sure 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 135 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting No or low reagent gas signal Carbon has built up on the filament or filament has sagged out of alignment Inspect the filament If necessary replace the filament Too much air or water in the system Run the methane pretune Peaks at m z 32 and 19 usually indicate air and water respectively Bake out and purge the instrument until there is no visible peak at m z 32 and the peak at m z 19 is reduced to a very low level If the peak at m z 32 does not decrease an air leak is likely See the Leaks section at the end of this chapter for more information The signal cable is not connected Check and if necessary reconnect the signal cable The filament or filament support is shorted to the ion source body or repeller Inspect the filament If necessary realign th
54. ions are normal 138 Excessive noise or low signal to noise ratio 140 Large peak at m z 19 141 Peak at m z 32 142 Tuning related symptoms overview 144 Reagent gas ion ratio is difficult to adjust or unstable 145 High electron multiplier voltage 147 Can not complete autotune 148 Peak widths are unstable 149 CI Troubleshooting Troubleshooting This chapter outlines the troubleshooting of 5973N MSDs equipped with PCI NCI Most of the troubleshooting information in the previous chapter also applies to CI MSDs Common ClI specific problems Because of the added complexity of the parts required for CI there are many potential problems added By far the greatest number and most serious problems with CI are associated with leaks or contamination in the reagent gas introduction system NCI is especially sensitive to the presence of air and air leaks small enough to 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 e Wrong reagent gas e Reagent gas not hooked up or hooked up to wrong reagent gas inlet port e Wrong ions entered in tune file e Wrong tune file selected e Not enough bake out time has elapsed since vent background is too high e Wrong column positioning extending gt 2 mm past tip of interface e Interface tip seal not installed e El source installe
55. loss of H20 or NH3 observed as a subsequent loss of 18 or 17 amu respectively is also common 380 Appendix A Chemical lonization Theory Positive CI theory Charge exchange Charge exchange ionization can be described by the reaction Xt M gt MEK 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 car bon monoxide hydrogen and other gases that do not react chemically with the analyte Each of these reagent gases once ionized has a recombination energy expressed as Xt e7 gt X or simply the recombination of the ionized reagent with an electron to form a neu tral species If this energy is greater than the energy required to remove an elec tron from the analyte then the first reaction above is exothermic and thermodynamically allowed Charge exchange chemical ionization is not widely used for general analytical applications It can however be used in some cases when other chemical ioniza tion processes are not thermodynamically favored 381 Appendix A Chemical lonization Theory Negative Cl theory Negative CI theory Negative chemical ionization NCI is performed with analyzer voltage polarities reversed to select negative ions There are several chemical mechanisms for nega tive chemical ionization Not all mechan
56. mass spectra No peaks e Jon source cables not connected e Bad connections to or from the detector e HED power supply output cable has failed white cable e Other electronics failure Isotopes are missing or isotope ratios are incorrect e Peaks are too wide or too narrow e Scan speed is too high scan mode e Dwell time is too short SIM mode e Electron multiplier voltage is too high e Repeller voltage is too high e High background e Dirty ion source High background e Pressure in the analyzer chamber is too high e Air leak e Contamination 103 4 Troubleshooting the MSD Mass spectral symptoms High abundances at m z 18 28 32 and 44 or at m z 14 and 16 e System was recently vented residual air and water e Air leak Large peaks at m z 14 and 16 are symptomatic of especially large leaks Mass assignments are incorrect Small shape changes at the top of the mass peaks can cause 0 1 amu shifts in mass assignments Shifts greater than 0 2 amu indicate a possible malfunction e MSD has not had enough time to reach thermal equilibrium e Large variations in the temperature of the laboratory e MSD has not been tuned recently or at the temperature at which it is operating e Incorrect tune file inappropriate parameters Peaks have precursors The tune report lists the size of the precursors for the tune masses Small precur sors are not unusual If the precursors are unacceptably large for your application
57. mole 185 Methyl amine 188 Methyl chloride 202 Methyl cyanide 178 Methyl sulfide 197 Methyl cyclopropane 179 Nitroethane 190 Nitromethane 121 n Propyl acetate 198 Propylene 175 Toluene 140 trans 2 Butene 141 Trifluoroacetic acid 190 Xylene 182 Positive CI theory Proton affinity kcal mole 211 165 186 185 80 185 180 207 17 18 18 16 1 Nx oOo N 8 N 379 Appendix A Chemical lonization Theory Positive Cl theory Hydride abstraction In the formation of reagent ions various reactant ions can be formed that have high hydride ion H7 affinities If the hydride ion affinity of a reactant ion is higher than the hydride ion affinity of the ion formed by the analyte s loss of H7 then the thermodynamics are favorable for this chemical ionization process Examples include the hydride abstraction of alkanes in methane chemical ioniza tion In methane CI both CHs and CjHs5 are capable of hydride abstraction These species have large hydride ion affinities which results in the loss of H for long chain alkanes according to the general reaction Rt M gt M H RH For methane R is CH and CoH5 and M is a long chain alkane In the case of CHs the reaction proceeds to form M H t CH 4 H The spectra resulting from hydride abstraction will show an M 1 amu peak resulting from the loss of H This reaction is exothermic so fragmentation of the M H ion is often observed Often both hy
58. 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 the Leaks section at the beginning of this chapter The reagent gas supply is at the wrong pressure Check the regulator on the reagent gas supply It should be adjusted to 20 psi 140 kPa A leak in the reagent gas delivery path This is especially likely if you have set the methane flow much higher than normal and the ratio is still too low Check the reagent gas path Tighten fittings 145 Possible Cause The Cl ion source is dirty Action Clean the ion source See the Maintenance chapter of this manual for more infor mation 146 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting High electron multiplier voltage High electron multiplier voltage The electron multiplier voltage can range from a few hundred volts to 3000 V If the CI autotune program consistently sets the electron multiplier voltage at or above 2600V but can still find peaks and complete the tune it may indicate a problem The filament is worn out The CI filament may wear out without actually breaking Check the Electron Energy ramp the curve should have a definite maximum with an inflection point If the curve is linear with a positive slope and no inflection point and the EMV is high the filament has st
59. 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 Technologies service representative 318 Source power cable Side board control cable Side board front Lut ash Signal cable o 11 Electronics Signal amplifier board MS control card Main board HED power cable Detector focus cable Side board rear High voltage HED power supply AC board Low voltage power supply Toroid transformer TT ck Sa 319 See also 11 Electronics Control panel and power switch CAUTION Control panel and power switch Control panel The MSD has a control panel on the front of the instrument You can view MSD system status and perform some control functions from the control panel Functions available through the control panel include e Prepare to vent cool analyzer and turn off high vacuum pump e Monitor MSD status e Run autotune e Run method e Run sequence e View and set analyzer tempe
60. oil trap to the trap adapter The oil trap will contain traces of oil solvents and analytes Treat it as hazardous Dispose of the oil trap in accordance with local environmental and safety regulations If the trap has turned brown quickly the MSD probably has a large air leak which is causing pump oil to get blown out the exhaust port Find and repair the air leak before installing a new trap See the 5973N MSD Maintenance CD ROM 166 ao a of iN YOO 5 Materials needed 6 Maintaining the MSD To check the diffusion pump fluid WARNING WARNING To check the diffusion pump fluid Screwdriver Torx T 15 8710 1622 Remove the upper and lower MSD covers See page 52 Do not remove any other covers Removing other covers may expose hazardous voltages Check the diffusion pump fluid level The diffusion pump fluid level can be seen through the window below the fan at the front of the MSD The diffusion pump fluid level should be between the top and bottom of one of the FULL ranges There are two sets of marks Use the HOT marks if the diffusion pump 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 diffusion pump fluid Do not just add fluid The pump fluid should be clear or almost
61. operate at very high temperatures Do not touch any part until you are sure it is cool Always wear clean gloves to prevent contamination when working in the analyzer chamber If you feel resistance stop Do not try to force the side plate open Verify that MSD is vented Verify that both the front and rear side plate screws are completely loose 56 2 Operating the MSD To open the analyzer chamber f omin HE a asp if M WU Front thumbscrew l D oc 2s ED 5 2 fae S 2 S oOo E O Source power cable Side board control cable Side plate 57 Materials needed WARNING CAUTION 2 Operating the MSD To close the analyzer chamber To close the analyzer chamber Gloves clean lint free large 8650 0030 small 8650 0029 Make sure all the internal analyzer electrical leads are correctly attached Check the side plate O ring Make sure the O ring has a very light coat of Apiezon L high vacuum grease If the O ring is very dry it may not seal well If the O ring looks shiny it has too much grease on it See page 200 for instructions for lubricating the side plate O ring Close the side plate Reconnect the side board control cable and source power cable to the side board Make sure the vent valve is closed Pump down the MSD page 60 Gently hand tighten the front side plate thumbscrew This is
62. parameters affecting 302 reinstalling 220 removing 218 selection 302 Flow control display reagent gas flow control module 293 Flow control module 293 schematic 295 state diagram 74 296 Flow rate See Column flow Foreline gauge 274 reinstalling 188 removing 186 See also Foreline pressure Foreline pressure exceeding 300 mTorr 114 monitoring 35 38 40 too high 107 too low 108 typical 38 391 Index Foreline pump 272 ammonia use requires frequent oil changes 254 ballast control 272 ballasting in ammonia CI MSD 254 effect of low oil level 107 failure to turn on 97 incorrect operation 97 minimizing damage from ammonia reagent gas 254 oil trap replacing 166 part numbers 346 power cord receptacle 332 turned off during pumpdown 97 venting the exhaust 34 157 272 vibration 272 See also Foreline pump oil Foreline pump oil adding and checking 160 as a source of contamination 119 draining 162 refilling the pump with 164 replace every 6 months 152 Foreline pump power cord receptacle 332 Foreline trap See Oil trap Foreline vacuum gauge See Foreline gauge Front panel See Status Display Fuses on the back panel 332 part numbers 339 replacing the primary fuses 242 G Gas purifier methane isobutane replacing 255 Gauge controller 287 abnormal or blank display 46 86 108 indicated vs actual pressure 46 86 287 monitoring pressure with 35 46 86 overpressure shutdown 4
63. power cord receptacle provides ac power for the foreline pump If the power switch is off no power is supplied to the foreline pump Remote start connector The remote start connector is the external connector for the remote start circuitry on the LAN MS control card It receives remote start signals from the GC LAN 1 0 connector The LAN cable from the data system is connected to the I O LAN connector This cable carries all data communication between the PC and the MSD LAN MSD control card LEDs The upper two LEDs indicate network communication The two bottom LEDs are the power and the heartbeat indicator 332 11 Electronics Back panel and connectors Transmit Tx and Receive Rx LEDs Remote start cable High vacuum control cable High vacuum power cable ga L 5 p a Primary fuses x A a L Kom gem Power cord receptacle Al Keren Foreline pump power cord LAN cable Power PWR and Heartbeat Heart LEDs 333 MSD remote start connector 11 Electronics Interfacing to external devices Interfacing to external devices Remote control processor The remote control processor on the LAN MS control card synchronizes start run signals with GCs and other devices The functions of the remote control processor are extended to the remote start Remote connector on the back panel of the MSD The remote start cable c
64. pump 4 0x 10 8 0x 105 1 0 x 10 Not recommended Not supported Not supported If the pressure is consistently higher than those listed refer to the online help in the MSD ChemStation software for information on troubleshooting air leaks and other vacuum problems If the pressure rises above approximately 8 x 10 Torr the gauge controller will turn off the triode gauge tube The gauge tube does not turn back on automatically 47 Materials needed 2 Operating the MSD To measure column flow linear velocity To measure column flow linear velocity Syringe Set Data Acquisition for splitless manual injection and selected ion monitoring SIM of m z 28 Press the Prep Run button on the GC keypad Inject 1 ul of air into the injection port and press the Start Run button Wait until a peak elutes at m z 28 Note the retention time Calculate the average linear velocity Average linear velocity cm sec 100 L t where L length of the column in meters t retention time in seconds Be sure to account for any pieces of column broken off A 1 meter section missing from a 25 meter column can yield a 4 error Use this value to verify the MSD ChemStation flow calculations page 49 If the numbers disagree click the Change button to calibrate the column dimen sions To calculate the volumetric flow rate 0 785 D L t Volumetric flow rate ml min where D internal column diameter in mi
65. temperature from a 6890 Plus GC 67 To remove the MSD covers 52 To vent the MSD 54 To open the analyzer chamber 56 To close the analyzer chamber 58 To pump down the MSD 60 To connect the gauge controller 63 To move or store the MSD 65 To vent the MSD without the ChemStation 68 Operating the MSD How to perform some basic operating procedures for the MSD Operating the MSD Operation of the MSD from the data system The software performs tasks such as pumpdown monitoring pressures setting temperatures tuning and preparing to vent These tasks are de scribed in this chapter Data acquisition and data analysis are described in the manuals and online help supplied with the MSD ChemStation software Operation of the MSD from the control panel You can use the 5973N MSD control panel to perform many of the same tasks that the ChemStation can perform See the 5973N Control Panel Quick Reference G2589 90011for more information Some conditions must be met before you turn on the MSD Verify the following before you turn on or attempt to operate the MSD e The vent valve must be closed the knob turned all the way clockwise e All other vacuum seals and fittings must be in place and fastened correctly The the front side plate screw should not be tightened unless hazardous carrier or reagent gasses are being used e The MSD is connected to a grounded power source e The GC MSD interface extends into the GC oven e A
66. terminates in spade lugs Care must be taken to ensure that the sys tem is actually ready before the start run signal is sent If necessary the remote start connector on the back of the MSD can be used to send the start run signal A contact closure between the start and ground pins will start the run if the system is ready 335 336 12 Electronics 339 Vacuum system 344 Analyzer 352 EI GC MSD interface 358 Consumables and maintenance supplies 360 Ferrules 362 CI Parts 364 Parts This chapter lists parts that can be ordered for your MSD General Parts This chapter lists parts that can be ordered for use in maintaining your 5973N MSD It includes most of the parts or assemblies in the MSDs This chapter is organized so that related parts are grouped together Some of the parts listed are not user replaceable They are listed here for the convenience of Agilent Technologies service representatives To order parts To order parts for your MSD address the order or inquiry to your local Agilent Technologies office Supply them with the following information e Modeland serial number of your MSD located on a label on the lower left side near the front of the instrument See page 9 e Part number s of the part s needed e Quantity of each part needed Some parts are available as rebuilt assemblies Rebuilt assemblies pass all the same tests and meet all the same specifica tions as new parts Rebuilt
67. the methane flow adjust panel Tell if a gross air leak is present by monitoring the ions at m z19 protonated water and 32 Confirm if the MS is generating real ions and not just background noise It is nearly impossible to perform any diagnostics on the system in NCI In NCI there are no reagent gas ions to monitor for any gas It is difficult to diagnose an air leak and difficult to tell whether a good seal is being created between the interface and the ion volume The PCI standard turbo pump MSD requires lower reagent gas flows and lower reagent ion ratios than the PCI NCI MSD 3 Operating the CI MSD To switch from El to Cl operating mode CAUTION CAUTION To switch from EI to CI operating mode Always verify MSD performance in El before switching to Cl operation See page 51 Always set up the Cl MSD in PCI first even if you are going to run NCI Vent the MSD See page 54 Open the analyzer Remove the EI ion source 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 Electrostatic discharge is a threat to the MSD electronics during maintenance on page 158 Take anti static precautions before you open the analyzer chamber 4 Install the CI ion source See page 248 5 Install the interface tip seal See page 250 6 Close the analyzer 7 Pump down the MSD See page 60
68. the Diagnostics menu e Inthe Instrument Control view in the Edit Parameters dialog box select MS OFF from the Execute menu e Inthe Manual Tune view select MS OFF from the Execute menu If your MSD is equipped with a gauge controller switch off the triode gauge and the gauge controller Remove the analyzer cover See page 52 Loosen the calibration vial collar by turning it counterclockwise Counterclockwise as viewed from the bottom vial side of the collar Do not remove the collar Pull the calibration vial out You may feel some resistance due to residual vacuum 181 6 Maintaining the MSD To remove the El calibration vial Calibration valve Collar Calibration vial 182 Materials needed 6 Maintaining the MSD To refill and reinstall the El calibration vial CAUTION To refill and reinstall the EI calibration vial PFTBA 05971 60571 or other tuning compound Remove the calibration vial See page 190 Pour PFTBA into the vial or use a pipette Leave the top 6 mm of the vial unfilled Push the calibration vial into the valve as far as possible Withdraw the vial 1 mm This prevents damage when you tighten the collar Turn the collar clockwise to tighten it Clockwise as viewed from the bottom vial side of the collar 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
69. the MSD To remove the ion source 207 Materials needed 6 Maintaining the MSD To disassemble the ion source To disassemble the ion source Gloves clean lint free large 8650 0030 small 8650 0029 Hex ball driver 1 5 mm 8710 1570 Hex ball driver 2 0 mm 8710 1804 Hex nut driver 5 5 mm 8710 1220 Wrench open end 10 mm 8710 2353 Remove the ion source See page 206 Remove the filaments Separate the repeller assembly from the source body The repeller assembly includes the source heater assembly repeller and related parts Remove the repeller Unscrew the interface socket A 10 mm open end wrench fits on the flats on the interface socket Remove the setscrew for the lenses Push the lenses out of the source body 208 6 Maintaining the MSD To disassemble the ion source Interface socket Source body Set scr ew Repeller Repeller insulator Filament S Source heater assembly Repeller insulator Washe r Repeller nut do not over tighten on foc us lens Drawo ut cylinder Drawo ut plate Lens in sulator one of a pair Entrance lens 209 Materials needed CAUTION 6 Maintaining the MSD To clean the ion source To clean the ion source Abrasive paper 5061 5896 Alumina abrasive powder 8660 0791 Aluminum foil clean Cloths clean 0598
70. the autotune that is currently loaded in the PC memory See the 5973N Control Panel Quick Reference Guide for more information In the Instrument Control View select Perform MS Autotune from the Instrument menu Select the tune program you wish to use The tune will start immediately For most applications Autotune gives the best results Standard Tune is not recommended as it may reduce sensitivity Quick Tune is used to adjust peak width mass assignment and abundance without changing ion ratios Always tune the MSD with the same GC oven temperature and column flow and the same analyzer temperatures that will be used for data acqui sition Wait for the tune to complete and to generate the report Save your tune reports To view history of tune results select View Tunes under the Qualify menu To manually tune your MSD or to perform special autotunes select Manual Tune from the View menu In the Manual Tune view you can manually adjust most tune parameters to suit special needs From the Tune menu in addition to the tunes available from Instrument Control you can select special autotunes for specific spectral results DFTPP Tune BFB Tune or Target Tune See the manuals or online help provided with your MSD ChemStation software for additional information about tuning 50 Materials needed 2 Operating the MSD To verify system performance To verify system performance 1 pg ul 0 001 ppm OFN sample
71. 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 261 Note that you must power cycle the MSD to recover from this state Control panel says No server found e Disconnected LAN cable between MSD and the hub or the hub and the PC e PC is turned off 97 4 Troubleshooting the MSD Chromatographic symptoms Chromatographic symptoms This section describes symptoms you may observe in the chromatograms gener ated by data acquisition In general these symptoms do not prevent you from operating your GC MSD system They indicate however that the data you are acquiring may not be the best data obtainable These symptoms can be caused by instrument malfunctions but are more likely caused by incorrect chromatographic technique Two of the symptoms If sensitivity is low and If repeatability is poor also apply to mass spectral data 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 e Incorrect sample concentration e No analytes present e Syringe missing from the ALS or not installed correctly e Injection
72. the sides of the pump and the liquid drains down to the bottom The liquid is boiled again and is reused continuously A cooling fan is located between the diffusion pump and the front cover of the MSD The fan draws air through the cover and blows it over the pump Without this cooling the pump fluid vapor would not condense correctly but would diffuse into the analyzer chamber The foreline pump is connected by the foreline hose to the outlet of the diffusion pump It removes the gas molecules that reach the outlet The diffusion pump operation is controlled by the ac board The ac board turns on the diffusion pump heater automatically as soon as the foreline pump lowers the pressure in the analyzer chamber below approximately 300 mTorr 0 3 Torr Until the foreline pressure drops below 300 mTor the diffusion pump heater will not turn on If the pressure does not drop below 300 mT within seven minutes of turn ing the MSD on the foreline pump will shut off During operation if the foreline pressure rises 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 x 10 Torr for GC helium carrier gas flows up to 2 ml minute High vacuum manifold pres sure can only be measured if your MSD is equipped with the optional gauge con troller 276 See Also See Also Table 7
73. turned off 185 Materials needed 6 Maintaining the MSD To remove the foreline gauge WARNING CAUTION To remove the foreline gauge Screwdriver flat blade large 8730 0002 Vent the MSD See page 54 Separate the MSD from the GC See page 171 The foreline pump and diffusion pump may still be hot Unplug the foreline gauge cable from the foreline gauge Disconnect the foreline gauge assembly from the diffusion pump outlet Loosen the hose clamp Pull the foreline gauge assembly out of the foreline hose Be sure the MSD is vented to atmosphere before breaking the seal at the foreline gauge Never vent the MSD at the pump end use the vent valve 186 6 Maintaining the MSD To remove the foreline gauge Foreline hose and hose clamp MA N Foreline gauge assembly NS Pls 4 o NS 1 rae Cae Diffusion pump outlet i o Foreline gauge E H o D Foreline gauge cable 187 Materials needed 6 Maintaining the MSD To reinstall a foreline gauge To reinstall a foreline gauge Foreline gauge assembly G1099 60545 Screwdriver flat blade large 8730 0002 Connect a new foreline gauge assembly to the foreline hose Tighten the hose clamp
74. types of inlets refer to your 6890 Series Gas Chromatograph Operating Manual Prepare the column for installation page 22 Position the column so it extends 4 to 6 mm past the end of the ferrule Slide the septum to place the nut and ferrule in the correct position Insert the column in the inlet Slide the nut up the column to the inlet base and finger tighten the nut Adjust the column position so the septum is even with the bottom of the column nut Tighten the column nut an additional 1 4 to 1 2 turn The column should not slide with a gentle tug Start carrier gas flow Verify flow by submerging the free end of the column in isopropanol Look for bubbles 24 1 Installing GC Columns To install a capillary column in a split splitless inlet Insulation cup Reducing nut Capillary column Ferrule not visible Inlet column nut Septum 25 Materials needed 1 Installing GC Columns To condition a capillary column WARNING CAUTION See Also To condition a capillary column Carrier gas 99 999 pure or better Wrench open end 1 4 inch x 5 16 inch 8710 0510 Do not condition your capillary column with hydrogen Hydrogen accumulation in the GC oven can result in an explosion If you plan to use hydrogen as your carrier gas first condition the column with ultrapure 99 999 or better inert gas such as helium nitrogen or argon Install the column in the GC inl
75. you are going to run NCI Verify that the MSD performs correctly in EI mode first See page 51 Load the PCICH4 U tune file or an existing tune file for the reagent gas you are using If you use an existing tune file be sure to save it with a new name if you don t want to over write the existing values Accept the default settings Perform methane setup See page 76 Under the Tune menu click CI Autotune Avoid tuning more often than is absolutely necessary this will minimize PFDTD background noise and help prevent ion source contamination There are no tune performance criteria If autotune completes it passes If the tune sets the electron multiplier voltage EMVolts at or above 2600V however you may not be able to acquire data successfully if your method sets EMVolts to 400 or higher The autotune report contains information about air and water in the system The 19 29 ratio shows the abundance of water The 32 29 ratio shows the abundance of oxygen 80 3 Operating the Cl MSD To perform a positive Cl autotune methane only PCI mode Methane Tune Instrument GC_MS Instrument 1 Wed Aug 25 11 19 30 1999 C HPCHEM 1 5973N PCICH4 U Flow 20 Gas A Mass 41 00 Mass 267 00 Mass 599 00 Ab 315018 Ab 725285 Ab 691110 Ion Pol POS MassGain 199 Pw50 0 61 Pw50 0 59 Pw50 0 61 ee MassOffs 11 Emission 242 3 AmuGain 1537 EleEnergy 54 2 AmuOffs 120 Filament 1 Wid219 0 058 DC Pol NEG Repeller
76. 0 60051 Cotton swabs 5080 5400 Glass beakers 500 ml Gloves clean lint free large 8650 0030 small 8650 0029 Solvents acetone reagent grade methanol reagent grade methylene chloride reagent grade Ultrasonic bath Disassemble the ion source See page 208 Collect the following parts to be cleaned e Repeller e Interface socket e Source body e Drawout plate e Drawout cylinder e Ton focus lens e Entrance lens These are the parts that contact the sample or ion beam The other parts normally should not require cleaning lf insulators are dirty clean them with a cotton swab dampened with reagent grade methanol If that does not clean the insulators replace them Do not abrasively or ultrasonically clean the insulators 210 6 Maintaining the MSD To clean the ion source Source body Repeller Interface socket Drawout plate Drawout cylinder lon focus lens Entrance lens 211 Major contamination CAUTION WARNING WARNING 6 Maintaining the MSD To clean the ion source In the event of a diffusion pump backstream or other major contamination the other source components must be cleaned ultrasonically but not abrasively or replaced The filaments source heater assembly and insulators cannot be cleaned ultrasonically Replace these components if major contamination occurs Abrasively clean the surfaces that contact the sample or ion
77. 0 Hz or 220 240 V ac 50 Hz single phase nominal e 850 VA diffusion pump or 700 VA turbomolecular pump e Main supply voltage not to exceed 10 of the nominal voltage e IEC Transient Overvoltage Category Overvoltage Category II e IEC pollution Degree 2 Environmental Specifications e Indoor use e Altitude up to 4000 meters e Operating environment 15 to 35 C at constant temperature constant temperature 2 C per hour e Operating humidity 25 to 50 relative humidity Non operating humidity 10 to 95 relative humidity non condensing 2 Agilent Technologies 999e Innovating the HP Way Printed on recycled paper Copyright 1999 Manual Part Number Agilent Technologies G2589 90001 Printed in USA 11 99
78. 099 69001 G1099 60229 62589 60584 G1099 69015 None of the parts in this table are user replaceable parts Refer service to your Agilent Technologies service representative 342 12 Parts Electronics Main board G1099 69010 Side board 61099 69015 Signal amplifier board G1099 69001 LAN MS control card 05990 69410 AC board G2589 69005 High voltage HED power supply Fan for electronics module 3160 1038 Control panel assembly G2589 60584 Low voltage ac dc power supply 0950 3067 Toroid transformer G1099 60229 343 Table 12 12 Parts Vacuum system Vacuum system This section lists replacement parts available for the vacuum system It includes clamps O rings and seals foreline pump and related components diffusion pump vacuum system components and turbomolecular pump vacuum system components O rings and seals Description Part number Calibration valve O ring 1 4 inch 0905 1217 End plate O ring for front and rear end plates 0905 1441 GC MSD interface O ring 0905 1405 HED feedthrough G1099 80012 HED feedthrough O ring 0905 0490 KF10 16 seal foreline pump inlet and diffusion pump outlet 0905 1463 KF25 O ring assem
79. 1 Transfer line See GC MSD interface Transformer toroid 331 Trap See Oil trap Triode gauge tube 285 baffle in stem 285 connecting a gauge controller to 63 ignition of hydrogen by 46 86 285 287 implosion hazard 46 86 monitoring high vacuum pressure 46 86 reinstalling 198 removing 196 shield 285 turning on 46 86 Troubleshooting 93 119 121 air leaks determining presence of leak 124 air leaks finding location of leak 126 common Cl specific problems 122 See also Symptoms of malfunctions tips and tricks 95 123 Tube triode gauge 285 Tune report 50 400 Index Tuning 50 cannot begin 117 compound 283 See also Autotune See also the online help in the software Turbo pump controller 328 Turbomolecular turbo pump monitoring the speed of 38 40 part numbers 350 Turn on failure of the MSD to 96 See also Pumpdown See Pumpdown U Ultrasonic cleaning of ion source parts 212 V Vacuum gauge See Foreline gauge See Triode gauge Vacuum gauge controller monitoring pressure with 86 Vacuum manifold diffusion pump version 266 turbo pump version 267 Vacuum manifold pressure monitoring 46 typical 274 280 Vacuum seals 270 part numbers 344 Vacuum system 259 288 determining type 20 diffusion pump system overview 264 maintaining 159 maintenance schedule 152 159 overview 260 part numbers 344 status monitoring 38 40 turbo pump system overview 265 Valve calibration
80. 112 4 Troubleshooting the MSD Error messages Difficulty with the fan If a cooling fan fault occurs the vacuum control electronics automatically shut off the high vacuum pump and the ion source and mass filter heaters Therefore the message The system is in vent state may also appear It is important to note that even though the high vacuum pump is off the analyzer chamber may not actually be vented See The system is in vent state in this section for precautions to take e One of the fans is disconnected e One of the fans has failed e MSD electronics are not working correctly Difficulty with the HED supply The only time this error occurs is if the output of the supply cannot get to its des tination the HED e Large peak such as the solvent peak eluted while the analyzer was on e Pressure in the analyzer chamber is too high e Detector is not working correctly e MSD electronics are not working correctly Difficulty with the high vacuum pump In an MSD equipped with a diffusion pump this indicates the diffusion pump became too hot In an MSD equipped with a turbomolecular pump this indicates the pump failed to reach 50 of full speed within 7 minutes or experienced a fault You must switch the MSD off and back on to remove this error message Be sure the diffusion pump has cooled or the turbo pump has slowed down before switch ing off the MSD The message will reappear if the underlying problem has not been corrected Diff
81. 181 8836 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 Gloves clean large 8650 0030 small 8650 0029 Inlet column nut 5181 8830 Magnifying glass Septum may be old used inlet septum Slide a septum column nut and conditioned ferrule onto the free end of the column The tapered end of the ferrule should point away from the column nut Use the column cutter to score the column 2 cm from the end Break off the end of the column Hold the column against the column cutter with your thumb Break the column against edge of the column cutter Inspect the end for jagged edges or burrs If the break is not clean and even repeat steps 2 and 3 Wipe the outside of the free end of the column with a lint free cloth moistened with methanol 22 Capillary column Column cutter Ferrule Inlet column nut Septum 1 Installing GC Columns To prepare a capillary column for installation 23 Materials needed 1 Installing GC Columns To install a capillary column in a split splitless inlet To install a capillary column in a split splitless inlet Gloves clean large 8650 0030 small 8650 0029 Metric ruler Wrench open end 1 4 inch x 5 16 inch 8710 0510 To install columns in other
82. 1999 80410 7157 0210 61999 00411 5180 4110 5180 4116 5080 8751 5080 8751 366 Rear flow module cover 61999 00411 analyzer cover 999 60440 aoa Front flow module cover 999 20422 rp isplay module 999 65461 Qo Isolation valve G1999 80402 Cl calibration valve assembly G1999 60456 Mass flow controller 0101 1006 Reagent gas select valve G1999 80401 12 Parts CI Parts Reagent gas supply tubing 7157 0210 367 Table 27 Cl ion source parts Description Box for ion source shipping and storage Cl ion source tested Cl drawout cylinder Cl drawout plate Cl filament Cl heater block Cl interface tip seal Cl ion focus lens Cl lens insulators set Cl repeller Cl repeller insulator Cl source body Cl source heater assembly Dummy filament Entrance lens Screw socket head cap for mounting filaments Setscrew for mounting heater and lens stack Screw M3 X 4L socket head for mounting RTD Screw M2 x 8L mounts source to radiator Part number 61999 65001 61999 65402 61999 20444 61999 20446 G1099 80053 G1999 20431 G1999 60412 61999 20443 G1999 20445 G1999 20432 G1999 20433 G1999 20430 61999 60414 61999 60454 05971 20126 G1999 20021 61999 20021 0515 2903 0515 1046 368 Cl ion source body 61999 20430 Setscrew 0515 1446 Cl repeller G1999 20432 Cl repeller insulator 61999 20433
83. 284 8 Vacuum System Triode gauge tube WARNING WARNING Triode gauge tube The MSD is equipped with a triode gauge tube connected to the analyzer chamber With the optional 59864B Gauge Controller the triode gauge can be used to mea sure the pressure high vacuum in the analyzer chamber The triode gauge will not operate at pressures above 8 x 10 Torr The triode gauge cannot be used without the gauge controller Parts of the triode gauge tube operate at approximately 150 V dc Turn off the triode gauge before working near it The triode filament can ignite hydrogen Never turn on the tube if there is a possibility that hydrogen has accumulated in the manifold The triode gauge relies on the ionization of gas molecules to establish a pressure dependent current flow In the triode gauge a regulated electrical current is passed through a filament called the cathode causing it to emit electrons The electrons accelerate from the filament toward a surrounding grid which is held at a higher potential 150 V dc The emitted electrons ionize gas molecules in the tube Positive ions are driven to a grounded wire mesh collector At the collector the positive ions regain missing electrons This generates current in the collector The number of ions formed is a function of the number of gas molecules present that is the gas pressure There fore pressure can be calculated based on the current applied to the filament c
84. 3 339 353363 379389399 a S ne rt r 100 150 200 250 350 400 Scan 1542 9 780 min FAMESO1A D 265 74 87 97 111 129 143 157 171 185 199 213 227237 251 r DEE a rr 316 ammonia PCI 63 75 87 101 115 rN 100 129 143153 171 185195 209 227 241 258 272284 298 330 360 T rrr m rr T T T T 150 200 250 300 350 377 Appendix A Chemical lonization Theory Positive Cl theory Proton transfer Proton transfer can be expressed as BH M gt MHt B 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 The most frequently used example is the proton transfer from CH_ to the molec ular analyte which results in the protonated molecular ion MH The relative proton affinities of the reagent gas and the analyte govern the proton transfer reaction If the analyte has a greater proton affinity than the reagent gas then proton transfer can take place Methane CH H is the most common reagent gas because its proton affinity is very low Proton affinities can be defined according to the reaction B H gt 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
85. 42 10 29 83 Materials needed 3 Operating the CI MSD To verify positive CI performance CAUTION See also To verify positive CI performance Benzophenone 100 pg ul 8500 5440 Always verify MSD performance in El before switching to Cl operation See page 51 Always set up the Cl MSD in PCI first even if you are going to run NCI Verify that the PCICH4 U tune file is loaded On the flow control panel turn Purge off Set Gas A to 20 flow for PCI NCI MSDs or 10 for PCI MSDs In Manual Tune view perform CI setup See page 76 Run Cl Autotune See page 78 Run the PCI sensitivity method BENZ_PCI M using 1 ul of 100pg ul Benzophenone Verify that the system conforms to the published sensitivity specification The 5973Network Series Mass Selective Detector Specifications 5968 7358E 84 3 Operating the Cl MSD To verify negative Cl performance Materials needed CAUTION See also To verify negative CI performance This procedure is for EI PCI NCI MSDs only OFN 1 pg ul 8500 5441 Always verify MSD performance in El before switching to Cl operation See page 51 Always set up the Cl MSD in PCI first even if you are going to run NCI Verify that the MSD performs correctly in EI mode Load the NCICH4 U tune file and accept the temperature setpoints Turn Purge and Gas A on and let the system stabilize for 90 minutes Turn Purge off and set Gas A to 40 flow In Manual T
86. 437 G1099 20552 G1099 20553 3160 1037 G1099 60545 0905 1463 0100 1397 0905 1463 0100 1395 0100 1884 61099 00003 61099 60021 0960 0897 61099 20549 61099 20554 348 12 Parts Vacuum system Calibration valve assembly diffusion pump version G1099 60201 Vent valve knob G1099 20554 Analyzer chamber diffusion pump version G1099 20549 Side plate G1099 60021 Triode gauge tube 0960 0897 ae S Diffusion pump baffle adapter Vc 5 lt 7 61099 20021 FPF OE IL KF50 clamp 0100 1395 Diffusion pump 120V G1099 80500 220V G1099 80501 Foreline gauge assembly G1099 60545 Fan diffusion pump position 3160 1037 349 Table 15 12 Parts Vacuum system Turbomolecular pump MSD vacuum system components Description Baffle inside stem of triode gauge tube not shown Calibration valve assembly for performance turbo MSD Calibration valve assembly for standard turbo and diffusion pump MSDs Calibrant vial Claw clamps for turbo pump Collar for triode gauge tube Fan KF25 clamp for turbo pump outlet KF25 O ring assembly for turbo pump outlet Manifold end plates front rear Shield for triode gauge tube port Side plate includes thumbscrews Triode gauge tube Performance turbomolecular pump Standard turbomolecular pump Elbow foreli
87. 5972 60053 Filament assemby CI G1099 80053 Foreline pump oil 1 liter 6040 0834 Foreline exhaust oil mist trap G1099 80037 Heater sensor assemblies GC MSD interface 05972 60106 ion source G1099 60177 mass filter G1099 60172 Octafluoronapthalene OFN 1 pg ul 8500 5441 Perfluorotributylamine PFIBA certified 10 gram 8500 0656 Perfluorotributylamine PFIBA sample kit 05971 60571 Sample evaluation A hydrocarbons 05970 60045 Vacuum gauges foreline gauge assembly G1099 60545 triode gauge tube 0960 0897 Do not use an exhaust oil mist trap if you are analyzing hazardous samples or if you are using hazardous carrier gas or if you are running Cl Plumb the pump exhaust to a fume hood 363 CI Parts This section lists parts that may be required to maintain the 5973N MSD with CI The parts listed in this section are related directly to the accessory other parts for the MSD can be found in the previous section of this chapter 364 Table 25 12 Parts Cl Parts Miscellaneous parts for CI MSD Description Benzophenone 100 pg ul Bipolar HED power supply EI PCI NC MSDs only Foreline pump secondary containment tray Methane isobutane gas purifier PFDTD calibrant Reagent gas line 20 ft 1 8 ID stainless steel cleaned Wipes industrial 300 package Swagelok fittings for gas purifier and inlet to flow module Ferrule front for 1 8 inch tubing 20 package Ferrule rear for 1 8 inch tubing 20 package
88. 6 Maintaining the MSD To reinstall a triode gauge tube WARNING CAUTION To reinstall a triode gauge tube Gloves clean lint free large 8650 0030 small 8650 0029 Triode gauge tube 0960 0897 Remove the old triode gauge tube See page 196 Slide the baffle into the open end of the new triode gauge tube Wear clean gloves when handling the baffle and new triode gauge tube If you set the baffle down make sure it is on a clean surface Slide the triode gauge tube into the collar Leave 3 mm of the metal sleeve exposed Be sure the pins are oriented as in the illustration Gently hand tighten the collar by turning it clockwise Do not overtighten you can break the tube or damage the O ring Reconnect the cable from the gauge controller to the triode gauge tube Route the cable so it does not put stress on the triode gauge tube Be careful when attaching the cable Too much force can break the tube Do not move the controller or cable while connected to the tube Pump down the MSD See page 60 198 6 Maintaining the MSD To reinstall a triode gauge tube ee CRS Cc Baffle N N BERE I Triode gauge tube AA Triode gauge cable f n Triode gauge collar al 199 Materials needed 6 Maintaining the MSD To lubrica
89. 7 power indicator does not light 109 pressure range 46 86 relative sensitivity to different gases 86 Gauge Controller 59864B 287 Gauge controller connecting 63 Gauge controller required for CI 7 Gauge tube See Triode gauge tube GC components responsible for air leaks 118 does not turn on 96 sources of contamination in 119 GC interface See GC MSD interface GC keypad setting GC MSD interface temperature from 67 GC MSD interface 289 296 failure to heat up 111 heated zone controlling 290 heater 36 290 maintaining 232 part numbers 358 reinstalling a heater and sensor 236 removing the heater and sensor 234 See also GC MSD interface temperature sensor thermocouple 290 GC MSD interface temperature 36 range 290 setting from the ChemStation 44 setting from the GC 67 GC MSD interface CI 292 tip seal 292 GC MSD interface CI See CI interface Grounded wrist strap 158 392 Index H Half splitting to find air leaks in CI MSD 126 Heater clamp CI interface 233 292 Heaters GC MSD interface reinstalling 236 GC MSD interface removing 234 heated zone used to power the GC MSD inter face heater 36 ion source reinstalling 224 ion source removing 222 mass filter reinstalling 228 mass filter removing 226 setting temperature monitors 40 viewing temperature and vacuum status 38 HED 312 difficulty with the HED power supply 113 HED feedthrough seal 271 HED power supply 331 High
90. 710 1570 Vent the MSD See page 54 Open the analyzer chamber See page 56 Remove the ion source See page 206 Remove the filament s to be replaced The analyzer operates at high temperatures Do not touch any part until you are sure itis cool 218 6 Maintaining the MSD a filament To remove Filament 1 Filament 2 219 Materials needed 6 Maintaining the MSD To reinstall a filament To reinstall a filament Filament assembly G1099 60053 Gloves clean lint free large 8650 0030 small 8650 0029 Hex ball driver 1 5 mm 8710 1570 Install the new filament Reinstall the ion source See page 216 Close the analyzer chamber See page 58 Pump down the MSD See page 60 Autotune the MSD See page 50 In the Edit Parameters dialog box Instrument Edit MS Tune Parameters select the other filament Autotune the MSD again Select and use the filament that give the best results If you decide to use the first filament run Autotune again to make sure the tune parameters are compatible with the filament Select Save Tune Parameters from the File menu 220 6 Maintaining the MSD To reinstall a filament Filament 1 Filament 2 221 Materials needed 6 Maintaining the MSD To remove the heater and sensor from the ion source To remove the heater and sensor from the ion source Gloves clean lint free large
91. 73N Mass Selective Detector MSD Related symptoms are grouped in these categories e General symptoms e Chromatographic symptoms e Mass spectral symptoms e Pressure symptoms e Temperature symptoms e Error messages e Contamination e Air leaks For each symptom one or more possible causes are listed The possible causes listed are not in a strict order In general however the possible causes listed first are the most likely causes or the easiest to check and correct See CI Troubleshooting 121 for help with Cl specific problem s This section is only a quick reference No corrective actions are listed for the possible causes for each symptom For more extensive troubleshooting information see the Troubleshooting 5973N MSD section in the online help of the MSD ChemStation software The online troubleshooting provides more explanation and in many cases corrective actions 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 you know the correct procedure and the dangers involved See the Troubleshooting 5973N MSD section in the online help and the other chapters in this manual for more information 94 4 Troubleshooting the MSD If the material in this chapter and in the online help proves insufficient to help you diagnose a problem contact your Agilent Te
92. 8 e Excessive noise See page 140 e Low chromatographic signal abundance See page 140 e Low signal to noise ratio See page 140 e Large peak at m z 19 See page 141 e Peak at m z 32 See page 142 132 5 Cl Troubleshooting No peaks 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 meth ane 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 e Wrong tune file loaded or tune file corrupted e Wrong ion polarity there are no reagent ions visible in NCI e No reagent gas flow look for background ions and check pressure e Wrong reagent gas selected for the tune file ooking for wrong ions e Large air leak e Dirty ion source e Poor vacuum pump problem See page 128 If MSD was recently switched from EI to CI e Interface tip seal not installed e No reagent gas flow e Analyzer not sealed big air leak e Wrong tune file loaded or tune file corrupted e Jon source not assembled or connected correctly e Wrong reagent gas selected for the tune file looking for wrong ions 133 5 Cl Troubleshooting No peaks No PFDTD peaks in PCI e Incorrect reagent gas There are no PCI PFDTD peaks created with isobutane or ammonia Switch to methane e Analyzer not sealed big air leak e No calibrant in v
93. 8500 5441 Verify the tune performance Verify that the system has been pumping down for at least 60 minutes Set the GC oven temperature to 150 C and the column flow to 1 0 ml min In the Instrument Control view select Checkout Tune from the Qualify menu The software will perform an autotune and print out the report When the autotune has completed save the method and then select Tune Evaluation from the Qualify menu The software will evaluate the last autotune and print a System Verification Tune report Verify the sensitivity performance Set up to inject 1 ul of OFN either with the ALS or manually In the Instrument Control view select Sensitivity Check from the Qualify menu Click the appropriate icons in the Instrument Edit window to edit the method for the type of injection Click OK to run the method When the method is completed an evaluation report will print out Verify that rms signal to noise ratio meets the published specification See the 59738Network Mass Selective Detector Specifications 5968 7358E 51 Materials needed 2 Operating the MSD To remove the MSD covers WARNING To remove the MSD covers Screwdriver TORX T 15 8710 1622 The analyzer cover is removed for venting and for many maintenance procedures The lower MSD cover is removed to check the fluid level in the diffusion pump and for a few maintenance procedures If you need to remove one of the MSD covers follo
94. AUGE button After a few seconds the pressure should be displayed Pressure is displayed in the format X X X where X is the base 10 exponent Units are Torr The gauge controller will not turn on if the pressure in the MSD is above approxi mately 8 x 10 Torr The gauge controller will display all 9s and then go blank The triode gauge tube can measure pressures between approximately 8 x 10 and less than 2 x 10 Torr The gauge controller is calibrated for nitrogen but all pressures listed in this manual are for helium Refer to the manual for the 59864B for infor mation on relative sensitivity to different gases The largest influence on operating pressure in EI mode 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 from instrument to instrument by as much as 30 46 Table 2 2 Operating the MSD To monitor high vacuum pressure Typical MSD pressure readings for various helium carrier gas flow rates Diffusion pump MSD Column flow ml min Triode gauge reading Torr Foreline gauge reading Torr 1 0 5 0 x 10 40 1 5 75x 10 53 2 0 1 0 x 10 Not 66 recommended Turbo pump MSDs Column flow ml min 1 0 2 0 24 3 0 40 Triode gauge reading Torr Performance turbo pump 1 5 x10 3 0 x 10 3 5x 10 45 x10 5 0 x 10 Triode gauge reading Torr Standard turbo
95. CI interface tip seal J G1999 60412 Ke Vacuum manifold Yj 7 J J af ee Z fd 7 Lin p ia es G1099 60107 Screws to attach interface to manifold 0515 0380 Screws for heater clamp 0515 0383 371 372 Appendix A Chemical ionization overview 374 References on chemical ionization 375 Positive CI theory 376 Proton transfer 378 Hydride abstraction 380 Addition 380 Charge exchange 381 Negative CI theory 382 Electron capture 384 Dissociative electron capture 385 Ion pair formation 385 Ion molecule reactions 386 Chemical Ionization Theory Appendix A Chemical lonization Theory Chemical ionization overview WARNING Chemical ionization overview Chemical ionization CI is a technique for creating ions used in mass spectromet ric 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 These collisions produce primarily positive ions Upon ionization the molecules of a given substance fragment in fairly predictable pat terns El is a direct process energy is transferred collisionally from electrons to the sample molecules For CI in addition to the sample and carrier gas large amounts of reagent gas are introduced into the ionization chamber Since the
96. Every As week 6months year needed Tune the MSD y Check the foreline pump oil level y Check the calibration vial s y Replace the foreline pump oil y Replace the diffusion pump fluid v Clean the ion source Check the carrier gas trap s on the GC Replace the worn out parts S ININIS Lubricate sideplate or vent valve O rings 1 Every 3 months for Cl MSDs using ammonia reagent gas 2 Vacuum seals other than the side plate O ring and vent valve O ring do not need to be lubricated Lubricating other seals can interfere with their correct function 152 Table 5 6 Maintaining the MSD Maintenance requires the proper tools spare parts and supplies Some of the required tools spare parts and supplies are included in the MSD shipping kit or MSD tool kit You must supply others yourself Each maintenance procedure includes a list of the materials required for that procedure Tables 5 and 6 summarize these Tools Description Part number Ball driver 1 5 mm 8710 1570 2 0 mm 8710 1804 2 5 mm 8710 1681 Funnel _ _ Hex nut driver 5 5 mm 8710 1220 Pliers long nose 1 5 inch nose 8710 1094 Screwdriver flat blade large 8730 0002 orx I 10 8710 1623 orx 1 15 8710 1622 orx T 20 8710 1615 Tweezers non magnetic 8710 0907 Wrench open end 1 4 inch x 5 16 inch 8710 0510 10 mm 8710 2353 Wrist strap anti static small 9300 0969 medium 9300 1257 large 9300 0970
97. Hi vac power cable Controller cable eee oe HI VAC Power MSD electronics pp y gs module ac board Turbo Fan pump Harness Cal valve Controller harness Turbo pump control with integrated power supply controller Hi vac power cable EXDC cable HI VAC Power Turbo power supply eet MSD electronics __ gt _ module ac board EXDC Fan Turbo 4 mini pump ctlr g Harness gt S e a Cal eec valve EXDC controller harness Turbo pump control with separate power supply and EXDC mini controller 327 11 Electronics AC board Diffusion pump control The power regulator ensures that the diffusion pump heater receives constant power even if there are fluctuations in the ac line voltage It measures the voltage across the heater and the current through it multiplies them together and com pares the result with a standard value Any discrepancy is applied as an error sig nal 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 Pumpdown failure shutdown The ac board will shut down both the high vacuum and the foreline pump if the system fails to pump down correctly The conditions that trigger shutdown are
98. Peak at m z 32 142 Tuning related symptoms overview 144 Reagent gas ion ratio is difficult to adjust or unstable 145 High electron multiplier voltage 147 Can not complete autotune 148 Peak widths are unstable 149 Maintaining the MSD Before starting 152 Maintaining the vacuum system 159 To check and add foreline pump oil 160 To drain the foreline pump 162 To refill the foreline pump 164 To replace the oil trap 166 To check the diffusion pump fluid 168 To replace the turbo pump 170 To separate the MSD from the GC 171 To remove the diffusion pump 173 14 Contents To replace the diffusion pump fluid 175 To reinstall the diffusion pump 177 To reconnect the MSD to the GC 179 To remove the EI calibration vial 181 To refill and reinstall the EI calibration vial 183 To purge the calibration valves 185 EI calibration valve 185 CI calibration valve 185 To remove the foreline gauge 186 To reinstall a foreline gauge 188 To remove the EI calibration valve 190 To reinstall the EI calibration valve 192 To replace the fan for the high vacuum pump 194 To remove the triode gauge tube 196 To reinstall a triode gauge tube 198 To lubricate the side plate O ring 200 To lubricate the vent valve O ring 202 Maintaining the analyzer 204 To remove the ion source 206 To disassemble the ion source 208 To clean the ion source 210 To reassemble the ion source 214 To reinstall the ion source 216 To rem
99. Reconnect the foreline gauge cable to the foreline gauge Reconnect the foreline gauge assembly to the diffusion pump outlet Reconnect the MSD to the GC See page 179 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 the analyzer chamber at the back of the MSD Pump down the MSD See page 60 188 6 Maintaining the MSD To reinstall a foreline gauge Foreline hose and hose clamp f Foreline gauge assembly AAAA Diffusion pump outlet Foreline gauge Abe A Foreline gauge cable 189 6 Maintaining the MSD To remove the El calibration valve To remove the EI calibration valve Materials needed Screwdriver Torx T 15 8710 1622 1 Vent the MSD See page 54 2 Disconnect the calibration valve cable from the connector next to the fan 3 Loosen the collar and remove the calibration vial Turn the collar counterclockwise as viewed from the bottom vial side of the thumbscrew Just loosen the collar do not remove 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 w
100. accidentally made in split mode instead of splitless mode e Empty or almost empty sample vial e Dirty injection port e Leaking injection port e Loose column nut at the injection port These could cause a fault condition in the GC that would prevent the GC from operating 98 A 4 Troubleshooting the MSD Chromatographic symptoms Does not pass tune Calibration vial is empty Excessive foreline or analyzer chamber pressure Very dirty ion source Calibration valve is not working correctly Bad signal cable connection Filament has failed or is not connected correctly Bad ion source wiring connection Bad detector wiring connection Failed electron multiplier horn Peaks are tailing Active sites in the sample path Injection is too large Incorrect injection port 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 Injection port pressure too high Insufficient column flow 99 IE HE VE fel Te 4 Troubleshooting the MSD Chromatographic symptoms Peaks have flat tops e Insufficient solvent delay e Incorrect scale on the display e Injection is too large e Electron multiplier voltage is too high Peaks have split tops e Bad injection technique e Inje
101. al of its oxygen and moisture traps To install the methane isobutane gas purifier follow the instructions on the label for installation and replacement intervals Be sure not to remove the caps until you are ready to install the gas purifier Only remove the caps in the gas flow to prevent contamination by air Methane is flammable Extinguish all flames in the area before turning on gas flow Disconnect the fittings on the old filter 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 Install the new filter Purge the new filter Cap the old filter and prepare it to be sent for regeneration See the instructions on the label 255 Materials needed 7 CI Maintenance To clean the reagent gas supply lines tubing WARNING CAUTION To clean the reagent gas supply lines tubing Clean dry nitrogen Heat gun Tubing cutter 8710 1709 If the reagent gas lines become contaminated they can be cleaned Disconnect the reagent gas tubing from the gas supply the gas purifier and the MSD Cap the gas purifier following the instructions on the label Connect one end of the tubing to a supply of clean dry nitrogen and turn on gas flow Use the heat gun to warm the tubing starting at the supply end and working your way to the free end Repeat for any other pieces of tubing that need to be cleaned Reconne
102. amage it and have a Serious negative effect on instrument performance Do not touch the HED ceramic insulator More information is available If you need more information about the locations or functions of analyzer components refer to Chapter 10 Analyzer on page 297 Most of the procedures in this chapter are illustrated with video clips in the 5973N MSD Maintenance CD ROM 205 Materials needed 6 Maintaining the MSD To remove the ion source CAUTION WARNING To remove the ion source Gloves clean lint free large 8650 0030 small 8650 0029 Pliers long nose 8710 1094 Vent the MSD See page 54 Open the analyzer chamber See page 56 Make sure you use an anti static wrist strap and take other anti static precautions before touching analyzer components Disconnect the seven wires from the ion source Do not bend the wires any more than necessary Pull on the connectors not on the wires Disconnect the wires for the ion source heater and temperature sensor from the feedthrough board Remove the thumbscrews that hold the ion source in place Pull the ion source out of the source radiator The analyzer operates at high temperatures Do not touch any part until you are sure itis cool 206 Source radiator Feedthrough board lon source Thumbscrew Thumbscrew Source heater and temperature sensor wires 6 Maintaining
103. ance and stability of your MSD 238 CAUTION CAUTION 6 Maintaining the MSD When you work on or near printed circuit boards or when you work on components with wires contacts or cables connected to printed circuit boards always use a grounded anti static wrist strap and take other anti static precautions The wrist strap should be connected to a known good Earth ground If that is not possible it should be connected to a conductive metal part of the assembly being worked on but not to electronic compo nents exposed wires or traces or pins on connectors Take extra precautions such as a grounded anti static mat if you must work on components or assemblies that have been removed from the MSD This includes the analyzer In order to be effective an anti static wrist strap must fit snugly not tight A loose strap provides little or no protection Anti static precautions are not 100 effective Handle electronic circuit boards as little as possible and then only by the edges Never touch the components exposed traces or pins on connectors and cables More information is available If you need more information about the functions of electronic components refer to Chapter 8 Electronics on page 317 Most of the procedures in this chapter are illustrated with video clips in the 5973N MSD Maintenance CD ROM 239 Materials needed 6 Maintaining the MSD To adjust the RF coils WARNING
104. and foreline pressure or turbo pump speed signal Monitors the signals from the vacuum system and fans and monitors the filament status HV fault and RF fault signals from the side board Activates the shutdown line when the analyzer electronics must be disabled Generates the control signals on and off used by the ac board for the high vacuum pump and calibration valve Generates 280 V dc nominal power for main board lens amplifiers and side board dc amplifiers Supplies and controls the power for the ion source and quadrupole mass filter heaters Provides 24 V dc power for the cooling fans 324 11 Electronics Signal amplifier board Signal amplifier board The signal amplifier board amplifies the output of the detector The signal ampli fier circuit produces an output voltage of 0 to 10 volts dc proportional to the loga rithm of the input current of 3 picoamps to 50 microamps An analog to digital converter converts the amplifier output voltage to digital information The LAN MS control card unlogs the data into abundance counts proportional to the detector signal current 325 11 Electronics AC board 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 distribu tion vacuum control board The ac board performs the following functions e Provides input voltage transparency for the MSD
105. 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 difference in proton affinities is large as with methane substantial excess energy may be present in the protonated molecular ion This can result in subsequent fragmentation For this reason isobutane with a proton affinity of 195 kcal mole may be preferred to methane for some analyses Ammonia has a proton affinity of 207 kcal mole making it less likely to protonate most analytes Proton transfer chemical ionization is usually considered to be soft ionization but the extent of the softness is dependent on the proton affinities of both the ana lyte and the reagent gas as well as on other factors including ion source tempera ture 378 Reagent gas proton affinities Appendix A Chemical lonization Theory Species Proton affinity Reactant ion formed kcal mole H2 100 CH 127 C2H4 160 H20 165 H2S 170 CH 0H 182 tCyHig 195 NH3 207 H3 m z 3 CHg m z 17 CoH5 m z 29 H40 H3S m z 19 m z 35 CH30H4 m z 33 t CaHa m z57 NH t m z 18 Proton affinities of selected organic compounds for PCI Molecule Acetaldehyde Acetic acid Acetone Benzene 2 Butanol Cyclopropane Dimethyl ether Ethane Ethyl formate Formic acid Hydrobromic acid Hydrochloric acid Isopropyl alcohol Methanol Proton affinity Molecule kcal
106. assemblies can be identified by their part numbers The first two digits of the last five digits of the part number are 69 or 89 i e XXXXX 69XXX 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 you need a part that is not listed in this chapter check the Agilent Technologies Analytical Supplies Catalog or the on line catalogue on the worldwide web at lt http www agilent com gt If you still cannot find it contact your Agilent Technologies service representative or your Agilent Technologies office 338 Table 8 Table 9 12 Parts Electronics Electronics The printed circuit boards in the MSD are available only as complete assemblies Individual electronic components are not available This section contains the following parts cables fuses printed circuit boards electronic assemblies External cables Description Part number Remote start cable G1530 60930 LAN cable shielded 8121 0008 Power cord Australia China 8120 1369 Power cord Denmark 8120 2956 Power cord Europe 8120 1689 Power cord India South Africa 8120 421 on t it1 Power cord Japan 200 V G2025 60189 Power cord Switzerland 8120 2104 Power cord UK Hong Kong Singapore 8120 1351 Power cord US 8120 1378 Triode gauge cable triode gauge tube to gauge control
107. assembly parts Description Repeller assembly insulator 2 required nut 5 5 mm repeller setscrew source heater assembly includes heater sensor and heater block washer Part number 1099 60170 1099 20133 0535 0071 1099 20132 0515 1446 G1099 60177 3050 0891 Gd Ga Gd 356 12 Parts Analyzer Repeller G1099 20132 nsulator G1099 20133 Setscrew 0515 1446 Insulator 61099 20133 Washer 3050 0891 Nut 5 5 mm 0535 0071 Source heater assembly G1099 60177 357 Table 20 12 Parts EI GC MSD interface EI GC MSD interface This table lists the replacement parts related to the GC MSD interface GC MSD interface Description GC MSD interface complete interface column nut not shown heater sleeve heater sensor assembly insulation setscrew for heater sensor assembly not shown screws M4 x 0 7 panhead for heater sleeve welded interface assembly GC MSD interface O ring Interface cover Screws for mounting interface and cover to analyzer chamber Part number 61099 60300 05988 20066 G1099 20210 G1099 60107 G1099 20301 0515 0236 0515 0383 G1099 60301 0905 1405 G1099 00005 0515 0380 358 12 Parts El GC MSD interface Heater sleeve G1099 20210 Screws for heater sleeve o y 0515 0383 Wee E i Welded interface assembly i SZ Se G1099 60301
108. ast the end of the tool Hand tighten the nut Slide the septum to touch the end of the nut The septum will help assure that the position is correct Use two wrenches to tighten the nut 1 4 to 1 2 turn The column should not slide when tugged gently 30 1 Installing GC Columns To install a capillary column using the installation tool Column Interface column nut Column installation tool 1 to 2mm gt lt Interface ferrule Septum 10 11 12 CAUTION Remove the column and nut from the installation tool The total length from the septum to the end of the column is 176 mm Clean the outside of the end of the column with a lint free cloth moistened with methanol Insert the column into the GC MSD interface Tighten the nut 1 4 to 1 2 turn Check tightness after one or two heat cycles Pump down the MSD The column installation tool must be kept clean to prevent contaminating the column and the ion source Keep it in its storage tube and clean it by flushing with methanol after each use 31 32 To view MSD analyzer temperature and vacuum status 38 To set monitors for MSD temperature and vacuum status 40 To set the MSD analyzer temperatures 42 To set the GC MSD interface temperature from the PC 44 To monitor high vacuum pressure 46 To measure column flow linear velocity 48 To calculate column flow 49 To tune the MSD 50 To set the interface
109. ate reactions to occur The EI CI interface has special plumbing for reagent gas A spring loaded insulating seal fits onto the tip of the interface Switching back and forth between CI and EI takes less than an hour although a 1 to 2 hour wait is required in order 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 The Agilent Technologies 5973Network Mass Selective Detector 6890 Series ALS tower 6890 Series ALS tray 59864B High Vacuum Gauge Controller Cl gas flow module EI PCI and El PCI NCI MSDs only 5973 A L Sees Mass Selective Detector M 5 EED Succes Coa O DOCO 5973N MSD control panel poooos 5 DOPE 6890 Plus Gas Chromatograph 5973N MSD serial number sticker 10 Chapter 1 Chapter 2 Table of Contents Installing GC Columns To prepare a capillary column for installation 22 To install a capillary column in a split splitless inlet 24 To condition a capillary column 26 To install a capillary column in the GC MSD interface 28 To install a capillary column using the installation tool 30 Operating
110. athode and the current measured in the collector Since one end of the triode gauge tube is open to the analyzer chamber the pres sure in the triode gauge is essentially the same as the pressure in the analyzer chamber To prevent electronic noise from the triode gauge tube from interfering with the detector a small z fold baffle is inserted into the stem of the triode gauge tube and a shield is installed in the analyzer chamber between the tube port and the ion source Unlike some other pressure gauges that work by ionization the triode gauge does not require degassing to remove accumulated ions from the surfaces in the gauge In some cases however new gauge tubes will not display pressures accurately until they have been turned on for several hours 285 Filament voltage and emission current regulated by gauge controller Grid voltage supplied by gauge controller Filament voltage and emission current regulated by gauge controller Collector ion current measured by gauge controller Grid Filament cathode Collector POR AOE PENEAN AN Open to analyzer chamber The glass around the connector pins is easily cracked if the pins are moved too much Be very careful when connecting and disconnecting the cable to avoid dam age to the tube and creating air leaks 286 See Also 8 Vacuum System Gauge controller WARNING Gauge controller The opti
111. beam Use an abrasive slurry of alumina powder and reagent grade methanol on a cotton swab Use enough force to remove all discolorations Polishing the parts is not nec essary small scratches will not harm performance Also abrasively clean the dis colorations where electrons from the filaments enter the source body Rinse away all abrasive residue with reagent grade methanol Make sure all abrasive residue is rinsed way before ultrasonic cleaning If the methanol becomes cloudy or contains visible particles rinse again Separate the parts that were abrasively cleaned from the parts that were not abrasively cleaned Ultrasonically clean the parts for 15 minutes in each of the following solvents Ultrasonically clean each group of parts separately e Methylene chloride reagent grade e Acetone reagent grade e Methanol reagent grade All of these solvents are hazardous Work in a fume hood and take all appropriate precautions Place the parts in a clean beaker Loosely cover the beaker with clean aluminum foil dull side down Dry the cleaned parts in an oven at 100 150 C for 30 minutes Let these parts cool before you handle them 212 6 Maintaining the MSD To clean the ion source NOTE Take care to avoid recontaminating cleaned and dried parts Put on new clean gloves before handling the parts Do not set the cleaned parts ona dirty surface Set them only on clean lint free cloths 213 Mate
112. bing and flow module Purge the reagent gas supply lines for at least 60 minutes See the Maintenance chapter Contaminated reagent gas supply Replace the reagent gas supply and purge the lines and flow module Saturated methane isobutane gas purifier Replace the gas purifier 141 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting Peak at m z 32 Peak at m z 32 A visible peak at m z 32 in methane pretune often indicates air in the system Residual air from recent venting check for water indicated by a large peak at m z 19 Bake out the system as described in the Maintenance chapter of this manual New or dirty reagent gas supply tubing Purge the reagent gas supply lines and flow module for at least 60 minutes See To set up your MSD for CI operation on page 247 Air leak 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 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 the capillary column Make sure it is not broken and it is installed cor rectly 142 5 Cl Troubleshooting Peak at m z 32
113. bles 3 Unauthorized modifications or misuse 4 Operation outside of the environmental and electrical specifications for the product 5 Improper site preparation and maintenance 6 Customer induced contamination or leaks This warranty may be modified in accordance with the laws of your country Please consult your local Agilent Technologies office for the period of the warranty for shipping instructions and for the applicable wording of the local warranty Warranty Claims If physical damage is found or if operation is not as specified when the instrument is first received notify the carrier and the nearest Agilent Technologies office immediately The Agilent Technologies office will arrange for repair or replacement of the instrument without waiting for settlement of a claim with the carrier For other than initial inspection warranty claims contact your local Agilent Technologies office Service Agreements Several service agreements are available each designed to meet a specific need In addition to a preventive maintenance agreement others cover specific repair maintenance services for the 5973 Mass Selective Detector and can provide for the extension of warranty beyond the initial warranty period Details of these agreements together with prices applicable to the particular installation can be obtained from your local Agilent Technologies office Power Specifications e 120 V ac 6
114. bly turbo pump outlet 0100 1551 KF elbow adapter for standard turbo pump outlet G2589 20041 KF50 seal diffusion pump inlet 0100 1884 O ring for diffusion pump baffle adapter and standard turbo pump inlet 0905 1443 Seal performance turbo pump inlet 0100 1879 Side plate O ring 0905 1442 Triode gauge tube O ring 0905 1070 Vent valve O ring 1 4 inch 0905 1217 Drain plug for the foreline pump 0100 2041 O ring for the foreline pump drain plug 0905 1515 1 The turbo pump and its seal are not user replaceable parts Refer service to your Agilent Technologies service representative 344 Face seal KF seal with internal centering ring KF seal with external centering ring Compression seal 000 12 Parts Vacuum system 345 Table 13 12 Parts Vacuum system Foreline pump and related parts Description Foreline hose assembly hose and internal spring Foreline pump 120V 230V Foreline pump inlet seal KF10 16 Hose clamp KF10 16 clamp foreline inlet KF16 hose adapter KF25 clamp turbo pump end of foreline hose not shown KF25 hose adapter turbo pump end of foreline hose not shown Exhaust oil mist trap not shown Oil drip tray 1 Do not use an exhaust oil mist trap if you are analyzing hazardous samples or if you are using hazardous carrier gas or if you are running Cl Plumb the pump exhaust to a fume exhaust
115. ch open end 1 4 inch x 5 16 inch 8710 0510 Note that the column installation procedure for the 5973 MSDs is different from that for all previous MSDs Using the procedure from another instrument result in poor sensitivity and possibly damage the MSD Condition the column page 26 Vent the MSD page 54 and open the analyzer chamber page 56 Be sure you can see the end of the GC MSD interface Slide an interface nut and conditioned ferrule onto the free end of the GC column The tapered end of the ferrule must point towards the nut Slide the column into the GC MSD interface until you can pull it out through the analyzer chamber Break 1 cm off the end of the column page 22 Do not let any column fragments fall into the analyzer chamber They could dam age the turbo pump 28 1 Installing GC Columns To install a capillary column in the GC MSD interface Column nterface column nut GC MSD interface GC end Analyzer chamber GC MSD interface MSD end J 1 to 2 mm MSD A GC oven Clean the outside of the free end of the column with a lint free cloth moistened with methanol Adjust the column so it projects 1 to 2 mm past the end of the GC MSD interface Use the flashlight and hand lens if necessary to see the end of the column inside the analyzer chamber Do not use your finger to feel for the column
116. chnologies service representative Troubleshooting tips and tricks The following are general rules for troubleshooting with specific 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 e Ifthe MSD was just pumped down after maintenance suspect air leaks or incorrect assembly e Carrier gas or helium gas purifier were just changed suspect leaks or contaminated or incorrect gas e Ifthe GC column was just replaced suspect air leaks or contaminated or bleeding column 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 e Ifyou re having trouble detecting your sample verify that autotune is successful Rule 3 Divide and conquer This technique is known as half split troubleshooting If you can isolate the problem to only part of the system it is much easier to locate e To determine whether an air leak is in the GC or the MSD you can vent the MSD remove the column and install the blank interface ferrule If the leak goes away it was in the GC 95 4 Troubleshooting the MSD General symptoms General symptoms This section describes symptoms you might observe when first turning on the GC MSD system All of these symptoms would prevent op
117. ct the tubing to the gas supply gas purifier and MSD Follow the instructions on the gas purifier label Do not heat the gas tubing when reagent gas is flowing Do not put liquids into the tubing Do not heat the tubing when it is connected to the MSD 256 Materials needed CAUTION 10 11 12 CAUTION 7 Cl Maintenance To refill the CI calibrant vial To refill the CI calibrant vial PFDTD calibrant 8500 8130 Set the reagent gas flow to Gas Off Vent the MSD Remove the capillary column from the GC MSD interface Pull the MSD away from the GC See page 171 Loosen the nut holding the vial in place Remove the calibrant vial 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 Cl sensitivity Fill the vial to no closer than 6 mm of the top with fresh PFDTD calibrant 8500 8130 Replace the vial and tighten the nut Reposition the MSD next to the GC See page 179 Reinstall the capillary column Pump down the MSD See page 60 Purge the calibration valve See page 185 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 filament and electron multiplier 257 258 Diffusion pump MSD vacuum system 264 Turbo pump MSD vacuum system 265 Diffusion pump a
118. ction is too large Baseline is rising e Column bleed e Other contamination Baseline is high e Column bleed e Other contamination e Electron multiplier voltage is too high Baseline is falling A falling baseline indicates contamination is being swept away Wait until the base line reaches an acceptable level Common causes include e Residual water air and water from a recent venting e Column bleed e Septum bleed e Splitless injection time too long inlet is not properly swept resulting in excess solvent on the column and slow solvent decay 100 4 Troubleshooting the MSD Chromatographic symptoms Baseline wanders e Insufficient carrier gas supply pressure e Malfunctioning flow or pressure regulator e Intermittent leak in the injection port These could cause a fault condition in the GC that would prevent the GC from operating Retention times for all peaks drift shorter e Column has been shortened e Initial oven temperature was increased e Column is getting old Retention times for all peaks drift longer e Column flow has been reduced e Initial oven temperature was decreased e Active sites in the sample path e Leaks in the injection port This could cause a fault condition in the GC that would prevent the GC from operating 101 4 Troubleshooting the MSD Chromatographic symptoms Poor sensitivity e Incorrect tuning e Tune file that does not match the type of analysis e Re
119. cylindrical body with its inlet open to the interior of the ana lyzer chamber Inside the pump body is a central shaft or cylinder Sets of small blades airfoils radiate from the central shaft The shaft spins at up to 60 000 rev olutions per minute in the performance turbo pump and 90 000 rpm in the stan dard turbo pump The turbo pump transports gas by momentum transfer The turbine blades are angled so that when they strike a gas molecule it is deflected downward Each set of blades pushes the gas molecules further down toward the pump outlet The foreline pump is connected by a hose to the outlet of the turbo pump It removes the gas molecules that reach the outlet A controller regulates current 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 turns on automatically as soon as the MSD power is switched on The system will allow the analyzer to be turned on when the turbo pump is greater than 80 speed but the pump normally operates at 100 speed Turbo pump MSDs typically maintain an indicated pressure below 8 x 10 Torr for helium col umn flows up to 4 ml minute for the performance turbo pump and up to 2 ml minute for the standard turbo pump Pressure vacuum can only be measured if your MSD is equipped with the optional gauge controller The turbo pump spins up
120. d Gently check the alignment of the analyzer and the interface When the analyzer is aligned correctly the analyzer can be closed all the way with no resistance except the spring tension from the interface tip seal Forcing the analyzer closed if these parts are misaligned will damage the seal or the interface or the ion source or will keep the sideplate from sealing You can align the analyzer and interface by wiggling the side plate on its hinge If the analyzer still won t close contact your Agilent Technologies service representative The figure opposite shows the alignment of the interface tip seal and CI ion source 250 7 Cl Maintenance To install the CI interface tip seal Cl ion source body Cl filament Cl source heater assembly Cl interface tip seal CI GC MSD pe interface tip a Cl interface cover Source heater and sensor cables lon focus lens pin oN Entrance lens pin 251 See Also 7 Cl Maintenance To clean the CI ion source CAUTION To clean the CI ion source The Clion source has slightly different cleaning requirements than the standard EI ion source See the procedure in the 5973N MSD Maintenance CD ROM Frequency of cleaning Because the Clion source operates at much higher pressures than the El ion source it will probably require more frequent cleaning than the EI ion source Cleaning of the source is
121. d in CI mode e EI filament or other EI source parts in CI ion source e Air leaks in reagent gas flow path e CI filament has stretched and sagged High EMV Linear no inflection point electron energy EleEnergy ramp 122 5 Cl Troubleshooting Troubleshooting tips and tricks Troubleshooting tips and tricks The following are general rules for troubleshooting with specific Cl exam ples 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 e Ifthe MSD was just pumped down after maintenance suspect air leaks or incorrect assembly e Ifthe reagent gas bottle or gas purifier were just changed suspect leaks or contaminated or incorrect gas e Ifthe GC column was just replaced suspect air leaks or contaminated or bleeding column e Ifyou have just switched ion polarity or reagent gas suspect the tune file you have loaded 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 e If you re having trouble with NCI verify that PCI still works e Ifyou re having trouble with other reagent gases verify that methane still works e If youre havi
122. d the air leak Look for the last seal that was disturbed e Ifyou 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 e Ifyou just replaced the reagent gas bottle or gas purifier check the fittings you just opened and refastened Check for tightness of seals at injection port and interface column nuts Ferrules for capillary columns often loosen after several heat cycles Do not over tighten the interface nut If any of the VCR fittings in the flow module have been loosened and then retightened the gasket must be replaced These gaskets are good for one use only Do not loosen the nuts on any VCR fittings unless you intend to replace the gaskets Otherwise you will create an air leak 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 analyzer chamber are not likely to be seen in CI because of the higher pressure inside the ionization chamber Half split the system e By closing valves starting at the gas select valves Gas Off and Purge turned on then moving farther downstream to the isolation valve Gas Off turned on and Purge turned off e You can cool and vent the MSD remove the GC column and cap off the interface If you are used to using argon or other introduced gas to find air leaks note that
123. dride abstraction and proton transfer ionization can be evident in the sample spectrum One example is the methane CI spectrum of long chain methyl esters where 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 favorable In these cases reagent gas ions are often reactive enough to combine with the analyte molecules by condensation or association addition reactions The resulting ions are called adduct ions Adduct ions are observed in methane chemical ionization by the presence of M Co Hs and M Cs3Hs ions which result in M 29 and M 41 amu mass peaks Addition reactions are particularly important in ammonia CI Because the NH has a high proton affinity few organic compounds will undergo proton transfer with ammonia reagent gas In ammonia CI a series of ion molecule reactions takes place resulting in the formation of NH4 NH4NHs and NH4 NH3 9 In par ticular the ammonium ion NH4 will give rise to an intense M NH ion observed at M 18 amu either through condensation or association If this result ing ion is unstable subsequent fragmentation may be observed The neutral
124. drupole mass filter The fused quartz quadrupole is fragile and will break if dropped or handled roughly The material in the cusps of the quadrupole is very hygroscopic If exposed to water the quadrupole must be dried very slowly to prevent damage 311 10 Analyzer Detector Detector The detector in the MSD analyzer is a high energy conversion dynode HED cou pled to an electron multiplier EM The detector is located at the exit end of the quadrupole mass filter It receives the ions that have passed through the mass fil ter The detector generates an electronic signal proportional to the number of ions striking it The detector has three main components the detector focus lens the high energy dynode and the electron multiplier horn Detector focus lens The detector focus lens directs the ion beam into the HED which is located off axis The voltage on the detector focus lens is fixed at 354 V High energy dynode The high energy dynode HED operates at 10 000 volts for EI and PCI and 10 000 volts for NCI The HED is located off axis from the center of the quadru pole 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 emit ted These electrons are attracted to the more positive electron multiplier horn Do not touch the ceramic insulator Electron multiplier horn The electron multiplier horn carries a voltage
125. e Physical description The 5973N MSD is arectangular box approximately 42 cm high 26 cm wide 65 cm deep The weight is 25 kg for the diffusion pump mainframe 26 kg for the standard turbo pump mainframe and 29 kg for the performance turbo pump mainframe The attached rough pump weighs an additional 11 kg The basic components of the instrument are the frame cover assemblies the control panel the vacuum system the GC interface the electronics and the analyzer The control panel allows local monitoring and operation of the MSD The control panel acts as a local user interface to the MSD You can perform some basic tasks such as running a tune a method or a sequence and monitor MSD status from the control panel The Agilent Technologies 5973Network Mass Selective Detector An optional gauge controller is available for measuring vacuum The 5973N MSD is equipped with a triode ionization gauge tube With an 59864B Gauge Controller the tube can be used to measure pressure high vacuum in the vacuum manifold Installation and operation of the gauge controller is described in this manual The gauge controller is required for chemical ionization CI operation 5973N MSD models and features Feature G2577A G2578A G2579A G2588A G2589A High vac pump Diffusion pump Standard turbo Performance turbo Standard turbo Performance turbo Optimal He column flow 1 1 1 to2 1 1 to 2 ml min Maximum recommended 1 5 2 0 4 2 0 4 gas flow
126. e 9 On CI upgrades a serial number is located under the cover of the flow module When corresponding with Agilent Technologies about your instrument be sure to include the model number and both full 10 character serial numbers Write the serial number of your 5973N MSD here for reference 5973N MSD version 5973N MSDs are equipped with either a diffusion pump or one of two turbomolecular turbo pumps Chemical Ionization is available for the turbo MSDs only The serial number label displays a product number that tells what kind of MSD you have G2577A Diffusion Pump EI MSD G2578A Standard turbo EI MSD G2579A Performance turbo EI MSD G2588A Standard turbo EI PCI MSD G2589A Performance turbo EI PCI NCI MSD 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 Agilent Technologies part numbers are generally listed in parentheses after the name of the part or in tables in the Parts chapter Most part numbers are either four digit by four digit 1234 1234 numbers or five digit by five digit 12345 12345 numbers A few tools and supplies listed have no part numbers and are not available from Agilent Technologies Most of th
127. e Diffusion pump MSD foreline pressure still above 300 mTorr after 7 minutes e Turbo pump MSD turbo pump speed below 80 after 7 minutes This is usually because of a large air leak either the sideplate has not sealed cor rectly 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 To correct the problem power cycle the MSD and troubleshoot You have seven minutes to find and correct the air leak before the system shuts down again Be sure to press on the sideplate when turning on the MSD power to ensure a good seal 328 Hi vac power cable Diffusion pump heater cable Fan Fore line gauge Diffusion pump heater 11 Electronics AC board HI VAC Power sensorse Harness Cal valve Diffusion pump harness Diffusion pump control MSD electronics module ac board 329 11 Electronics LAN MSD control card LAN MSD control card The LAN MS control card is located to the left of the main board on the electronics panel The LAN MS control card has two main functions e Providing a communication interface between the MSD and the data system e Providing real time control of the MSD freeing the data system for other tasks Functional areas of the LAN MS control card include e Instru
128. e MSD electronics do not require any scheduled maintenance None of the electronic components of the MSD need to be replaced on a regular schedule None of the electronic components in the MSD need to be adjusted or calibrated on a regular schedule Avoid unnecessary handling of the MSD electronics Very few of the electronic components are operator serviceable The primary fuses can be replaced by the operator The RF coils can be adjusted by the operator All other maintenance of the electronics should be performed by your Agilent Technologies service representative Improper use of these procedures could create a serious safety hazard Improper use of these procedures could also result in serious damage to or incorrect operation of the MSD Vent the MSD and disconnect its power cord before performing any of these procedures except adjusting the RF coils Electrostatic discharge is a threat to the MSD electronics during maintenance All of the printed circuit boards in the MSD contain components that can be damaged 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 gradually degrade the perform
129. e body help the vacuum system to pump away carrier gas and un ionized sample molecules or fragments Filament Source body P oh a lonization chamber a Figg Entrance lens on focus lens Lens insulators Drawout cylinder Drawout plate Repeller 300 Source radiator Feedthrough board lon source Thumbscrew Thumbscrew Source heater and sensor wires lon focus pin orange wire Entrance lens pin blue wire 10 Analyzer lon source 301 10 Analyzer lon source Filaments Two filaments are located on opposite sides of the outside of the ion source The active filament carries an adjustable ac emission current The emission current heats the filament causing it to emit electrons these electrons ionize the sample molecules In addition both filaments have an adjustable dc bias voltage The bias voltage determines the energy on the electrons usually 70 eV The Cl ion source has only one filament of a different design from the EI filaments A dummy filament provides connections for the Filament 2 wires The filament is shut off automatically if there is a general ins
130. e detector Generates and adjusts filament emission current and electron energy as controlled by the main board Switches the filament power from one filament to the other Monitors for RF faults and shuts down the analyzer one is detected 322 11 Electronics Electronics module Electronics module Most of the electronics in the MSD are contained in the electronics module The whole electronics module can be replaced if necessary by your Agilent Technolo gies service representative The electronics module contains e Main board e Signal amplifier board e LAN MS control card e AC board power distribution vacuum control board e Low voltage ac dc power supply e High voltage HED power supply e Toroid transformer assembly 323 11 Electronics Main board Main board The main board is mounted on the outer side of the electronics module The main board performs the following functions Receives 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 alternate filament selection filament emission current and electron energy Generates control signals for quadrupole RF drive dc RF ratio adjustment dc polarity selection and all detector voltages Performs analog to digital conversion for the coil DIP signal ion source and mass filter temperature signals
131. e filament support arms The electron inlet hole is blocked Inspect the electron inlet hole If necessary clean the hole with a clean toothpick and a slurry of aluminum oxide powder and methanol If the electron inlet hole is that dirty the entire ion source probably needs to be cleaned See the Mainte nance chapter in this manual for more information Ion source wires are not connected or incorrectly connected Inspect the repeller Make sure 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 136 Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting No or low reagent gas signal One of the detector leads in the analyzer chamber is not connected Check and if necessary reconnect the electron multiplier leads 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 137 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting No or low PFDTD signal but reagent ions are normal No or low PFDTD signal but reagent ions are normal You are f
132. e manifold and the plates provide attachment points for the triode gauge tube calibration valve vent valve GC MSD interface and high vacuum pump 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 Calibration valve port Vent valve port Side plate O ring groove Front end plate GC MSD interface port Triode gauge port behind shield Rear end plate Triode gauge port shield Cooling fins Vapor baffle 266 8 Vacuum System Turbo pump analyzer chamber Turbo pump analyzer chamber The manifold for the turbo pump does not have a baffle or cooling fins The turbo pump and the mounting bracket for the turbo controller are clamped directly to the manifold In every other respect the two manifolds are identical Calibration valve port Vent valve port Side plate O ring groove Front end plate GC MSD interface port Triode gauge port behind shield Rear end plate Triode gauge port shield 267 CAUTION CAUTION 8 Vacuum System Side plate Side plate The side plate is a flat stainless steel plate that covers the large ope
133. e mass filter and reach the detector The ratio of dc to RF voltage determines the resolution widths of the mass peaks There are several parameters that control the dc and RF voltages All these parameters are set by Autotune but also can be manually adjusted in the Edit Parameters window e AMU gain AmuGain e AMU offset AmuOffs e 219 width Wid219 e DC polarity DC Pol e Mass axis gain MassGain e Mass axis offset MassOffs AMU gain AMU gain AmuGain affects the ratio of dc voltage to RF frequency on the mass filter This controls the widths of the mass peaks e Higher gain yields narrower peaks e AMU gain affects peaks at high masses more than peaks at low masses 308 10 Analyzer Quadrupole mass filter AMU offset AMU offset AmuOffs also affects the ratio of dc voltage to RF frequency on the mass filter e Higher offset yields narrower peaks e 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 compound other than PFTBA there may not be an ion at m z 219 In that case set the 219 width to the last value found for it by Autotune or set it to 0 309 CAUTION 10 Analyzer Quadrupole mass filter DC polar
134. e when reagent flow is changed The reagent gas regulator is closed Check and if necessary open the reagent gas regulator The reagent gas regulator is set to the wrong pressure Set the reagent gas regulator to 10 psi 70 kPa for methane or to 3 10 psi 20 70 kPa for isobutane or ammonia 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 make sure the reagent line is connected to the rear of the flow module Be sure the methane line is connected to the Gas A inlet GC MSD interface clogged or damaged Check for flow and repair or replace components as indicated 131 5 Cl Troubleshooting Signal related symptoms overview 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 Error messages in autotune due to insufficient signal may vary The following symptoms are covered in more detail in this section e No peaks e No or low reagent gas signal See page 135 e No or low PFDTD signal See page 13
135. ed 382 autotune 82 buffer gas 382 dissociative electron capture 385 effect of contamination 384 electron capture 384 ion pair formation 385 ion molecule reactions 386 sensitivity 384 theory 382 thermal electrons 382 NH3 preventing damage to the foreline pump due to 254 No peaks in CI MSD 133 Noise declaration inside front cover O Oil drip tray for foreline pump 272 Oil trap 272 replacing 166 Oil tray for foreline pump 272 On off switch See Power switch Opening the analyzer chamber 56 Operating the MSD 33 67 Operation switching from EI to CI 72 Ordering parts 338 O rings and O ring assemblies 270 part numbers 344 Oxygen effect of on column bleed 21 P Part numbers inside front cover See also Parts Parts 337 372 analyzer 352 CI interface 370 consumables 360 diffusion pump vacuum system 348 electronic 339 external cables 339 ferrules 362 foreline pump 346 GC MSD interface 358 370 if you cannot find a part you need 338 ion source 354 maintenance supplies 361 miscellaneous 363 365 366 368 370 ordering 338 O rings and O ring assemblies 344 printed circuit boards 342 rebuilt assemblies 338 samples 363 365 366 368 370 seals 344 turbomolecular pump vacuum system 350 vacuum system 344 396 Index Parts replacement 337 PCI See Positive CI Peak widths inconsistent 104 Peaks at m z 18 28 32 and 44 or at m z 14 and 16 104 flat tops 100 fr
136. electron multiplier voltage in CI MSD 147 High pressure electron capture mass spectrome try See Negative Cl High vacuum gauge installing 198 relative sensitivity to different gases 86 removing 196 High vacuum pump difficulty with 113 diffusion pump 276 not ready 116 High vacuum See Vacuum manifold pressure High voltage feedthrough See HED feedthrough History Autotune 50 Horn electron multiplier 312 HPECMS See Negative CI Hydride abstraction 380 Hydrogen carrier gas danger of ignition by triode gauge tube 46 86 flow turned off while MSD is vented 34 hazards during pumpdown 35 60 I Indicated pressure 287 Installing GC columns 19 31 Interface socket reinstalling 214 removing 208 Interface tip seal CI installing 250 Interface See CI interface Interface See GC MSD interface Interfacing to external devices 334 start run input 335 system ready signal 335 Ion focus 304 Ion source 300 body 300 cleaning 210 213 disassembling 208 drawout plate and cylinder 304 drying cleaned parts 212 entrance lens 304 filament care 303 filament reinstalling 220 filament removing 218 filaments 302 heater 314 heater and sensor reinstalling 224 heater and sensor removing 222 ion focus lens 304 magnet 303 part numbers 354 parts that should not be cleaned 210 reassembling 214 reinstalling 216 removing 206 repeller 303 393 Index Ion source temperature 36 setting 42 setti
137. encing is not appropriate for automating methods that use different reagent gases or gas flows as these parameters must be set manually 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 General guidelines e Always use the highest purity methane and other reagent gases if applicable Methane must be at least 99 99 pure e Always verify that the MSD is performing well in EI mode before switching to CI See To verify system performance on page 51 e Make sure the Clion source and GC MSD interface tip seal are installed e Make sure the reagent gas plumbing has no air leaks This is determined in PCI mode checking for m z 32 after the methane pre tune To operate the CI MSD 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 Temperatures for Cl operation lon source Quadrupole GC MSD interface PCI 250 C 150 C 320 C NCI 150 C 150 C 280 C NOTE Start the system in PCI mode first By bringing the system up in PCI mode first you will be able to do the following Set up the MSD with methane first even if you are going to use another reagent gas Check the interface tip seal by looking at the m z 28 to 27 ratio in
138. ended Not recommended Ammonia Performance turbo pump 5 0x 10 7 0x 107 8 5x10 10x10 1 2 x107 1 5 x107 20x10 Standard turbo pump 1 5 x107 20x 10 3 0x 104 Not recommended Not recommended Not recommended Not recommended Familiarize yourself with the measurements on your system under operating con ditions and watch for changes that may indicate a vacuum or gas flow problem 124 Special negative CI notes 5 Cl Troubleshooting Air leaks Always look for small air leaks when setting up methane flow Run the methane pretune starting with a good PCI tune file The abundance of m z 19 protonated water should be less 50 of m z 17 for acceptable PCI performance for NCI the abundance of m z 19 protonated water should be less than 25 that of m z 17 If the MSD was just pumped down look for the abundance of m z 19 to be decreas ing There should not be any peak visible at m z 32 O2 This almost always indicates an air leak Mass 17 25 Mass 29 05 Mass 41 05 Ab 115776 Pw50 0 60 Ab 216065 Pw50 0 61 Ab 79405 Pw50 0 61 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 greater than that of m z 272 you have an air leak 125 CAUTION 5 Cl Troubleshooting Air leaks How do I fin
139. endix A Chemical lonization Theory Negative Cl theory hundance J sooo 4 El 75 109121 methane NCI 150 C source 35 50 50 100 71 82 99 113124136148 143 150 150 Scan 1464 11 133 min PESTO6 D 195 241 207 170 229 183 T pee 50 100 150 200 250 300 350 400 450 bundance Scan 1464 11 133 min PESTO4 D 406 242 206 21923 254 270 284 200 250 169 183 358371 387 406417429 449 aa 338 300 350 400 450 383 Appendix A Chemical lonization Theory Negative Cl theory 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 sam ples and under ideal conditions electron capture can provide sensitivity as much as 10 to 1000 times higher than positive ionization Note that all the reactions associated with positive CI will also occur in NCI mode usually with contaminants The positive ions formed do not leave the ion source because of the reversed lens voltages and their presence can quench the electron capture reaction The electron capture reaction is described by MX e thermal gt MX where MX is the sample molecule and the electron is a thermal slow electron generated by the interaction between high en
140. eration of the system GC does not turn on This refers to a condition in which nothing happens when the GC is switched on The GC fans do not turn on and the keypad display does not light e Disconnected GC power cord e No voltage or incorrect voltage at the electrical outlet e Failed fuse in the GC e GC power supply is not working correctly MSD does not turn on This refers to a condition in which 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 The control panel is not on e Disconnected MSD power cord e No voltage or incorrect voltage at the electrical outlet e Failed primary fuses e MSD electronics are not working correctly Foreline pump is not operating This refers to a condition where the MSD is receiving power the fan is operating and the control panel is lit but the foreline pump is not operating e Large air leak usually the analyzer door open has caused pumpdown failure See Pumpdown failure shutdown on page 261 Note that you must power cycle the MSD to recover from this state e Disconnected foreline pump power cord e Malfunctioning foreline pump 96 4 Troubleshooting the MSD General symptoms MSD turns on but then the foreline pump shuts off MSDs will shut down both the foreline pump and the high vacuum pump if the sys tem fails to pump down correctly This is usually because of a large air leak either
141. erature setpoint e lon source heater cartridge is not connected e lon source temperature sensor is not connected e lon source heater failed burned out or shorted to ground e Jon source temperature sensor failed e Source power cable is not connected to the side board e MSD electronics are not working correctly These will cause an 110 4 Troubleshooting the MSD Temperature symptoms Mass filter quad heater will not heat up e High vacuum pump is off or has not reached normal operating conditions e Incorrect temperature setpoint e Mass filter has not had enough time to reach temperature setpoint e Mass filter heater cartridge is not connected e Mass filter temperature sensor is not connected e Mass filter heater failed burned out or shorted to ground e Mass filter temperature sensor failed e Source power cable is not connected to the sideboard e MSD electronics are not working correctly These will cause an error message GC MSD interface will not heat up e Incorrect setpoint e Setpoint entered in wrong heated zone e GC MSD interface has not had enough time to reach temperature setpoint e GC is off e GC experienced a fault and needs to be reset e GC MSD interface heater sensor cable is not connected e GC MSD heater failed burned out e GC MSD sensor failed e GC electronics are not working correctly These will cause a GC error message GC error messages are described in the docu
142. ergy electrons and the reagent gas In some cases the MX radical anion is not stable In those cases the reverse reac tion can occur MX gt 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 stabilized through collisions or other reactions Electron capture is most favorable for molecules that have hetero atoms For example nitrogen oxygen phosphorus sulfur silicon and especially the halo gens fluorine chlorine bromine and iodine The presence of oxygen water or almost any other contaminant interferes with the electron attachment reaction Contaminants cause the negative ion to be formed by the slower ion molecule reaction This generally results in less sensitiv ity All potential contamination sources especially oxygen air and water sources must be minimized 384 Appendix A Chemical lonization Theory Negative Cl theory 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 Dissociative electron capture is illustrated by the reaction equa tion MX hen gt M X This reaction does not yield the same sensitivity as electron capture and
143. es 86 Sensitivity poor 102 poor at high masses 106 verifying NCI performance 85 verifying PCI performance 84 Septum bleed as a source of contamination 119 Septum leaking 118 Sequencing not appropriate for CI methods using different reagent gases or gas flows 70 Service agreements inside back cover Shutdown See Venting Side plate lubricating the O ring 200 O ring 270 thumbscrews 268 Signal amplifier board 325 Signal not enough to begin tune 117 398 Index Smartcard III SeeLAN MS control card Software using to pump down the MSD 60 Solvent peak effect if analyzer is on 112 113 effect on triode gauge 108 Specifications sensitivity 84 85 Standard Tune 50 Startup failure of the MSD to 96 methane pre tune showing acceptable levels of air and water 77 See also Pumpdown setting up methane flow 76 setting up the software for CI operation 73 too much air and water 77 State diagram reagent gas flow control module 74 296 Static discharge See Electrostatic discharge Status display 320 Storing the MSD 65 Supplies for maintaining the MSD 154 Switch power See Power switch Switching from CI to EI operating mode 92 from EI to CI operating mode 72 Switching between EI and CI 8 Symptoms of malfunctions analyzer chamber pressure is too high 107 baseline is falling 100 baseline is high 100 baseline is rising 100 baseline wanders 101 can not complete CI autotune 148 chromatographic
144. ese can be obtained from laboratory supply companies Safety Information Safety Symbols on equipment N Refer to operating instructions ndicates hazardous voltage ndicates hot surface ndicates earth ground terminal A A Safety class The 5973N Mass Selective Detector MSD is a Safety Class I instrument and has been designed and tested in accordance with IEC Publication 1010 1 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use WARNING Connecting an MSD to a power source which is not equipped with a protective earth contact creates a shock hazard for the operator and can damage the instrument Likewise interrupting the protective conductor inside or outside the MSD or disconnecting the protective earth terminal creates a shock hazard for the operator and can damage the instrument WARNING Make sure that only fuses with the required current rating and of the specified type are used for replacement The use of incorrect or makeshift fuses or the short circuiting of fuse holders creates a shock hazard for the operator and can damage the instrument WARNING Any adjustment maintenance or repair of the opened instrument while it is connected to a power source should be avoided if possible and if required should be carried out only by trained persons who are aware of the hazards involved Safety Information is contin ued on the inside of the bac
145. essages e Amu gain or offset is too high e Calibration vial is empty or almost empty e Excessive pressure in the analyzer chamber e Air leak e Electron multiplier voltage is too low e Signal cable is not connected e Electrical leads to the detector are not connected correctly e HED power supply output cable failed e Electrical leads to the ion source are not connected correctly e Filament shorted to the source body Temperature control disabled e One of the heater fuses has failed e MSD electronics are not working correctly Temperature control fault This indicates that something has gone wrong with the temperature control of either the ion source or mass filter quad heater The cause can be further iso lated by selecting Status MS Temp Ctlr Status in the Diagnostics Vacuum Control view One of the following should be displayed as the cause e Source temperature sensor is open e Source temperature sensor is shorted e Mass filter quad temperature sensor is open e Mass filter quad temperature sensor is shorted e No heater voltage heater fuse has probably failed e Heater voltage is too low e Temperature zone has timed out heater failed bad heater wiring or loose temperature sensor e Problem with the temperature control electronics 115 4 Troubleshooting the MSD Error messages The high vacuum pump is not ready e Diffusion pump is on but has not had enough time 10 15 minutes to reach its normal ope
146. et page 24 Allow the carrier gas to flow through the column for 5 minutes without heating GC oven Ramp the oven temperature at 5 C minute to 10 C above your highest analytical temperature Once the oven temperature exceeds 80 C inject 5 ul methanol into GC repeat two more times at 5 minute intervals This will help remove any contamination from the column before it is installed into the GC MSD interface Do not exceed the maximum temperature rating of the column Hold this temperature Allow the carrier gas to flow for several hours Return the GC oven temperature to a low standby temperature For more information about installing a capillary column refer to the application note Optimizing splitless injections on your GC for high performance MS analysis publication number 5091 4587E 26 1 Installing GC Columns To condition a capillary column 27 Materials needed 1 Installing GC Columns To install a capillary column in the GC MSD interface CAUTION To install a capillary column in the GC MSD interface Column cutter 65181 8836 Ferrules 0 3 mm id for 0 10 mm id columns 5062 3507 0 4 mm id for 0 20 and 0 25 mm id columns 5062 3508 0 5 mm id for 0 32 mm id columns 5062 3506 0 8 mm id for 0 53 mm id columns 5062 3538 Flashlight Hand lens magnifying glass Gloves clean large 8650 0030 small 8650 0029 Interface column nut 05988 20066 Safety glasses Wren
147. etector focus volt age 350 volts with a handheld voltmeter will give a typical reading of 90 to 100 volts where the polarity matches that of the HED voltage Toroid transformer The toroid transformer is mounted next to the ac board It provides 24 V ac for the mass filter and source heater circuits The input wires take 120 V ac or 200 260 V ac from the ac board The AC board samples the line voltage and uses a relay to appropriately strap the toroid primary The output wires connect to the main board 331 11 Electronics Back panel and connectors Back panel and connectors The back panel contains several connectors the primary fuses several status LEDs Most of these components are part of the ac board or the LAN MS control card and extend through the back panel High vacuum control HIVAC SIGNAL connector The high vacuum signal connector is on the ac board See Turbo pump control 326 and Diffusion pump control 328 High vacuum power HIVAC POWER connector The high vacuum power 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 fore line 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 power cord receptacle The foreline pump
148. etpoint The typical setpoint is 280 C The limits are 0 C and 350 C A setpoint below ambient temperature turns off the interface heater Never exceed the maximum temperature of your column Make sure that the carrier gas is turned on and the column has been purged of air before heating the GC MSD interface or the GC oven Press the Enter key to download the new setpoint If you want the new setpoint to become part of the current method click Save under the Method menu Otherwise the first time a method is loaded all the set points in the method will overwrite those set from the GC keyboard 67 2 Operating the MSD To vent the MSD without the ChemStation WARNING CAUTION See Also To vent the MSD without the ChemStation If the MSD ChemStation is functioning use the procedure on page 54 This proce dure should only be used if it is absolutely necessary if communication has failed If your system is equipped with a gauge controller switch off the triode gauge tube and gauge controller From the GC keypad turn off the GC zone controlling the GC MSD interface heater and set the GC oven to 30 C see page 67 Disconnect the HIVAC POWER cable from the back panel This turns off the MS heaters and the diffusion pump heater or turbo pump but the cooling fans and foreline pump stay on After 45 minutes turn off the MSD power switch Unplug the MSD power cord If you are using hydrogen as a car
149. filter 219 width 309 amu gain 308 amu offset 309 dc polarity 310 dc voltage 308 difficulty with the mass filter electronics 112 heater 314 heater and sensor reinstalling 228 heater and sensor removing 226 maintenance 311 mass axis offset 310 parameters 308 radiator 314 RF voltage 308 Mass filter temperature monitor 40 setting 42 viewing 38 Mass gain 310 Mass offset 310 Mass spectra high abundances at m z 18 28 32 and 44 or at m z 14 and 16 104 high background 103 inconsistent peak widths 104 incorrect mass assignments 104 isotopes missing or ratios are incorrect 103 precursors 104 Mass to charge ratio 308 Methane PCI methyl stearate spectrum 376 setting up gas flow 76 Methane isobutane gas purifier 8 replacing 255 Methyl stearate spectra for methane and ammonia PCI 376 Mist filter for foreline exhaust 272 395 Index Monitoring foreline pressure 38 turbo pump speed 38 vacuum manifold pressure 46 MonitoringAnalyzer chamber pressure 86 Monitors 40 Moving the MSD 65 MS error numbers 112 MSD dangerous voltages in 155 dangerously hot parts in the 156 does not turn on 96 electronics 317 335 hazards from chemical residue 157 interfacing to external devices 334 maintaining 151 244 measuring column flow with the 48 moving or storing 65 operating 33 68 troubleshooting 93 119 N NCI See Negative CI Negative CI analyzer voltage polarities revers
150. fluid between the center stack and the side wall Watch the sight glass while pouring Do not overfill 7 Reinstall the diffusion pump See page 177 176 Materials needed 6 Maintaining the MSD To reinstall the diffusion pump To reinstall the diffusion pump Gloves oil resistant Vacuum cleaner non ESD generating 92175V or equivalent This procedure works best with two people one to hold the pump and one to install the clamp Vacuum the fan that cools the diffusion pump Keeping the fan clean helps ensure maximum cooling This is one of the few times you will have convenient access to the pump side of the fan Slide the diffusion pump into the MSD You may have to tilt the pump slightly to get it into the MSD Do not tilt it past 45 Install the O ring assembly on the diffusion pump Lift the diffusion pump into its normal position Install the KF50 clamp Reconnect the diffusion pump temperature sensor wires to the wiring harness Reconnect the high vacuum power cable to the HIVAC POWER connector on the back panel of the MSD This is the thick black cable that emerges near the bottom of the pump Reconnect the foreline gauge fitting to the outlet of the diffusion pump If you disconnected the foreline gauge cable reconnect it to the foreline gauge Move the MSD back to its normal position See page 179 177 6 Maintaining the MSD To reinstall the diffusion pump Foreline gauge assembly
151. g maintenance 204 Closing the analyzer chamber 58 Column bleed 21 as a source of contamination 119 Column conditioning assisted by solvent injection 26 C Column flow 36 calculating average linear velocity 48 effect on Analyzer chamber pressure 47 for optimum sensitivity 37 maximum for diffusion pump MSD 20 maximum for turbo pump MSDs 20 measuring with the MSD 36 48 Column installation tool 30 Column nut leaking 118 part numbers 22 30 Column capillary preparing for installation 22 Columns conditioning 21 26 installing 19 31 installing in a split splitless inlet 24 installing in the GC MSD interface 28 30 table of size pressure and flow 20 tips and hints 21 types that can be used with the MSD 20 See also Column flow Communication failure venting the MSD in case of 68 Compression seals 270 Conditioning capillary columns importance of 21 procedure for 26 Conditioning column assisted by solvent injection 26 Conditioning ferrules 21 Connectors 332 foreline pump cord receptacle 332 high vacuum power HIVAC POWER 332 high vacuum signal HIVAC SIGNAL 332 power cord receptacle 332 remote start 332 334 Consumables part numbers of 360 389 Index Contamination 119 avoiding after cleaning the ion source 204 table of common contaminants 120 Control panel 6 34 Control panel reagent gas flow control module 293 Controller high vacuum gauge 63 D Data syste
152. g the foreline pump oil box screws first oil change after installation e Replacing the diffusion pump fluid once a year Failure to perform these tasks as scheduled can result in decreased instru ment performance It can also result in damage to your instrument Other procedures should be performed as needed Tasks such as replacing a foreline vacuum gauge or triode gauge tube should be performed only when needed See Chapter 4 Trowbleshooting the MSD on page 107 and see the online help in the MSD ChemStation software for symptoms that indicate this type of maintenance is required More information is available If you need more information about the locations or functions of vacuum system components refer to Chapter 8 Vacuwm System on page 259 Most of the procedures in this chapter are illustrated with video clips in the 5973N MSD Maintenance CD ROM 159 Materials needed See also 6 Maintaining the MSD To check and add foreline pump oil WARNING To check and add foreline pump oil Foreline pump oil 6040 0834 Funnel A video demonstration of this procedure is on the 5973N MSD Maintenance CD ROM A slow loss of oil is normal for the foreline pump Therefore it is especially impor tant to check the oil level regularly Examine the oil level window The oil level should be above the lower line The foreline pump oil should be almost clear If the oil level is near or below the lower line f
153. gative CI It has obvious advan tages of availability and safety 91 3 Operating the CI MSD To switch from CI to El operating mode CAUTION CAUTION To switch from CI to EI operating mode Press the Gas Off button to close the isolation valve Vent the MSD See page 54 The software will prompt you for the appropriate actions Open the analyzer Remove the CI interface tip seal See page 250 Remove the CI ion source See page 248 Install the EI ion source See page 216 Place the CI ion source and interface tip seal in the ion source storage box Pump down the MSD See page 60 Load your EI tune file Always wear clean gloves while touching the analyzer or any other parts that go inside the analyzer chamber 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 before you open the analyzer chamber See page 158 92 General symptoms 96 Chromatographic symptoms 98 Mass spectral symptoms 103 Pressure symptoms 107 Temperature symptoms 110 Error messages 112 Air leaks 118 Contamination 119 Troubleshooting the MSD How to identify the symptoms and causes of problems in your MSD WARNING Troubleshooting the MSD This chapter is a quick reference to symptoms and possible causes of the most common problems experienced by the 59
154. ge 48 for instructions on how to measure actual flow in your column Use the Flow Calculation software to determine whether a given column will give acceptable flow with realistic head pressure Feature G2577A G2578A G2579A G2588A G2589A High vac pump Diffusion pump Standard turbo Performance turbo Standard turbo Performance turbo EI PCI EI PCI NCI Optimal gas flow ml min 1 1 1 to 2 1 1 to 2 Maximum recommended 1 5 2 0 4 2 0 4 gas flow ml min Maximum gas flow 2 24 6 5 2 4 4 ml min Max column id 0 25mm 30m 0 32mm 30m 0 53 mm 30m 0 32mm 30m 0 53mm 30m a Total gas flow into the MSD column flow plus reagent gas flow if applicable b Expect degradation of spectral performance and sensitivity 20 WARNING WARNING 1 Installing GC Columns Conditioning a column before it is installed into the GC MSD interface is essential A small portion of the capillary column stationary phase is often carried away by the carrier gas This is called column bleed Column bleed deposits traces of the stationary phase in the MSD ion source This decreases MSD sensitivity and makes cleaning the ion source necessary Column bleed is most common in new or poorly cross linked columns It is much worse if there are traces of oxygen in the carrier gas when the column is heated To minimize column bleed all capillary columns should be condi tioned before they are installed in the GC MSD interface Conditioning ferru
155. ghten the knob before pumping down WARNING Allow the analyzer to cool to near room temperature before touching it CAUTION Always wear clean gloves while handling any parts that go inside the analyzer chamber WARNING When the MSD is vented do not put the ChemStation into Top view Doing so will turn on the interface heater 55 Materials needed 2 Operating the MSD To open the analyzer chamber CAUTION WARNING CAUTION CAUTION To open the analyzer chamber Gloves clean lint free large 8650 0030 small 8650 0029 Wrist strap anti static small 9300 0969 medium 9300 1257 large 9300 0970 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 see page 158 before you open the analyzer chamber Vent the MSD page 54 Disconnect the side board control cable and the source power cable from the side board Loosen the side plate thumbscrews if they are fastened The rear side plate thumbscrew should be unfastened during normal use It is only fastened during shipping The front side plate thumbscrew should only be fas tened for CI operation or if hydrogen or other flammable or toxic substances are used for carrier gas Gently swing the side plate out The analyzer GC MSD interface and other components in the analyzer chamber
156. h is on potentially dangerous voltages exist on e Electronic circuit boards e Toroidal transformer e Turbomolecular pump controller e Wires and cables between these boards e Wires and cables between these boards and the connectors on the back panel of the MSD e 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 difficult to accidentally make contact with dangerous voltages Perform no maintenance with the MSD turned on or plugged into its power source unless you are instructed to by one of the procedures in this chapter 155 WARNING WARNING 6 Maintaining the MSD One or two procedures in this chapter require access to the inside of the MSD while the power switch is on Do not remove any of the electronics safety covers in any of these procedures To reduce the risk of electric shock follow the procedures carefully If your instrument is equipped with the optional gauge controller potential ly dangerous voltage also exists where the cable from the gauge controller connects to the triode gauge tube Turn off the gauge controller if you are going to be working near the triode gauge tube Many parts are hot enough to be dangerous Many parts in the MSD operate at or reach temperatures high enough to cause serious burns These parts include but are not limited to
157. h voltage HED eedthrough Rear side plate thumbscrew 8 Vacuum System Side plate Analyzer chamber Side plate O ring 269 8 Vacuum System Vacuum seals Vacuum seals 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 must 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 are lightly lubricated with Apiezon L vacuum grease the side plate O ring and the vent valve O ring 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 pumpdown in order to assure 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 baff
158. hardware overview 8 methane reagent gas 374 molecular ion 374 overview 374 references 375 water contamination 374 Chemical residue hazardous 157 ChemStation controlling temperatures with 36 monitoring temperatures and vacuum 38 setting monitors 40 setting the GC MSD interface temperature 44 using to pump down the CI MSD 62 using to pump down the MSD 60 using to set up methane reagent gas flow 76 using to tune the MSD 50 using to vent the MSD 54 68 Chromatography abnormal results 98 CI autotune 78 Methane PCI only 80 CI calibrant vial refilling 257 CI calibration valve 283 294 CI filament 306 388 Index Cl interface heater clamp 233 292 interface tip seal 306 installing 250 Cl ion source cleaning 252 installing 248 repeller 306 CI maintenance 245 258 CI MSD maintenance 245 installing the CI interface tip seal 250 CI operating mode switching to 72 CI operation 69 CI autotune 78 general guidelines 70 72 247 installing the Cl ion source 248 NCI autotune 82 PCI autotune 80 setting up methane gas flow 76 setting up the software for 73 start up in methane PCI first 71 typical pressure readings 87 using other reagent gases 88 using the reagent gas flow control module 74 CI reagent gas flow control module see Reagent gas flow control module CI spectra classical 8 endosulfan methane NCI 383 methyl stearate methane and ammonia PCI 377 Cleanliness importance durin
159. he MSD Of greater concern are changes in pressure from hour to hour or day to day These changes can indicate air leaks or other problems with the vacuum system All the pressures listed in this manual are indicated pressures for helium carrier gas The gauge controller setpoints are also indicated pressures To monitor high vacuum pressure page 46 The filament in the triode gauge tube can ignite hydrogen Never turn on the tube if there is a possibility that hydrogen has accumulated in the manifold 287 8 Vacuum System Gauge controller Hew 3 Ea T ASE s saasa an ne GAUGE CONTROLLER 1 Pressure display il a TORR Power indicator Gauge on off switch Power cord Power switch Cable to triode gauge tube Fuse Ground point 288 EI GC MSD interface 291 EI CI GC MSD interface CI interface 292 Reagent gas flow control module 293 GC MSD Interfaces and CI Flow Control This chapter describes the function of the GC MSD interfaces and the CI reagent gas flow control module See Also CAUTION WARNING GC MSD interface The GC MSD interface is a heated conduit into the MSD for the capillary column It is bolted onto the right side of the analyzer chamber with an O ring seal A channel machined into the flange for the seal provides thermal isolation between the heated interface and the O ring and manifold The GC MSD interface is covered by a pr
160. he calibration vial See page 183 Pump down the MSD See page 60 Select Purge Cal Valve from the Vacuum menu in the Diagnostics Vacuum Control view Failure to purge the calibration valve will result in damage to the filaments and detector 192 Calibration valve O ring Front end plate 6 Maintaining the MSD To reinstall the El calibration valve Calibration valve Collar Calibration vial 193 Materials needed WARNING 5 6 7 WARNING 10 6 Maintaining the MSD To replace the fan for the high vacuum pump To replace the fan for the high vacuum pump Fan 3160 1037 Screwdriver Torx T 15 8710 1622 Vent the MSD See page 54 Remove the upper and lower MSD covers See page 52 Disconnect the fan wiring from the connector on the MSD frame Remove the 4 fan screws and remove the fan Keep the 4 screws Do not touch the high vacuum pump The high vacuum pumps especially the diffusion pump operate at dangerously high temperatures and could still be hot enough to burn you Disconnect the fan wiring and safety grill from the old fan The fan wiring ends in a small connector on the back of the fan Connect the fan wiring and safety grill to the new fan Install the new fan and reinstall the 4 screws The flow arrow on the side of the fan points towards the pump Make sure the safety grill that shields the fan blades is in place
161. hood Part number 05971 60119 G1099 89023 61099 89024 0905 1463 1400 1234 0100 1397 61099 20531 0100 0549 61099 20532 61099 80037 61099 00015 346 12 Parts Vacuum system Foreline hose 05971 60119 Hose clamp 1400 1234 EZ KF16 hose adapter G1099 20531 wz F 10 16 clamp 0100 1397 wz F10 16 seal 905 1463 Foreline pump 120 V ac G1099 89023 230 V ac G1099 89024 Exhaust outlet use 11 mm id hose Oil drip tray G1099 00015 347 Table 14 12 Parts Vacuum system Diffusion pump MSD vacuum system components Description Baffle inside stem of triode gauge tube not shown Calibration valve assembly calibration vial Claw clamps for baffle adapter Collar for triode gauge tube not shown Diffusion pump 120V 220 240V Diffusion pump baffle adapter Diffusion pump baffle adapter O ring Diffusion pump control cable End plate front rear Fan for high vacuum pump Foreline gauge assembly Foreline gauge seal KF10 16 clamp diffusion pump outlet KF10 16 seal diffusion pump outlet KF50 clamp KF50 seal foreline pump to baffle adapter Shield for triode gauge tube port not shown Side plate includes feedthroughs and thumbscrews Triode gauge tube Analyzer chamber Vent valve knob Part number 05972 00015 61099 60201 05980 20018 0100 1881 05972 60210 G1099 80500 G1099 80501 G1099 20021 0905 1443 G1099 60
162. horn replacing 230 electronics 238 fan high vacuum pump replacing 194 filament reinstalling 220 filament removing 218 foreline gauge reinstalling 188 foreline gauge removing 186 foreline pump in CI 254 foreline pump oil draining 162 foreline pump refilling 164 GC MSD interface 232 GC MSD interface heater and sensor reinstall ing 236 394 Index GC MSD interface heater and sensor remov ing 234 increased need for ion source cleaning in CI MSD 246 ion source heater and sensor reinstalling 224 ion source heater and sensor removing 222 ion source disassembling 208 ion source reassembling 214 ion source reinstalling 216 ion source removing 206 mass filter quadrupole 311 mass filter heater and sensor reinstalling 228 mass filter heater and sensor removing 226 methane isobutane gas purifier 255 primary fuses replacing 242 purging thecalibration valve after refilling the calibrant vial 185 reconnecting the MSD to the GC 179 refilling the CI calibrant vial 257 RF coils adjusting 240 safety during 155 158 schedule 152 separating the MSD from the GC 171 side plate O ring lubricating 200 supplies for 154 tools for 153 361 triode gauge tube reinstalling 198 triode gauge tube removing 196 vacuum system 159 vent valve O ring lubricating 202 Maintenancem CI 258 Malfunctions See Symptoms of malfunctions Manual tune 50 Mass assignments incorrect 104 Mass
163. hrough the data system and or control panel and through the optional gauge controller 260 8 Vacuum System Common vacuum system problems The most common problems associated with any vacuum system are air leaks Symptoms of air leaks include e Loud gurgling noise from the foreline pump very large leak e Inability of the turbo pump to reach 95 speed e High foreline pressure in diffusion pump MSDs e Higher than normal high vacuum gauge controller readings The 5973N MSD will not pump down successfully unless you press on the side plate analyzer door when you turn on the MSD power Continue to press until the sound from the foreline pump becomes quieter Pumpdown failure shutdown The system will shut down both the high vacuum and the foreline pump if the system fails to pump down correctly The conditions that trigger shut down are e Diffusion pump MSD foreline pressure above 300 mTorr after 7 minutes e Turbo pump MSDs turbo pump speed below 80 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 foreline pump from sucking air through the system which can damage the analyzer and pump To restart the MSD find and correct the air leak then switch the power off and on Be sure to press on the sideplate when turning on the MSD power to ensure a good seal 261 8 Vacuum System Many component
164. ial e Defective calibration valve e Air leak in carrier or reagent gas path No reagent gas peaks in NCI e Reagent gases do not ionize in NCI look for background ions instead e Verify tune parameters e Ifno background ions are visible go back to methane PCI No PFDTD calibrant peaks in NCI e Look for background ions 17 OH 35 Cl and 235 ReO3 e Verify tune parameters e Go back to methane PCI No sample peaks in NCI e Look for background ions 17 OH 35 Cl and 235 ReO3 e Go back to methane PCI e Poor quality reagent gas purity less than 99 99 Large peak at m z 238 in NCI OFN spectrum e Look for background ions 17 OH 35 Cl and 235 ReO3 e Find and fix your small air leak 134 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting No or low reagent gas signal No or low reagent gas signal If you have just installed the CI ion source and have an air leak or large amounts of water in the system and have run one or more autotunes the ion source is proba bly dirty now Fix the air leak Clean the ion source Then bake out for two hours before tuning See To set up your MSD for CI operation on page 247 The wrong reagent gas is flowing Turn on the correct reagent gas for your tune file Ion polarity is set to Negative No reagent gas
165. ill prevent diffusion of PFIBA into the analyzer chamber for tuning If this happens the valve should be replaced 4 Remove the calibration valve from the front end plate 190 Calibration valve O ring Front end plate 6 Maintaining the MSD To remove the El calibration valve Calibration valve Collar Calibration vial 191 Materials needed 6 Maintaining the MSD To reinstall the El calibration valve CAUTION To reinstall the EI calibration valve Calibration valve for diffusion pump or standard turbo G1099 60201 for performance turbomolecular pump G1099 60204 O ring for calibration valve 0905 1217 replace if the old O ring is damaged PFTBA 05971 60571 or other tuning compound Screwdriver Torx T 15 8710 1622 Remove the old calibration valve See page 190 Make sure the calibration valve O ring is in place If the O ring is worn or damaged replace it Install the calibration valve Tighten the screws that hold it in place Make sure you use the calibration valve that matches the high vacuum pump in your MSD The different calibration valves have different restrictors Using the wrong valve will interfere with tuning Reconnect the calibration valve cable to the connector next to the fan Remove the vial from the new calibration valve See page 181 The valve is supplied with a vial already installed Fill and reinstall t
166. ill result in a heavily contaminated ion source Water contamination is most common immediately after new reagent gas tubing or reagent gas cylinders are connected This contamination will often decrease if the reagent gas is allowed to flow for a few hours purging the system 374 Appendix A Chemical lonization Theory Chemical ionization overview 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 14 327 348 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 6 375 Appendix A Chemical lonization Theory Positive Cl theory 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 than electron ionization producing less frag mentation This reaction usually yields high abundance of the molecular ion and is therefore often used for determining molecular weights of samples The most common reagent gas is methane Methane
167. ing 99 peaks are tailing 99 399 Index peaks have flat tops 100 peaks have precursors 104 peaks have split tops 100 poor repeatability 102 poor sensitivity 102 poor vacuum without reagent gas flow 129 power indicator on the gauge controller does not light 109 pressure does not change when reagent gas flow is changed 131 pressure symptoms 107 109 pressure related symptoms overview CI 128 reagent gas ion ratio is difficult to adjust or un stable 145 relative abundance of m z 502 less than 3 105 retention time drifts all peaks 101 signal related symptoms overview 132 temperature control disabled 115 temperature control fault 115 temperature symptoms 110 111 the high vacuum pump is not ready 116 the system is in standby 116 the system is in vent state 117 there is no emission current 117 tuning related symptoms overview for CI MSD 144 System ready signal 335 T Target tune 50 Temperature sensors GC MSD interface reinstalling 236 GC MSD interface removing 234 in the MSD analyzer 36 ion source reinstalling 224 ion source removing 222 mass filter reinstalling 228 mass filter removing 226 Temperatures controlled through the MSD Chem Station 36 Thermal Aux 2 290 Thermal electrons in NCI 382 Thermal equilibrium time to reach 314 Tipping the MSD caution against 66 To 68 72 248 254 Tools for maintaining the MSD 361 Toroid transformer 33
168. ionization chamber through the GC MSD interface by means of the gas flow control module After the system has been switched from El to Cl mode or vented for any other reason the MSD must be purged and baked out for at least 2 hours before tuning Longer bakeout is recommended before running samples requiring optimal sensitivity There is a PCI autotune for methane only as there are no PFDTD ions produced by other gases in positive mode PFDTD ions are visible in NCI for any reagent gas Always tune for methane PCI first regardless of which mode or reagent gas you wish to use for your analysis There are no tune performance criteria If CI autotune completes it passes EMVolts electron multiplier voltage at or above 2600V however indicates a problem If your method requires EMVolts set at 400 you may not have adequate sensitivity in your data acquisition Always verify MSD performance in El before switching to Cl operation See page 51 Always set up the Cl MSD in PCI first even if you are going to run NCI Default starting Cl tune parameters 78 Suggested starting parameters for El PCI NCI MSDs 3 Operating the Cl MSD Cl autotune Reagent gas Methane Isobutane Ammonia El on polarity Positive Negative Positive Negative Positive Negative N A Emission 50 uA 50 uA 50 uA 50 uA
169. 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 programs tune the 5973N MSD to achieve about a 0 8 ratio of m z 502 69 e Tune program tune file has a different relative abundance target 8 only applies to Autotune e Not enough time for the MSD to warm up and pump down e Analyzer chamber pressure is too high e Jon source temperature is too high e Column carrier gas flow is too high e Poor filament operation e Dirty ion source e Air leak e Incorrect dc polarity on the quadrupole mass filter Spectra look different from those acquired with other MSDs Ion ratios are different from those in older MSDs This is due to the HED detector and is normal To get spectra similar to older MSDs use Standard Spectra Tune avail able in the Manual Tune view Note that this tune takes much longer to complete than Autotune 105 4 Troubleshooting the MSD Mass spectral symptoms High mass sensitivity is poor This refers to a condition where the absolute abundance at the upper end of the mass range is poor Absolute abundance should not be confused with the relative abundance percentage of m z 502 to m z 69 Sensitivity at high masses can be excellent even if the relative abundance of m z 502 is low e Wrong tune program e Wrong tune file e Repelle
170. is the thick black cable that emerges near the bottom of the pump Support the diffusion pump with one hand Remove the KF50 clamp Lower the diffusion pump 173 6 Maintaining the MSD To remove the diffusion pump Foreline gauge assembly KF50 clamp O ring assembly Diffusion pump Diffusion pump outlet 9 Remove the O ring assembly from the top of the diffusion pump The O ring will have diffusion pump fluid on it and will be very sticky Place the O ring on clean aluminum foil shiny side down to keep your lab bench and the O ring clean 10 Remove the diffusion pump through the side of the MSD You may have to tilt the pump slightly to remove it Do not tilt the pump past 45 if the pump is warm 174 Materials needed 6 Maintaining the MSD To replace the diffusion pump fluid WARNING WARNING Charred or blackened pump fluid WARNING To replace the diffusion pump fluid Aluminum foil clean Cloths clean lint free 05980 60051 Container for old diffusion pump fluid Diffusion pump fluid 18 5 ml 6040 0809 2 required Gloves oil and solvent resistant thermally insulated Remove the diffusion pump from the MSD See page 173 Make sure you remove the O ring assembly from the top of the diffusion pump Cover the top of the diffusion pump with aluminum foil shiny side up Heat the diffusion pum
171. is used to adjust the flow When no gases are turned on the Flow Control display will show dashes e Purge sets the MFC to 100 of total flow fully open regardless of the position of the flow control knob or the state of the select valves e The flow control display shows the gas flow as a percentage of the total possible flow 5 ml min for methane If the display is flashing the controller cannot maintain the selected flow This usually means that the reagent gas supply does not have high enough pressure 293 9 GC MSD Interfaces and Cl Flow Control Reagent gas flow control module e 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 e The CI calibration valve is controlled by the ChemStation software and opens automatically during CI autotune or manual tuning allowing PFDTD to diffuse into the ion source e The isolation valve prevents contamination of the flow control module by atmosphere while the MSD is vented or by PFTBA during EI operation Rear flow module cover Isolation valve Flow control board under cover Control panel EI C GC MSD interface Cl calibration valve Mass flow controller Reagent gas select valve Reagent gas inlet lines CAUTION Try to avoid tuning any more often than absolutely necessary to minimize PFDTD background and ion sou
172. isms provide the dramatic increases in sensitivity often associated with negative chemical ionization The four most com mon mechanisms reactions are e Electron capture e Dissociative electron capture e Jon pair formation e Jon molecule reactions In all of the cases except the ion molecule reactions the reagent gas serves a func tion different from the function it serves in positive chemical ionization In nega tive CI the reagent gas is often 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 gt Reagent ions thermal If the reagent gas is methane the reaction is CH4 e 30ev gt CH4 2 thermal The thermal electrons have lower energy levels than the electrons from the fila ment It is these thermal electrons that react with the sample molecules There are no negative reagent gas ions formed This prevents the kind of back ground that is seen in PCI mode and is the reason for the much lower detection limits of NCI The products of negative chemical ionization can only be detected when the MSD is operating in negative ion mode This operating mode reverses the polarity of all the analyzer voltages Carbon dioxide is often used as a buffer gas in negative CI It has obvious cost availability and safety advantages over other gases 382 Endosulfan MW 404 El and methane NCI App
173. ity The dc polarity DC Pol parameter selects the orientation of the direct current applied to the quadrupole mass filter The dc polarity that works best for your MSD is determined at the factory It is listed on the final test sheet accompanying your MSD It is also listed on a label on the cover over the RF coils This cover can be viewed by removing the upper MSD cover Using the non preferred dc polarity may result in very poor performance Always use the factory specified polarity Mass axis gain Mass gain MassGain controls the mass assignment that is assignment of a par ticular peak to the correct m z value e A higher gain yields higher mass assignment e Mass gain affects peaks at high masses more than peaks at low masses Mass axis offset Mass offset MassOffs also controls the mass assignment e A higher offset yields higher mass assignment e Mass offset generally affects peaks equally at all masses 310 CAUTION CAUTION CAUTION CAUTION 10 Analyzer Quadrupole mass filter 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 Agi lent Technologies service personnel Never put the quadrupole in an ultrasonic cleaner Never change the physical orientation of the qua
174. k cover 5973Network Mass Selective Detector Hardware Manual In This Manual This manual describes the operation troubleshooting and maintenance of the Agilent Technologies 5973Network Mass Selective Detector 5973N MSD 5973N MSD Version 5973N MSDs are equipped with either a diffusion pump or one of two turbomolecular turbo pumps Chemical Ionization is available for the turbo pump MSDs only The serial number label displays a product number that tells what kind of MSD you have In this manual the term CI MSD applies to both the EI PCI MSD and the EI PCI NCI MSD Model number Description G2577A Diffusion Pump El MSD G2578A Standard turbo El MSD G2579A Performance turbo El MSD G2588A Standard turbo El PCI MSD G2589A Performance turbo EI PCI NCI MSD e Chapter 1 shows you how to prepare and install a capillary column e Chapter 2 describes basic tasks such as setting temperatures monitoring pressures tuning and venting and pumpdown e Chapter 3 describes basic tasks necessary to operate a CI MSD in CI mode e Chapter 4 provides a quick reference for identifying causes of poor instrument performance or malfunctions e Chapter 5 provides a quick reference for identifying problems unique to CI MSDs e Chapter 6 features maintenance procedures e Chapter 7 features maintenance procedures unique to CI MSDs The Agilent Technologies 5973Network Mass Selective Detector e Chapter 8 describes operation
175. late thumbscrews Overtightening will strip the threads in the analyzer chamber It will also warp the side plate and cause leaks Plug the MSD power cord in Switch the MSD on to establish a rough vacuum Verify that the foreline pressure is below 300 mTorr or the turbo pump speed greater than 50 Switch the MSD off Reinstall the analyzer cover 65 2 Operating the MSD To move or store the MSD e Front side plate thumbscrew Oo LOO OOIONY Rear side plate thumbscrew a AAA e Ss SS cS 13 Disconnect the LAN remote and power cables The MSD can now be stored or moved The foreline pump cannot be disconnected It must be moved with the MSD Make sure the MSD remains upright and is never tipped on its side or inverted 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 66 2 Operating the MSD To set the interface temperature from a 6890 Plus GC CAUTION CAUTION To set the interface temperature from a 6890 Plus GC Press the Aux key on the GC keypad Press 2 By default the GC MSD interface is powered by heated zone Thermal Aux 2 on the 6890 Series GC Verify that the display shows THERMAL AUX 2 MSD Use the number keys to type in the new temperature s
176. le adapter is clamped to the manifold with 4 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 the outside of the O ring The clamp presses two flanges against the O ring making a seal KF clamps must not be overtightened Compression seals A compression fitting consists of a threaded fitting on the analyzer chamber and a threaded collar with a ferrule and O ring A cylindrical part fits inside the collar Tightening the collar presses the ferrule compressing the O ring around the part The triode gauge tube and calibration vial use compression seals 270 8 Vacuum System Vacuum 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 Analyzer chamber OX Side plate O ring Side plate KF seal with internal centering ring KF flange clamp not shown KF flange clamp not shown KF seal with external centering ring Collar O ring Analyzer chamber ECR Ferrule 000 l Triode tube 271 WARNING CAUTION CAUTION See Also 8 Vacuum System Foreline pump Foreline pump
177. ler 8120 6573 Fuses and power switch Description Part number Fuse 4A 250V fast acting low breaking ac board and main board 2110 0734 Fuse 8A 250V time lag high breaking capacity primary fuses 2110 0969 Power button 5041 1203 Power switch extender rod G1099 40007 Switch adapter G 1099 20026 1 Notauser replaceable part Refer service to your Agilent Technologies service representative 339 Table 10 12 Parts Electronics Internal Cables Description AC board control cable AC board to main board Chassis ground wire Control panel ribbon cable Diffusion pump control cable Electronics module fan cable Fan high vacuum cable Feedthrough board inside analyzer chamber HED control cable HED power cable High vacuum power extender cable AC board to back panel Low voltage power supply input cable AC board to LV PS Low voltage power supply output cable LV PS to main board Mass filter contact cable kit inside analyzer chamber Side board control ribbon cable main board to side board Signal cable signal feedthrough on side plate to signal amplifier board Source power cable main board to side board Turbo pump control cable back panel to turbo controller Turbo pump power cable back panel to turbo controller HP part number 61099 60422 61099 60433 62589 60030 61099 60437 61099 60560 61099 60561 G1099 60425 G1099 60430 G1099 60431 G1099 60436 G1099 60426
178. les is also beneficial Heating ferrules to their maximum expected operating temperature a few times before they are installed can reduce chemical bleed from the ferrules Tips and hints e Note that the column installation procedure for the 5973 MSDs is different from that for all previous MSDs Using the procedure from another instrument will not work and may damage the column or the MSD e You can remove old ferrules from column nuts with an ordinary push pin e Always use carrier gas that is at least 99 999 pure e Because of thermal expansion new ferrules may loosen after heating and cooling a few times Check for tightness after two or three heating cycles e Always wear clean gloves when handling columns especially the end that will be inserted into the GC MSD interface If you are using hydrogen as a carrier gas do not start carrier gas flow until the column is installed in the MSD and the MSD has been pumped down If the vacuum pumps are off hydrogen will accumulate in the MSD and an explosion may occur Read the Hydrogen Carrier Gas Safety Guide 5955 5398 before operating the MSD with hydrogen carrier gas Always wear safety glasses when handling capillary columns Use care to avoid puncturing your skin with the end of the column 21 Materials needed 1 Installing GC Columns To prepare a capillary column for installation To prepare a capillary column for installation Capillary column Column cutter 5
179. ller is calibrated for methane and the high vacuum gauge controller is calibrated for nitrogen so these measurements are not accurate in absolute 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 150 C Interface temperature 320 C Helium carrier gas flow 1ml min MFC Pressure Torr Methane Ammonia Performance Standard Performance Standard turbo turbo pump turbo pump turbo pump pump 10 55x105 20x107 50x105 15x10 15 8 0x10 25x107 70x10 20x107 20 10x10 30x10 85x10 30x10 25 12x104 40x10 10x10 35x10 30 15x10 50x107 12x10 40x107 35 20x10 55x107 15x10 45x107 40 25x10 65x107 20x10 55x107 128 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting Poor vacuum without reagent gas flow CAUTION Poor vacuum without reagent gas flow Excess water in the background Scan from 10 40 amu A large peak at m z 19 gt m z 17 indicates water in the background If water is present allow the instrument to bake out more and flow reagent gas through the lines to purge any accumulated water Air leak Run Methane Pretune See page 76 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 The foreline pump is not working pro
180. llimeters L the column length in meters t the retention time in minutes 48 2 Operating the MSD To calculate column flow To calculate column flow 1 In the Instrument Control view click the Columns icon 2 Check that the correct column dimensions are entered 3 Type the desired value in the pressure field Instrument Edit Columns 6890 x Oven Temp Temperature C sas o T o Plot fo roe oe a Time min Column Installed Column oy Mode Const Flow x Inventory AB001 Inlet From x not calibrated Column Dimensions Detector MSD Z Capillary 30 0 m x 250 um x 0 25 pm Outlet psi Vacuum x He Flow Apply Setpoint Actual 2 Flow ml min ml min Hold min Run Time Initial 1 0 0 00 10 00 OK 8 s p Ramp 1 0 00 0 0 0 00 Flow 1 0 1 0 ml min Ramp 2 Average jz Ramp 3 Velocity cm sec Post Run 0 00 10 00 0 00 0 0 0 00 Cancel 0 00 0 0 0 00 4 Ifthe Average Velocity displayed is different from that obtained on page 48 click the Change button to calibrate the column dimensions 49 Software changes See also 2 Operating the MSD To tune the MSD To tune the MSD The software is revised periodically If the steps in this procedure do not match your MS ChemStation software refer to the manuals and online help supplied with the software for more information You can also use the Control Panel to run
181. lowing any reagent gas but methane in PCI Switch to methane Wrong or corrupted tune file loaded Check your tune file No PFDTD in the calibrant vial Inspect the calibration vial on the back of the flow controller If necessary fill the vial with PFDTD Do not fill the vial completely keep the level at least 0 5 cm from the top of the vial The pressure of the methane entering the flow controller is too high Make sure the regulator on the methane supply is set to 10 psig 70 kPa The Cl ion source is dirty Clean the ion source See the Maintenance chapter in this manual for more infor mation The calibration valve was not purged after the vial was refilled Purge the calibration valve as described in the Maintenance chapter Then clean the ion source 138 Possible Cause Action Possible Cause Action 5 Cl Troubleshooting No or low PFDTD signal but reagent ions are normal The calibrant vial was overfilled Excess PFDTD can quench the chemical ioniza tion reactions Check the level of the PFDTD in the calibration vial as described in Maintenance chapter 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 139 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action
182. ly Interface socket lonization chamber O ring Analyzer Screw Heater sensor assembly nterface cover nsulation Guide tube Capillary column 291 EI CI GC MSD interface CI interface The Cl interface mounts onto the side of the analyzer chamber 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 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 erface cover C erface insulator CI interface heater clamp CI interface weldment nterface tip seal Hs CI ionization chamber J z z r a pe N ZN YY JJ Source radiator g Analyzer chamber Heater sensor cable Reagent gas inlet GC inlet 292 9 GC MSD Interfaces and Cl Flow Control Reage
183. m control over pumpdown 35 controlling temperatures with 36 using to ensure correct venting 36 DC polarity 310 Detection limits high in PCI 376 lower in NCI 382 Detector 312 difficulty with the EM supply 112 electron multiplier horn 312 electron multiplier voltage 312 replacing the horn 230 steadily increasing EM voltage 313 Detector focus lens 312 DFTPP tune 50 Diffusion pump 276 automatic control of 276 277 effect of low fluid level in 107 error messages related to 113 part numbers 348 reinstalling 177 removing 173 thermal switches 277 See also Diffusion pump fluid Diffusion pump fluid 276 as a source of contamination 119 checking 168 replace once a year 152 replacing 175 Disassembling the ion source 208 Drawout plate and cylinder 304 Drying cleaned ion source parts 204 Dummy filament 306 E EI overview 374 EI CI GC MSD interface See CI interface EI CI GC MSD interface See CI interface Electronics 317 335 ac board 326 ac dc board See low voltage power supply danger to from electrostatic discharge 158 238 high voltage HED power supply 331 LAN MS control card 330 locations of major components 319 low voltage power supply 331 main board 324 maintaining 238 part numbers 339 power supplies 331 signal amplifier board 325 status display 320 toroid transformer 331 turbo pump controller 328 Electrostatic discharge danger to the electronics from 158 238 precaution
184. ment controller e Data processor e Main processor e Serial communication processor e Network communication controller e Remote start processor e Random access memory RAM e Status LEDs e Control panel firmware LEDs on the LAN MSD control card are visible on the rear panel The upper two LEDs indicate network communication The two bottom LEDs are the power good digital 5V and the heartbeat indica tor The flashing heartbeat LED indicates that the operating system of the MSD is functioning In case of catastrophic loss of flash memory the heartbeat flashes in an SOS pattern 330 11 Electronics Power supplies Power supplies Low voltage ac dc power supply The low voltage power supply is mounted next to the toroid transformer in the electronics module A universal input power supply it converts ac line voltage into the dc voltages used by the rest of the electronics The power supply generates the following dc voltages e 24 V nominal e 15 V nominal e 15 V nominal e 5 V nominal High voltage HED power supply The high voltage power supply provides the 10 000 volts dc for the high energy dynode HED in the detector for EI and EI PCI MSDs The EI PCI NCI MSD requires a bipolar power supply that can also provide 10 000 volts for NCI opera tion The HED power supply also provides the 350 volts dc for the detector focus lens Due to the high impedance of this circuit measuring the d
185. mentation supplied with your GC 111 4 Troubleshooting the MSD Error messages Error messages Sometimes a problem in your MSD will cause an error message to appear in the MSD ChemStation software Some error messages appear only during tuning Other messages will appear during tuning or data acquisition Sometimes instead of a message only a number will appear This number will represent one or more error messages To translate a number into an error message Note the number Select Diagnostics Vacuum Control from the View menu Select MS Error Codes from the Status menu Type in the error number and press Enter Kw Dd The corresponding error message s will appear Some error messages are latched These messages remain active in your data system even if the condition that caused the message has corrected itself If the cause is removed these messages can be removed by checking instrument status through the data system Difficulty in mass filter electronics e Pressure in the analyzer chamber is too high e RFPA is not adjusted correctly e Mass filter quad contacts are shorted or otherwise not working correctly e Mass filter is not working correctly e MSD electronics are not working correctly Difficulty with the electron multiplier supply e Large peak such as the solvent peak eluted while the analyzer was on e Pressure in the analyzer chamber is too high e MSD electronics are not working correctly
186. messages 112 Difficulty in mass filter electronics 112 Difficulty with the electron multiplier supply 112 Difficulty with the fan 113 Difficulty with the HED supply 113 Difficulty with the high vacuum pump 113 Foreline pressure has exceeded 300 mTorr 114 Internal MS communication fault 114 Lens supply fault 114 Log amplifier ADC error 114 No peaks found 114 Temperature control disabled 115 Temperature control fault 115 The high vacuum pump is not ready 116 The system is in standby 116 The system is in vent state 117 There is no emission current 117 There is not enough signal to begin tune 117 Air leaks 118 Contamination 119 13 Chapter 5 Chapter 6 Contents CI Troubleshooting Troubleshooting tips and tricks 123 Air leaks 124 How do I know if I have an air leak 124 How do I find the air leak 126 Pressure related symptoms overview 128 Poor vacuum without reagent gas flow 129 High pressure with reagent gas flow 130 Pressure does not change when reagent flow is changed 131 Signal related symptoms overview 132 No peaks 133 No reagent gas peaks in PCI 133 No PFDTD peaks in PCI 134 No reagent gas peaks in NCI 134 No PFDTD calibrant peaks in NCI 134 No sample peaks in NCI 134 Large peak at m z 238 in NCI OFN spectrum 134 No or low reagent gas signal 135 No or low PFDTD signal but reagent ions are normal 138 Excessive noise or low signal to noise ratio 140 Large peak at m z 19 141
187. ml min Maximum gas flow 2 2 4 6 5 2 4 6 5 ml min Max column id 0 25 mm 30m 0 32 mm 30m 0 53mm 30m 0 32 mm 30m 0 53 mm 30 m CI capability no no no PCI PCI NCI DIP capability yes yes yes no no 3rd Party a Total gas flow into the MSD column flow plus reagent gas flow if applicable b Expect degradation of spectral performance and sensitivity The Agilent Technologies 5973Network Mass Selective Detector CI MSD hardware description In this manual the term CI MSD applies to both the EI PCI MSD and the EI PCI NCI MSD The CI hardware allows the 5973N MSD to produce high quality classical CI spectra which include molecular adduct ions A variety of reagent gases can be used The 5973N CI system adds to the 5973N MSD e Redesigned EI CI GC MSD interface e Clion source and interface tip seal e Reagent gas flow control module e Bipolar HED power supply for PCI NCI MSDs only e Amethane sobutane gas purifier is provided and is required It removes oxygen water hydrocarbons and sulfur compounds A high vacuum gauge controller 59864B is required for CI MSDs To achieve the relatively high source pressure required for CI while still maintaining high vacuum in the quadrupole and detector the MSD CI system has been carefully optimized Special seals along the flow path of the reagent gas and very small openings in the ion source keep the source gases in the ionization volume long enough for the appropri
188. mn nut e Side plate O ring all the way around e Vent valve O ring e Triode gauge tube cracked at connector e Calibration valve e GC MSD interface O ring where the interface attaches to the analyzer chamber e Front and rear end plate O rings e Diffusion pump KF seal e Diffusion pump baffle adapter O ring e Turbomolecular pump O ring 118 4 Troubleshooting the MSD Contamination Contamination Contamination is usually identified by excessive background in the mass spectra It can come from the GC or from the MSD The source of the contamination can sometimes be determined by identifying the contaminants Some contaminants are much more likely to originate in the GC Others are more likely to originate in the MSD Contamination originating in the GC typically comes from one of these sources e Column or septum bleed e Dirty injection port e Injection port liner e Contaminated syringe e Poor quality carrier gas e Dirty carrier gas tubing e Fingerprints improper handling of clean parts Contamination originating in the MSD typically comes from one of the following sources e Air leak e Cleaning solvents and materials e Diffusion pump fluid e Foreline pump oil e Fingerprints Gmproper handling of clean parts The following table lists some of the more common contaminants the ions charac teristic of those contaminants and the likely sources of those contaminants 119 Table 3 4 Troublesho
189. mpete with electron capture reactions The more ion molecule reactions that occur the fewer electron capture reactions occur 386 Index Numerics 19 large peak at m z in CI MSD 141 219 width 309 32 visible peak at in CI MSD 71 76 142 59864B Gauge Controller 287 59864B gauge controller 63 5986B Gauge controller 7 A Abrasively cleaning ion source parts 212 parts to be cleaned 210 Abundance absolute 105 low for m z 502 105 relative 105 AC board 326 Adduct ion 380 Adjusting the RF coils 240 Air leaks 118 as a source of contamination 119 detecting in CI 77 finding in CI 126 small enough to cause no problems in PCI can destroy NCI sensitivity 122 visible peak at m z 32 in CI MSD 142 Alignment analyzer and CI interface checking 250 Ammonia ballasting of the foreline pump required due to 254 maintenance caution 374 PCI spectrum of methyl stearate 376 Ammonia reagent gas increased maintenance required 246 AMU gain 308 AMU offset 309 Analyzer 297 315 accessing 56 basic components of 298 heaters 314 ion source 300 maintaining 204 mass filter 308 part numbers 352 parts that should not be disturbed 205 radiators 314 Analyzer chamber closing 58 opening 56 Analyzer chamber pressure effect of column flow on 47 too high 107 too low 108 typical 47 Analyzer chamber diffusion pump 266 Analyzer chamber turbo pump 267 Analyzer temperatures 36 recommended 314
190. mpound table 379 reagent gas table 379 Proton transfer 378 Pump exhaust venting 157 Pump oil drip tray 272 Pump foreline failure to turn on 97 turned off during pumpdown 97 397 Index Pumpdown failure 328 procedure 60 62 procedure for CI MSD 62 safety shutdown 261 waiting for thermal equilibrium after 61 Pumpdown safety shutdown 328 Pumping problem 328 Pumps turned off 261 328 Q Quad temperature 36 See also Mass filter temperature Quadrupole See Mass filter Quick Tune 50 R Radiators 314 Reagent gas ammonia using 90 carbon dioxide using for NCI buffer gas 91 CI theory overview 374 cleaning supply tubing 256 delay in turning on 295 isobutane using 90 no negative ions 382 plumb methane to Gas A 293 plumbing into the CI interface 292 using other reagent gases 88 Reagent gas flow control module 293 Gas A always methane 293 Gas Off 293 isolation valve 294 mass flow controller 293 operating 74 schematic 295 state diagram 74 296 VCR fittings 293 Reagent gas ions not visible 135 Relative abundance 105 Remote start connector 332 334 Repeatability poor 102 Repeller parts for 356 Repeller CI 306 Replacing parts See Maintenance S Safety covers 155 during maintenance 155 158 Samples 363 366 368 370 part numbers 363 365 366 368 370 Seals vacuum 270 344 See also O rings and O ring assemblies Sensitity of high vacuum gauge to different gas
191. n 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 gt setpoint On gt 100 On gt 100 On 100 Off 0 Isolation valve Open Open Open Open Open Closed 296 10 Ion source 300 Cl ion source 306 Quadrupole mass filter 308 Detector 312 Analyzer heaters and radiators 314 Analyzer This chapter describes the parts of the analyzer Analyzer The analyzer is the heart of the MSD The analyzer ionizes the sample filters the ions and detects them The sample components exiting the GC column flow into the ion source In the ion source the sample molecules are ionized and fragmented The resulting positive ions are repelled from the ion source into the quadrupole mass 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 to allow easy access to the analyzer Both the ion source and the mass filter are independently heated Each is mounted inside a radiator for correct heat distribution Each of the parts of the analyzer is discussed in the
192. n 96 Foreline pump is not operating 96 MSD turns on but then the foreline pump shuts off 97 Control panel says No server found 97 Chromatographic symptoms 98 No peaks 98 Peaks are tailing 99 Peaks are fronting 99 Peaks have flat tops 100 Peaks have split tops 100 Baseline is rising 100 Baseline is high 100 Baseline is falling 100 Baseline wanders 101 Retention times for all peaks drift shorter 101 Retention times for all peaks drift longer 101 Poor sensitivity 102 Poor Repeatability 102 12 Contents Mass spectral symptoms 103 No peaks 103 Isotopes are missing or isotope ratios are incorrect 103 High background 103 High abundances at m z 18 28 32 and 44 or at m z 14 and 16 104 Mass assignments are incorrect 104 Peaks have precursors 104 Peak widths are inconsistent 104 Relative abundance of m z 502 is less than 3 105 Spectra look different from those acquired with other MSDs 105 High mass sensitivity is poor 106 Pressure symptoms 107 Foreline pressure is too high 107 Analyzer chamber pressure is too high EI operating mode 107 Foreline pressure is too low 108 Analyzer chamber pressure is too low 108 Gauge controller displays 9 9 9 and then goes blank 108 Power indicator on the gauge controller does not light 109 Temperature symptoms 110 Ion source will not heat up 110 Mass filter quad heater will not heat up 111 GC MSD interface will not heat up 111 Error
193. n about the locations or functions of GC MSD interface components refer to GC MSD Interface on page 291 Most of the procedures in this chapter are illustrated with video clips in the 5973N MSD Maintenance CD ROM 232 6 Maintaining the MSD erface cover C erface insulator 2 Cl interface heater clamp Cl interface weldment nterface tip seal fl Cl ionization chamber Tw Source radiator Analyzer chamber Heater sensor cable Reagent gas inlet GC inlet 233 Materials needed 6 Maintaining the MSD To remove the GC MSD interface heater and sensor WARNING CAUTION To remove the GC MSD interface heater and sensor Screwdriver Torx T 15 8710 1622 Hex driver 1 5 mm 8710 1570 Vent the MSD See page 54 Make sure you turn off the GC MSD interface heater This heater is controlled and powered by the GC Separate the MSD from the GC See page 171 Remove the cover from the GC MSD interface The GC MSD interface operates a very high temperatures It is also well insulated Make sure the interface is cool before you touch it Slide the insulation off of the GC MSD interface Loosen the two heater sleeve screws Slide the heater slee
194. nalyzer chamber 266 Turbo pump analyzer chamber 267 Side plate 268 Vacuum seals 270 Foreline pump 272 Foreline gauge 274 Diffusion pump and fan 276 Turbomolecular pump and fan 280 Calibration valves and vent valve 283 Triode gauge tube 285 Gauge controller 287 Vacuum System This chapter describes components of the vacuum system in the MSD Vacuum System The vacuum system is essential to MSD operation The vacuum system creates the high vacuum low pressure required for the MSD to operate Without the vacuum the molecular mean free path would be too short and ions would collide with air molecules before they could reach the detector Operation at high pressures also would damage analyzer components The 5973N MSD has one of three kinds of vacuum system diffusion pump or one of two turbomolecular turbo pumps this determines the maximum column flow that the MSD will support Model number Description Maximum recommended column flow G2577A Diffusion Pump El 1 5 ml min G2578A Standard Turbo Pump El 2 0 ml min G2588A Standard Turbo Pump El PCI 2 0 ml min G2579A Performance Turbo Pump El 4 0 ml min G2589A Performance Turbo Pump El PCI NCI 4 0 ml min Many parts of the vacuum system are common to both but some parts are specific to the high vacuum pump Most vacuum system operation is automated Operator interaction is through the data system or control panel Monitoring of the vacuum system is done t
195. nd ion source Cl ion source body Cl filament Cl source heater assembly Cl interface tip seal Cl interface tip Cl interface cover Source heater and sensor cables lon focus lens Entrance lens 306 10 Analyzer Cl ion source Cl ion source body Setscrew Cl repeller Cl repeller insulator Cl filament Cl source heater assembly Dummy filament Cl lens insulator Cl ion focus lens Cl drawout cylinder Cl drawout plate Cl lens insulator Entrance lens Cl interface tip seal 307 10 Analyzer Quadrupole mass filter Quadrupole mass filter The mass filter separates ions according to their mass to charge ratio m z At a given time only ions of a selected mass to charge ratio can pass through the filter to the detector The mass filter in the MSD is a quadrupole The quadrupole is a fused silica quartz tube coated with a thin layer of gold The four hyperbolic surfaces create the complex electric fields necessary for mass selection Opposing segments are connected adjacent segments are electrically isolated One pair has positive voltages applied the other negative 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 mass to charge ratio of the ions that pass through th
196. ndling analyzer parts If you are using hydrogen as a carrier gas the carrier gas flow must be off before turning off the MSD power If the foreline pump is off hydrogen will accumulate in the MSD and an explosion may occur Read the Hydrogen Carrier Gas Safety Guide 5955 5398 before operating the MSD with hydrogen carrier gas Never vent the MSD by allowing air in through either end of the foreline hose Use the vent valve or remove the column nut and column Do notvent or shut off the power on a diffusion pump MSD while the pump is hot Do notvent while the turbo pump is still spinning at more than 50 Do not exceed the maximum recommended total gas flow See 5973N MSD models and features on page 7 Moving or storing the MSD requires special care 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 atmosphere for long periods 37 Software changes See also 2 Operating the MSD To view MSD analyzer temperature and vacuum status To view MSD analyzer temperature and vacuum status 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 m
197. ne for the standard turbo pump Turbo pump seal large pump Turbo pump seal small pump Analyzer chamber Vent valve knob Turbo pump power supply controller Turbo pump harness for integrated PS controller Turbo pump power supply for use with EXDC mini turbo controller EXDC mini turbo pump controller Turbo harness for EXDC mini controller Part number 05972 00015 61099 60204 61099 60201 05980 20018 0100 1881 05972 60210 3160 1037 0100 0549 0100 1551 61099 20552 61099 20553 61099 00003 61099 60021 0960 0897 62589 89062 62589 89061 62589 20041 0100 1879 0100 1879 61099 20550 61099 20042 61099 89002 61099 60438 62589 80063 61946 80035 62589 60034 1 The turbo pumps and their seals are not user replaceable parts Refer service to your Agilent Technologies service representative 350 12 Parts Vacuum system Calibration valve assembly G1099 60201 standard turbo MSD G1099 60204 performance turbo MSD Vent valve knob G1099 20554 Analyzer chamber turbo pump version G0199 20550 Side plate G1099 60021 5 a7 Triode gauge tube l 0960 0897 E lle Turbo pump power supply controller G1099 89002 r G1946 80032 for use with G1946 80035 mini controller G2589 89062 performance turbo pump G2589 89061 s
198. ng a monitor for 40 viewing 38 Ion source CI cleaning 252 installing 248 Ion source CI See Cl ion source Isolation valve 294 K KF seals 270 part numbers 344 L LAN I O connector 332 LAN MS control card 330 interfacing to external devices 334 RAM on 330 remote control processor 334 Line voltage symptoms of incorrect or missing 96 108 Log amplifier See Signal amplifier Low sensitivity at high masses 106 general 102 Low signal to noise ratio in CI MSD 140 Low voltage ac dc power supply 331 Lubricating side plate O ring 200 vent valve O ring 202 M m z 308 m z 14 and 16 symptoms of a large air leak 104 m z 18 28 32 and 44 symptoms of an air leak 104 m z 502 low or decreasing abundance of 105 Maintenance 151 244 analyzer 204 analyzer chamber opening 56 avoiding dangerous voltages during 155 calibration vial removing 181 CI calibrant vial refilling 257 CI gas purifier replacing 255 Cl interface tip seal installing 250 Cl ion source cleaning 252 Cl ion source installing 248 CI MSD 245 cleaning reagent gas supply tubing 256 dangerous voltages 155 dangerously hot parts 156 diffusion pump fluid checking 168 diffusion pump fluid replacing 175 diffusion pump reinstalling 177 diffusion pump removing 173 EI calibration valve refilling 192 EI calibration valve removing 190 EI calibration vial refilling 183 EI calibration vial reinstalling 183 electron multiplier
199. ng trouble with CI verify that EI still works Rule 3 Divide and conquer This technique is known as half split troubleshooting If you can isolate the problem to only part of the system it is much easier to locate e To isolate an air leak start by shutting the gas select valve while leaving the isolation valve and MFC open turn on Purge and Gas Off If abundance of m z 32 decreases the problem is upstream of the flow module 123 5 Cl Troubleshooting Air leaks 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 Note that the mass flow controller is calibrated for methane and the high vacuum gauge controller is calibrated for nitrogen so these measurements are not accu rate in absolute terms but are intended as a guide to typical observed readings They were taken with the following set of conditions Source temperature Quad temperature Interface temperature Helium column flow MFC 10 15 20 25 30 35 40 Pressure Torr Methane Performance turbo pump 5 5 x105 8 0x10 5 1 0 x107 1 2 x107 1 5x 104 2 0 x10 25x107 250 C 150 C 320 C 1ml min Standard turbo pump 20x10 25x107 3 0x 10 4 Not recommended Not recommended Not recomm
200. ning in the side of the analyzer chamber The side plate is attached to the manifold with a hinge The analyzer assembly is attached to the side plate inside the analyzer chamber The hinge allows the side plate to swing away from the manifold for easy access to the analyzer Several electrical feedthroughs 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 Fasten both side plate thumbscrews for shipping or storage only For normal operation the both thumbscrews should be loose For operation with hydrogen carrier gas or with flammable or explosive Cl reagent gases the front thumbscrew should be fastened just finger tight Overtightening will warp the side plate and cause air leaks Do not use a tool to tighten the side plate thumbscrews When you turn on the power to pump down the MSD be sure to press on the side board to ensure a good seal 268 Side plate hinge EM voltage feedthrough Signal detector output eedthrough ass filter quadrupole eedthrough Side board Screws for radiator mounting brackets Front side plate humbscrew on source and heater eedthroughs on source and heater eedthroughs ass filter quadrupole eedthrough Detector focus feedthrough Hig
201. nitors for MSD temperature and vacuum status instrument Control HEWLETT Sample Name ARPA AnD 2 ee Idle Data File evaldemo d i Sample p Chromatography GC in gas saver mode MS Source Total lon GC Status Messages gt Oven Temperature Column 1 Flow Cal EM Volts Foreline 41 Software changes 2 Operating the MSD To set the MSD analyzer temperatures CAUTION To set the MSD analyzer temperatures Setpoints for the MSD ion source and mass filter quad temperatures are stored in the current tune u file When a method is loaded the setpoints in the tune file associated with that method are downloaded automatically 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 In Instrument Control view select Edit MS Tune Parameters from the Instrument menu Select the tune file you plan to use with your method from the Load MS Tune File dialog box Select Temperatures from the MoreParams menu Type the desired Source and Quad mass filter temperatures in the setpoint fields and click OK Table 1 on page 43 for recommended setpoints The GC MSD interface ion source and quadrupole heated zones interact The analyzer heaters may not be able to accurately control temperatures if the setpoint for one zone is much lower than that
202. nnect the other end of the power cord to an appropriate electrical outlet If you wish to share one controller among MSDs obtain one cable for each instru ment Leave a cable connected to the triode gauge tube on each MSD This will avoid having to vent the MSD before connecting the controller Pump down the MSD Do notuse a 59864A older model triode gauge controller during data acquisition This model can be used for diagnostic purposes only 63 2 Operating the MSD To connect the gauge controller Triode gauge tube Triode gauge cable OG Gauge controller INPUT Power 5 00240 WER 80 HZ 25 Wer Triode gauge cable Power cord ae PTT 64 Materials needed CAUTION 10 11 12 2 Operating the MSD To move or store the MSD To move or store the MSD Ferrule blank 5181 3308 Interface column nut 05988 20066 Wrench open end 1 4 inch x 5 16 inch 8710 0510 Vent the MSD page 54 Remove the column and install a blank ferrule and interface nut Tighten the vent valve If the MSD has a gauge controller disconnect the cable from the triode gauge tube Move the MSD away from the GC page 171 Unplug the GC MSD interface heater cable from the GC Install the interface nut with the blank ferrule Remove the analyzer cover page 52 Tighten the side plate thumbscrews to finger tight Do not overtighten the side p
203. not a scheduled periodic maintenance procedure The source should be cleaned whenever there are performance anomalies that are associated with a dirty ion source See the Troubleshooting chapter for symptoms that indicate a dirty ion source Visual appearance is not an accurate guide to cleanliness of the CI ion source The CI ion source can show little or no discoloration yet still need cleaning Let analytical 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 To clean the ion source 210 with the following exceptions e The Clion source may not look dirty but deposits left by chemical ionization are very difficult to remove Clean the CI ion source thoroughly e Use around wooden toothpick to gently clean out the electron entrance hole in the source body and the ion exit hole in the drawout plate e Do not use halogenated solvents and use hexane for the final rinse Refer to the MSD Reference Collection CD ROM for video demonstrations of ion source cleaning and other maintenance procedures Do not use any halogenated solvents to clean the CI ion source 252 7 Cl Maintenance To clean the CI ion source 253 7 CI Maintenance To minimize foreline pump damage from ammonia CAUTION CAUTION To minimize foreline pump damage from ammonia Gas ballasting for an hour every day removes most of the ammonia from
204. nstall the thumbscrews Connect the dummy filament repeller and CI filament wires Reconnect colored wires to the appropriate pins on the ion source Wire color Connects to Number of leads Blue Entrance lens 1 Orange lon focus 1 White Filament 1 top filament 2 Red Repeller 1 Black Dumny filament Filament 2 2 7 Connect the heater and sensor cables 248 Source radiator Feedthrough board Cl filament Repeller Dummy filament Source heater and sensor wires lon focus pin orange wire Entrance lens pin blue wire 7 Cl Maintenance To install the CI ion source 249 Materials needed 7 Cl Maintenance To install the CI interface tip seal CAUTION CAUTION To install the CI interface tip seal 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 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 before you open the analyzer chamber Remove the seal from the ion source storage box Place the seal over the end of the interface See the illustration on the previous page To remove the seal reverse the above steps Verify that the CI ion source is installe
205. nt gas flow control module 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 The back panel provides Swagelok inlet fittings for methane and one other reagent gas The other fittings in the flow module are VCR fittings VCR fittings have a disposable gasket that must be replaced every time the seal is opened Operation of the flow module is 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 Flow control knob Flow control display f L Nn Taas A A Purge ror m SASA a N A SS F pi N S7 pans gt gt X ae Jo Sa Gas N j ier Cle a A aEAGENTS FLOW CONTROL SS ee e Each button on the control pane has an LED light next to it When that button is active the light is on e Gas A or Gas B opens the chosen gas select valve Only one can be open at a time e Gas Off closes the gas select and isolation valves Gas Off also sets the MFC to 0 flow unless Purge is on The Gas Off LED must be off to turn on Gas A or Gas B e The flow control knob
206. o CI autotune for isobutane or ammonia in PCI If you wish to run NCI with isobutane or ammonia load NCICH4 U or load an existing NCI tune file for the specific gas Use of ammonia affects the maintenance requirements of the MSD See the maintenance chapter for more information 90 CAUTION See also CAUTION 3 Operating the Cl MSD To use other reagent gases 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 below the level of the flow module Coil the ammonia supply tubing into several vertical loops by wrapping the tubing around a can or bottle This will help keep any liquid ammonia out of the flow module Ammonia tends to break down vacuum pump fluids and seals Ammonia CI makes more frequent vacuum system maintenance necessary To minimize foreline pump damage from ammonia 254 When running ammonia for five or more hours a day the foreline pump must be ballasted for at least one hour a day to minimize damage to pump seals See page 254 Always purge the MSD with methane after flowing ammonia Frequently a mixture of 5 ammonia and 95 helium or 5 ammonia and 95 methane is used as a CI reagent gas This is enough ammonia to achieve good chemical ionization while minimizing its negative effects Carbon dioxide NCI Carbon dioxide is often used as a buffer gas for ne
207. od starts on 31st day from he date of shipment For international orders the grace period is 60 days and the warranty period starts on the 61st day from the date of shipment Agilent Technologies software and firmware products which are designated for use with a hardware product when properly installed on that hardware product are warranted not to fail to execute their programming instructions due to defects in materials and workmanship If Agilent Technologies receives notice of such defects during the warranty period it shall repair or replace software media and firmware which do not execute their programming instructions due to such defects Agilent Technologies does not warrant that the operation of the software firmware or hardware shall be uninterrupted or error free Within Agilent Technologies service travel areas warranty and installation services for products installed by Agilent Technologies and certain other products designated by Agilent Technologies will be performed at Buyer s facility at no charge For installation and warranty services outside of Agilent Technologies s service travel area Agilent Technologies will provide a quotation for the applicable additional services The foregoing warranty shall not apply to defects resulting from 1 Improper or inadequate maintenance adjustment calibration or operation by Buyer 2 Buyer supplied software hardware interfacing or consuma
208. of an adjacent zone Do not exceed 200 C for the quadrupole or 250 C for the source Click OK in the Edit Parameters window to apply the new temperature setpoints When the Save MS Tune File dialog box appears either click 0K to save your changes to the same file or type a new file name and click OK 42 2 Operating the MSD To set the MSD analyzer temperatures M5 Zones fone Actual Setpoint Limit MS Source MS Quad Table 1 Recommended temperature settings El operation PCI operation NCI operation MS Source 230 150 150 MS Quad 150 150 150 43 Software changes See also CAUTION CAUTION 2 Operating the MSD To set the GC MSD interface temperature from the PC To set the GC MSD interface temperature from the PC 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 You can also use the Control Panel to perform this task See the 5973N Control Panel Quick Reference Guide for more information Select Instrument Control from the View menu Click the Aux button to display the Instrument Edit Aux 6890 window Verify that MSD is selected under Type and Thermal Aux 2 is selected under Aux Channel Turn the heater on and type the setpoint in the Next C column Do not set temperature ramps The typical setpoint is 280 C The limits are 0
209. of the components of the vacuum system e Chapter 9 describes the GC MSD interface and the CI flow module e Chapter 10 describes operation of the analyzer ion source mass filter and detector e Chapter 11 describes the electronics that control the MSD e Chapter 12 contains illustrated parts identification and part numbers e Appendix A is an overview of chemical ionization theory For updated information check the Agilent Technologies Chemical Analysis web site at http www agilent com chem Other User Information 5973 Mass Selective Detector Reference Collection This CD ROM includes the following multimedia resources e Software tutorial hands on training e 5968 7358E 5973Network Mass Selective Detector Specifications e Mass Spectrometer Fundamentals Mass spectrometer hardware and Acquiring and evaluating mass spectra The 5973Network MSD The 5973N MSD is a stand alone capillary GC detector The 5973N Mass Selective Detector MSD is designed for use with the 6890 Plus Series Gas Chromatograph The MSD features e Control panel for locally monitoring and operating the MSD e One of three different high vacuum pumps e Rotary vane foreline pump e Independently heated electron ionization ion source e Independently heated hyperbolic quadrupole mass filter e High energy dynode HED electron multiplier detector e Independently heated GC MSD interface e Chemical ionization EI PCI or EI PCI NCI models availabl
210. of up to 3000 volts at its opening and 0 volts at the other end The electrons emitted by the HED strike the EM horn and cascade through the horn liberating more electrons as they go At the far end of the horn the current generated by the electrons is carried through a shielded cable outside the analyzer to the signal amplifier board The voltage applied to the electron multiplier horn determines the gain The volt age is adjustable from 0 to 3000 V dc Use the electron multiplier voltage found in autotune as a baseline for the electron multiplier voltage setting e To increase signal strength increase the electron multiplier voltage e For concentrated samples where less signal strength is needed decrease the electron multiplier voltage 312 See Also 10 Analyzer Detector As the EM horn ages the voltage EMVolts required by the electron multiplier increases over time If the electron multiplier voltage must always be set at or near 3000 V dc to complete Autotune with no other probable cause it may need to be replaced Check your tune charts for gradual degradation which indicates wearing out Select View Tunes from the Qualify menu in the Instrument Control view to see the tune charts Sudden changes usually indicate a different type of problem Troubleshooting 5973N MSD in the online help for more information about symptoms that may indicate electron multiplier problems Signal wire Mounting bracket
211. oller page 287 Table 2 Typical MSD pressure readings for various carrier gas flow rates page 47 274 Diffusion pump outlet Foreline gauge assembly KF10 16 seal KF10 16 clamp Foreline gauge cable part of high vacuum control cable 8 Vacuum System Foreline gauge Foreline hose and hose clamp 275 8 Vacuum System Diffusion pump and fan Diffusion pump and fan The diffusion pump in the MSD is an air cooled vapor diffusion pump with 90 liters second capacity It mounts with a KF50 fitting to a baffle adapter clamped to the bottom of the analyzer chamber The diffusion pump has a cylindrical body surrounded by fins to help dissipate heat 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 The diffusion pump transports gas by momentum transfer The heater boils a spe cial fluid a polyphenyl ether inside the stack As the vapor pressure increases the pump fluid vapor is forced out and downward through nozzles in the stack The vapor forced out of these nozzles 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
212. ollow the steps 2 6 to add foreline pump oil Never add oil while the foreline pump is on If your MSD is nearing its scheduled time for replacement of the foreline pump oil replace the oil instead of adding oil If the oil is dark or cloudy replace it See page 162 for instructions about replacing the foreline pump oil Vent the MSD See page 54 Remove the fill cap Add pump fluid until the oil level in the window is near but not above the upper line Reinstall the fill cap Pump down the MSD See page 60 160 6 Maintaining the MSD To check and add foreline pump oil Fill cap Upper line Oil level window Lower line 161 Materials needed See also 6 Maintaining the MSD To drain the foreline pump WARNING WARNING To drain the foreline pump Book or other solid object approximately 5 cm thick Container for catching old pump oil 500 ml Gloves oil and solvent resistant Screwdriver flat blade large 8730 0002 A video demonstration of this procedure is on the 5973N MSD Maintenance CD ROM Vent the MSD See page 54 If necessary slide the foreline pump out from 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 the analyzer chamber at the back of the MSD The foreline pump may be hot Place a book or other object under the pump motor
213. ommended 30 15x10 Notrecommended 1 2x10 Notrecommended 35 20x10 Notrecommended 1 5x10 Notrecommended 40 25x10 Notrecommended 2 0x10 4 Notrecommended Familiarize yourself with the measurements on your system under operating con ditions and watch for changes that may indicate a vacuum or gas flow problem Measurements will vary by as much as 30 from one MSD and gauge controller to the next 87 CAUTION CAUTION 3 Operating the Cl MSD 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 Cl equipped 5973N MSD with methane reagent gas before attempting to use other reagent gases Do not use nitrous oxide as a reagent gas It radically shortens the life span of the filament Changing the reagent gas from methane to either isobutane or ammonia changes the chemistry of the ionization process and yields different ions The principal chemical ionization reactions encountered are described in general in Appendix A Chemical Ionization Theory If you are not experienced with chemical ioniza tion we suggest reviewing that material before you proceed Not all setup operations can be performed in all modes with all reagent gases See the following table for details 88 Reagent gas mode Reagent ion PFDTD Flow adj ions Ratio masses Calibrantions El PCI NCI MSD Performance turbo pump Recommended
214. omponents with wires contacts or cables connected to printed circuit boards always use a grounded anti static wrist strap and take other anti static precautions The wrist strap should be connected to a known good Earth ground If that is not possible it should be connected to a conductive metal part of the assembly being worked on but not to electronic compo nents exposed wires or traces or pins on connectors Take extra precautions such as a grounded anti static mat if you must work on components or assemblies that have been removed from the MSD This includes the analyzer In order to be effective an anti static wrist strap must fit snugly not tight A loose strap provides little or no protection Anti static precautions are not 100 effective Handle electronic circuit boards as little as possible and then only by the edges Never touch components exposed traces or pins on connectors and cables 158 6 Maintaining the MSD Maintaining the vacuum system The vacuum system requires some periodic maintenance As listed earlier in Table 4 some maintenance tasks for the vacuum system must be performed periodically These include e Checking the foreline pump fluid every week e Checking the calibration vial every 6 months e Ballasting the foreline pump daily in MSDs using ammonia reagent gas e Replacing the foreline pump oil every 6 months every 3 months for CI MSDs using ammonia reagent gas e Tightenin
215. onal 59864B Gauge Controller allows you to use the triode gauge tube to monitor the pressure in the MSD analyzer chamber This can aid in everyday oper ation and in troubleshooting The 59864B Gauge Controller includes the controller and a cable for connecting the controller to the triode gauge A power cord is supplied with a plug appropri ate for the country from which the order was placed The gauge controller can operate on all voltages between 100 and 240 V ac nominal and at ac frequencies of 50 to 60 hertz The fuse in the gauge controller is appropriate for all allowed voltages The gauge controller regulates emission current to the filament of the triode gauge tube It also measures the ion current in the collector From these data the gauge controller calculates and displays the pressure present in the analyzer chamber The analyzer chamber pressure in Torr is displayed on the front panel of the controller The gauge controller is calibrated for nitrogen N3 The carrier gas is usually helium which has does not ionize as readily as nitrogen Therefore the indicated pressure for helium is approximately 6 times lower than the absolute pressure For example a reading of 2 0 x 10 Torr versus an absolute pressure of 1 2 x 10 Torr In a CI MSD the indicated pressure reflects the contribution of both the carrier gas and the reagent gas The distinction between indicated and absolute pressure is not important for normal operation of t
216. only necessary for CI MSDs or if hydrogen or other flammable or toxic sub stance is used for carrier gas This thumbscrew must be fastened for Cl operation or if hydrogen or other hazardous gas is being used as the GC carrier gas In the unlikely event of an explosion it may prevent the side plate from opening Do not overtighten the thumbscrew it can cause air leaks or prevent successful pumpdown Do not use a screwdriver to tighten the thumbscrew Once the MSD has pumped down reinstall the analyzer cover Wait until after pumpdown to reinstall the analyzer cover 58 2 Operating the MSD To close the analyzer chamber y N K Aj wonton A Z q SS SS Ss Ss ie Front thumbscrew Rear thumbscrew do not tighten x Source power cable ray ont EFA 4 o N Yi E a Side board control cable Side plate Le 59 Software changes See also WARNING WARNING 2 Operating the MSD To pump down the MSD To pump down the MSD 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 You can also use the Control Panel to perform this task See the 5973N Control Panel Quick Reference Guide for more information Make sure your MSD meets all the
217. onnects the GC and the MSD Remote start signals It is often necessary to communicate with external devices for example a purge and trap during arun Typically these communications are e Requests to send a system ready signal e Receive a start run signal from an external device e Program the timing of events during a run Ground Ready Start 334 11 Electronics Interfacing to external devices System ready When interfacing to an external device it is often desirable to send a system ready signal to the device In the case of a multi sample Tekmar purge and trap each sample is purged onto a trap where it waits for a ready signal On receipt of the ready signal the desorbtion cycle begins When a specific temperature has been reached the purge and trap closes a contact to indicate the run has started The ready pin on the remote start connector on the GC is held low at all times except when the GC MSD and data system are all ready On system ready a logic high of 5 V dc is present between that pin and any ground This same 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 which is also available
218. onting 99 inconsistent widths 104 missing 98 114 precursors 104 split tops 100 tailing 99 PFDTD avoiding persistent background of 80 82 294 not visible but reagent ions are present 138 PFDTD perfluoro 5 8 dimethyl 3 6 9 trioxidode cane 283 PFTBA perfluorotributylamine 283 Physical description of MSD 6 Polarity dc of the mass filter 310 Positive CI addition 380 charge exchange 381 hydride abstraction 380 reagent ion background 376 theory 376 Power cord ac 332 foreline pump 332 receptacle 332 Power supplies high voltage HED 331 low voltage ac dc 331 Power switch 320 Pressure analyzer chamber pressure too high 107 analyzer chamber pressure too low 108 Cl ion source 306 376 does not change when reagent gas flow is changed 131 foreline pressure too high 107 foreline pressure too low 108 indicated vs absolute 46 86 Ion source for CI 8 monitoring 35 analyzer chamber 86 monitoring analyzer chamber 46 86 monitoring foreline 38 monitoring vacuum manifold 46 symptoms indicating malfunctions 107 too high in analyzer chamber with reagent gas flow 130 too high in analyzer chamber without reagent gas flow 129 typical analyzer chamber pressure for various carrier gas flows 47 typical vacuum manifold pressure for various carrier gas flows 274 277 Pressure gauge See Triode gauge tube Printed circuit boards part numbers 342 Proton affinity importance in PCI 378 organic co
219. ontrolled through the data system Carrier gas flow through the GC column is controlled by head pressure in the GC For a given head pressure the column flow will decrease as the GC oven temperature increases With electronic pneumatic control EPC set to Const Flow constant flow the same column flow is be maintained regard less of oven temperature The MSD can be used to measure actual column flow You inject a small amount of air or other unretained chemical and time how long it takes to reach the MSD With this time measurement you can calculate the column flow See page 48 The data system aids in venting A program in the data system guides you through the venting process It switches off the GC and MSD heaters and the diffusion pump heater or turbo pump at the correct time It also lets you monitor temperatures in the MSD and indicates when to vent the MSD The MSD will be damaged by incorrect venting A diffusion pump will backstream vaporized pump fluid onto the analyzer if the MSD is vented before the diffusion pump has fully cooled A turbo pump will be damaged if it is vented while spinning at more than 50 of its normal operating speed 36 WARNING WARNING CAUTION CAUTION CAUTION 2 Operating the MSD Make sure the GC MSD interface and the analyzer zones are cool below 100 C before you vent the MSD 100 C is still hot enough to burn skin always wear cloth gloves when ha
220. ore information You can also use the Control Panel to perform this task See the 5973N Control Panel Quick Reference Guide for more information In Instrument Control view select Edit MS Tune Parameters from the Instrument menu Select the tune file you plan to use with your method from the Load MS Tune File dialog box Analyzer temperatures and vacuum status are displayed in the Zones field Unless you have just begun the pumpdown process the foreline pressure should be less than 300 mTorr or the turbo pump should be running at least 80 speed MSD heaters remain off as long as the diffusion pump is cold or the turbo pump is operating at less than 80 Normally the foreline pressure will be below 100 mTorr or the turbo pump speed will be at 100 The MSD heaters turn off at the beginning of the vent cycle and turn on at the end of the pumpdown cycle Note that the reported setpoints will not change during venting or pumpdown even though both the MSD zones are turned off 38 2 Operating the MSD To view MSD analyzer temperature and vacuum status Edit Parameters HP5973 ATUNE U File Execute Calibrate MoreParams View Mass 69 00 Mass 218 95 Mass 502 00 lon Pol POS MassGain Ab 244506 Ab 312200 Ab 24552 MassOffs Pw50 0 56 Pw50 0 58 Pw50 0 58 Emission 34 6 AmuGain EleEnergy 69 9 AmuOffs Filament 1 Wid219 DC Pol Repeller lonFocus HED ON EntLens EMVolts 1588 EntOffs 17 32 PFTBA OPEN Zones Source 231
221. ositive CI theory 376 Proton transfer 378 Hydride abstraction 380 Addition 380 Charge exchange 381 Negative CI theory 382 Electron capture 384 Dissociative electron capture 385 Ion pair formation 385 Ion molecule reactions 386 18 To prepare a capillary column for installation 22 To install a capillary column in a split splitless inlet 24 To condition a capillary column 26 To install a capillary column in the GC MSD interface 28 To install a capillary column using the installation tool 30 Installing GC Columns How to connect GC columns to the 5973N MSD Installing GC columns Before you can operate your GC MSD system you must select condition and install a GC column This chapter will show you how to install and condition a column For correct column and flow selection you must know what type of vacuum system your MSD has The serial number tag on the lower front of the left side panel shows the model number Many types of GC columns can be used with the MSD but there are some restrictions During tuning or data acquisition the rate of column flow into the MSD should not exceed the maximum recommended flow Therefore there are limits to column length and flow Exceeding recommended flow will result in degradation of mass spectral and sensitivity performance Remember that column flows vary greatly with oven temperature unless the GC is set for constant flow See To measure column flow linear velocity pa
222. otective cover which should be left in place One end of the GC MSD interface passes through the side of the gas chromatograph and extends into the GC oven This end is threaded thread size is 10 x 32 allowing connection of the column with a nut and ferrule The other end of the GC MSD interface fits into the ion source The last two millimeters of the capillary column extend past the end of the guide tube and into the ionization chamber The GC MSD interface is heated by an electric cartridge heater The heater is powered and controlled by Thermal Aux 2 heated zone of the 6890 Series GC The GC MSD interface temperature can be set from the MSD ChemSta tion or from the keypad of the gas chromatograph A sensor thermocouple in the GC MSD interface monitors the temperature The GC MSD interface should be operated in the 250 to 350 C range Subject to that restriction the GC MSD interface temperature should be slightly higher than the maximum GC oven temperature but never higher than the maximum column temperature To install a capillary column in the GC MSD interface 28 Never exceed the maximum column temperature either in the interface or the GC oven The GC MSD interface operates at high temperatures If you touch it when it is hot it will burn you 290 9 GC MSD Interfaces and CI Flow Control El GC MSD interface EI GC MSD interface Heater sleeve Heater sleeve screws Welded interface assemb
223. oting the MSD Contamination Common contaminants lons m z 18 28 32 44 or 14 16 31 51 69 100 119 131 169 181 214 219 264 376 414 426 464 502 576 614 31 43 58 78 91 92 105 106 151 153 69 73 147 207 221 281 295 355 429 77 94 115 141 168 170 262 354 446 149 Peaks spaced 14 amu apart Compound H30 No 0 CO or N 0 PFIBA and related ions Methanol Acetone Benzene Toluene or xylene Xylene Trichloroethane Foreline pump oil or PFIBA Dimethylpolysiloxane Diffusion pump fluid and related ions Plasticizer phthalates Hydrocarbons Possible source Residual air and water air leaks outgassing from Vespel ferrules PFTBA tuning compound Cleaning solvent Cleaning solvent Cleaning solvent Cleaning solvent Cleaning solvent Cleaning solvent Foreline pump oil vapor or calibration valve leak Septum bleed or methyl silicone column bleed Diffusion pump fluid Vacuum seals O rings damag ed by high temperatures vinyl gloves Fingerprints foreline pump oil 120 Common Cl specific problems 122 Air leaks 124 Pressure related symptoms overview 128 Poor vacuum without reagent gas flow 129 High pressure with reagent gas flow 130 Pressure does not change when reagent flow is changed 131 Signal related symptoms overview 132 No peaks 133 No or low reagent gas signal 135 No or low PFDTD signal but reagent
224. ove a filament 218 To reinstall a filament 220 To remove the heater and sensor from the ion source 222 To reinstall the heater and sensor in the ion source 224 To remove the heater and sensor from the mass filter 226 To reinstall the heater and sensor in the mass filter 228 To replace the electron multiplier horn 230 Maintaining the GC MSD interface 232 To remove the GC MSD interface heater and sensor 234 To reinstall the GC MSD interface heater and sensor 236 Maintaining the electronics 238 To adjust the RF coils 240 To replace the primary fuses 242 15 Chapter 7 Chapter 8 Contents CI Maintenance To set up your MSD for CI operation 247 To install the Cl ion source 248 To install the CI interface tip seal 250 To clean the CI ion source 252 Frequency of cleaning 252 Cleaning procedure 252 To minimize foreline pump damage from ammonia 254 To replace the methane isobutane gas purifier 255 To clean the reagent gas supply lines tubing 256 To refill the CI calibrant vial 257 Vacuum System Diffusion pump MSD vacuum system 264 Turbo pump MSD vacuum system 265 Diffusion pump analyzer chamber 266 Turbo pump analyzer chamber 267 Side plate 268 Vacuum seals 270 Face seals 270 KF NW seals 270 Compression seals 270 High voltage feedthrough seal 271 Foreline pump 272 Foreline gauge 274 Diffusion pump and fan 276 Turbomolecular pump and fan 280 Standard turbo pump 281 Performance t
225. p at 60 C for 15 minutes in your GC oven The pump and pump fluid will be hot Wear protective gloves when you remove the pump from the oven Pour the old diffusion pump fluid out the top of the pump Even after heating the pump fluid pours very slowly Treat the old pump fluid as hazardous It may contain traces of toxic chemicals If the diffusion pump has been heated with insufficient pump fluid or with a large air leak in the MSD the remaining pump fluid may be severely blackened Black ened pump fluid may also be baked onto the internal parts stack of the pump If so you may have to remove the diffusion pump 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 diffusion pump performance Methylene chloride is a hazardous solvent Work in a fume hood and take all appropriate precautions 175 6 Maintaining the MSD To replace the diffusion pump fluid Only use about half of the second bottle ae 5 Wipe clean the diffusion pump flange on the analyzer chamber Follow the instructions on the bottle for pre heating the diffusion pump fluid 6 Pour new diffusion pump fluid into diffusion pump until the fluid level is within the FULL COLD range The recommended charge for this pump is 30 ml It will require approximately 1 5 of the bottles 18 5 ml each of diffusion pump fluid Pour the
226. peller nut do not over tighten on foc us lens Drawo ut cylinder Drawo ut plate Lens in sulator one of a pair Entrance lens 215 Materials needed 6 Maintaining the MSD To reinstall the ion source To reinstall the ion source Gloves clean lint free large 8650 0030 small 8650 0029 Pliers long nose 8710 1094 Slide the ion source into the source radiator Install and hand tighten the source thumbscrews Do not overtighten the thumbscrews Reconnect the 7 wires to the appropriate pins on the ion source Wire color Connects to Number of leads Blue Entrance lens 1 Orange lon focus 1 White Filament 1 top filament 2 Red Repeller 1 Black Filament 2 bottom filament 2 Reconnect the source heater and temperature sensor wires to the pins on the feedthrough board 5 Close the analyzer chamber See page 58 6 Pump down the MSD See page 60 216 Source radiator Feedthrough board lon source Thumbscrew Thumbscrew Source heater and sensor wires lon focus pin orange wire Entrance lens pin blue wire 6 Maintaining the MSD To reinstall the ion source 217 Materials needed 6 Maintaining the MSD To remove a filament WARNING To remove a filament Gloves clean lint free large 8650 0030 small 8650 0029 Hex ball driver 1 5 mm 8
227. peller voltage is too low e Incorrect temperatures oven GC MSD interface ion source or mass filter e Incorrect sample concentration e Leaking injection port e Dirty injection port e Incorrect split ratio e Purge off time in splitless mode is too short e Excessive pressure in the MSD e Dirty ion source e Air leak e Poor filament operation e Detector HED electron multiplier is not working correctly e Incorrect mass filter polarity This could cause a fault condition in the GC that would prevent the GC from operating Poor Repeatability e Dirty syringe needle e Dirty injection port e Leaking injection port e Injection is too large e Loose column connections e Variations in pressure column flow and temperature e Dirty ion source e Loose connections in the analyzer e Ground loops This could cause a fault condition in the GC that would prevent the GC from operating 102 4 Troubleshooting the MSD Mass spectral symptoms Mass spectral symptoms This section describes symptoms you might observe in mass spectra Some of these symptoms will appear in the mass spectra of samples Others you will observe only in a tune report Some of these symptoms have causes that can be corrected by the operator Others however require service by an Agilent Technol ogies service representative Two symptoms listed under Chromatographic symptoms If sensitivity is poor and If repeatability is poor also apply to
228. perly Replace the pump oil If that does not help 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 at least 95 Contact your local Agilent Tech nologies service representative Use of ammonia as reagent gas can shorten the life of the foreline pump oil and possibly of the foreline pump itself See the Maintenance chapter in this manual 129 Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting High pressure with reagent gas flow High pressure with reagent gas flow The reagent gas flow rate is too high On the flow controller turn down reagent gas flow as appropriate Verify that reagent ion ratios are correct See page 76 Air leak Run Methane Pretune See page 76 Visible peak at m z 32 indicates air in the sys tem Check for and correct any leaks See the Leaks section at the beginning of this chapter Interface tip seal wasn t 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 130 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting Pressure does not change when reagent flow is changed Pressure does not chang
229. r on the lab bench next to or behind the MSD or under the analyzer chamber at the back of the MSD Move the MSD away from the GC until you have access to the GC MSD interface cable Place a column nut with a blank ferrule on the end of the interface This will help prevent contamination out of the MSD Disconnect the GC MSD interface cable Disconnecting the cable with the GC on can cause a fault condition Continue to move the MSD until you have access to the part requiring maintenance 171 6 Maintaining the MSD To separate the MSD from the GC U N 4 172 Materials needed See also 6 Maintaining the MSD To remove the diffusion pump WARNING To remove the diffusion pump Aluminum foil clean Gloves oil resistant The 5973N MSD Maintenance CD ROM Vent the MSD See page 54 Separate the MSD from the GC See page 171 The diffusion pump operates at very high temperatures Make sure it has cooled before handling it Disconnect the foreline gauge assembly from the diffusion pump outlet The foreline gauge cable can be disconnected or can remain connected to the fore line gauge Disconnect the diffusion pump temperature sensor wires from the wiring harness These are on the side of the diffusion pump not shown in the illustration Disconnect high vacuum power HIVAC POWER cable from the back panel of the MSD This
230. r leak will rapidly contaminate the ion source e Make sure that the peak at m z 19 protonated water is less than 50 of the peak at m z 17 Perform the Methane Flow Adjust Adjust the methane flow on the PCI NCI MSD to get the ratio of m z 28 27 between 1 5 and 5 0 Adjust the methane flow on the PCI MSD to get the ratio of m z 28 27 between 0 5 and 3 0 76 CAUTION 3 Operating the Cl MSD To set up methane reagent gas flow Continuing with Cl autotune if the MSD has an air leak or large amounts of water will result in severe ion source contamination If this happens you will need to vent the MSD and clean the ion source Mass 17 10 Mass 29 10 Mass 41 00 Ab 163354 Pw50 0 61 Ab 227524 Pw50 0 63 Ab 77288 Pw50 0 65 T 7 T 7 T 7 T y T 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 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 at first but the abundance of m z 19 should still be less than 50 of m z 17 77 3 Operating the Cl MSD Cl autotune CAUTION CAUTION 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 intro duced directly into the
231. r parts should be placed only on clean lint free cloths If not done correctly analyzer maintenance can introduce contaminants into the MSD The analyzer operates at high temperatures Do not touch any part until you are sure itis cool 204 CAUTION CAUTION 6 Maintaining the MSD Some parts can be damaged by electrostatic discharge The wires contacts and cables connected to the analyzer components can carry electrostatic discharges ESD to the electronics boards to which they are connected This is especially true of the mass filter quadrupole contact wires which can conduct ESD to sensitive components on the side board ESD damage may not cause immediate failure but will gradually degrade performance and stability See page 158 for more information 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 158 and take other anti static precautions before you open the analyzer chamber Some analyzer parts should not be disturbed The mass filter quadrupole requires no periodic maintenance In general the mass filter should never be disturbed In the event of extreme contami nation it can be cleaned but such cleaning should only be done by a trained Agilent Technologies service representative The HED ceramic must never be touched Incorrect handling or cleaning of the mass filter can d
232. r voltage is too low e Not enough time for the MSD to warm up and pump down e Analyzer chamber pressure is too high e Column carrier gas flow is too high e Poor filament operation e Dirty ion source e Air leak e Incorrect de polarity on the quadrupole mass filter 106 4 Troubleshooting the MSD Pressure symptoms Pressure symptoms This section describes unusual pressure readings and their possible causes The symptoms in this section are based on typical pressures At typical column flow rates 0 1 2 0 ml minute the foreline pressure will be approximately 20 to 100 mTorr The analyzer chamber pressure will be approximately 1 x 10 to 1 4 x 10 Torr These pressures can vary widely from instrument to instrument so it is very important that you are familiar with the pressures that are typical for your instrument at given carrier gas flows The foreline pressures listed can only be measured on diffusion pump equipped systems Turbomolecular pumps are controlled according to their speed and do not have foreline pressure gauges The analyzer chamber 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 is above 100 mTorr or if the pressure you observe for a given column flow has increased over time check the following e Column carrier gas flow is too high e Air leak usually the sideplate is not pushed in or vent val
233. rating temperature e Turbomolecular pump is on but has not had enough time 5 minutes to reach 80 of its normal operating speed e Level of fluid in the diffusion pump is too high e Diffusion pump stack is not aligned correctly e Turbomolecular pump is not working correctly e MSD electronics are not working correctly The system is in standby This message is triggered by a shutdown signal on the remote start cable It is usu ally caused by a GC fault an ALS fault or a bad cable connection Once the cause of the fault is corrected selecting MS ON or checking MSD status should remove the message 116 CAUTION 4 Troubleshooting the MSD Error messages The system is in vent state Although the message says the system is in vent state if the fault has just occurred the MSD may actually still be under vacuum and the diffusion pump may still be hot or the turbo pump may still be at high speed Wait at least 30 minutes after seeing this message before you actually vent the MSD Venting the MSD too soon after this message appears can result in the backstreaming of a diffusion pump or damage to a turbomolecular pump e System was vented on purpose no problem e Fan fault has turned off the high vacuum pump power cycle the MSD to clear the fault e Fuse for the high vacuum pump has failed e Diffusion pump heater cartridge has failed e MSD electronics are not working correctly There is no emission current e Filamen
234. ratures The 5973N MSD Control Panel Quick Reference 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 switch the MSD and foreline pump on and off Do not switch the MSD off unless it has completed the vent program Incorrect shutdown can seriously damage the MSD 320 11 Electronics Control panel and power switch 5973N control panel pooaeao D00000 opERRE ne ae a eee E as eS ee i Ss Power switch 321 11 Electronics Side board Side board The side board is mounted on the side plate It performs the following functions Provides the 1 MHz reference clock for the RF amplifier Generates the RF component of the voltage applied to the quadrupole mass filter according to a signal from the main board The amplitude of this voltage 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 th
235. rce contamination 294 Reagent gas flow control module schematic 9 GC MSD Interfaces and Cl Flow Control Reagent gas flow control module Gas A Methane supply Gas B Other gas supply Gas select valve A Mass Isolation i valve Flow Controller Gas select valve B light i EI Cl GC MSD interface Cl ion source A GC column When you turn off one gas and turn on the other the system sets a 6 minute delay with Gas Off and Purge both on to pump out the flow control module The light for the selected reagent gas will flash indicating the delay timer is active Once the delay is finished the Purge and Gas Off lights will turn off 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 gas last time 295 9 GC MSD Interfaces and CI Flow Control Reagent gas flow control module 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 El mode Control panel lights LEDs Gas A gree
236. re is so much more reagent gas than sample most of the emitted electrons collide with reagent gas molecules forming reagent ions These reagent gas ions react with each other in primary and secondary reaction processes that establish an equilibrium They also react in var ious ways with sample molecules to form sample ions CI ion formation involves much lower 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 Cl is often used to determine the molecular weights of sample compounds Methane is the most common CI reagent gas It yields certain characteristic ioniza tion patterns Other reagent gases yield different patterns and may result in better sensitivity for some samples Common alternative reagent gases are isobutane and ammonia Carbon dioxide is often used in negative CI Less common reagent gases are carbon dioxide hydrogen freon trimethylsilane nitric oxide and methy lamine Different ionization reactions occur with each reagent gas Ammonia is toxic and corrosive Use of ammonia requires special maintenance and safety precautions Water contamination in reagent gases may decrease CI sensitivity dramatically A large peak at m z 19 H30 in positive CI is a diagnostic symptom of water con tamination In high enough concentrations especially when combined with cali brant water contamination w
237. reline pump oil to break down more quickly Therefore the oil in the foreline vacuum pump must be checked and replaced more frequently Always purge the MSD with methane after flowing ammonia Be sure to install the ammonia so the tank is in an upright position This will help prevent liquid ammonia from getting into the flow module 246 7 Cl Maintenance To set up your MSD for CI operation To set up your MSD for CI operation Setting up your CI MSD for operation in CI mode requires special care to avoid contamination and air leaks General guidelines e Before venting in EI mode verify that the GC MSD system is performing correctly See To verify system performance 51 e Make sure the reagent gas inlet line s are equipped with gas purifiers not applicable for ammonia e Use extra high purity reagent gases 99 99 or better for methane and as pure as is available for other reagent gases 247 CAUTION 7 Cl Maintenance To install the CI ion source To install the CI ion source 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 before you open the analyzer chamber Vent the MSD and open the analyzer See page 54 Remove the EI ion source See page 206 Remove the CI ion source from its storage box and insert the ion source into the radiator Rei
238. retched 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 default source tempera ture is 250 C for PCI and 150 C for NCI The quadrupole temperature is 150 C for both CI modes The Cl ion source is dirty Clean the ion source See the Maintenance chapter in this manual for more infor mation The electron multiplier detector is failing Switch to EI mode and confirm Replace the electron multiplier 147 Possible Cause Action Possible Cause Action Possible Cause Action Possible Cause Action 5 Cl Troubleshooting Can not complete autotune Can not complete autotune Wrong or corrupted tune file Check the tune parameters The m z 28 27 ion ratio for methane is incorrect The correct ratio should be between 1 5 and 5 0 If the ion ratio is incorrect adjust it See page 88 The CI ion source is dirty Clean the ion source See the Maintenance chapter in this manual for more infor mation Too much air or water in the system See the Leaks section of this chapter for more information After eliminating these problems clean the ion source 148 5 Cl Troubleshooting Peak widths are unstable Peak widths are unstable Possible Cause Wrong or corrupted tune file
239. rials needed 6 Maintaining the MSD To reassemble the ion source CAUTION CAUTION To reassemble the ion source Gloves clean lint free large 8650 0030 small 8650 0029 Hex ball driver 1 5 mm 8710 1570 Hex ball driver 2 0 mm 8710 1804 Hex nut driver 5 5 mm 8710 1220 Wrench open end 10 mm 8710 2353 Slide the drawout plate and the drawout cylinder into the source body Assemble the ion focus lens entrance lens and lens insulators Slide the assembled parts into the source body Install the setscrew that holds the lenses in place Reinstall the repeller repeller insulators washer and repeller nut into the source heater assembly The resulting assembly is called the repeller assembly Do not overtighten the repeller nut or the ceramic repeller insulators will break when the source heats up The nut should only be finger tight Reconnect the repeller assembly to the source body The repeller assembly includes the source heater assembly repeller and related parts Reinstall the filaments Reinstall the interface socket Do not overtighten the interface socket Overtightening could strip the threads 214 6 Maintaining the MSD To reassemble the ion source Interface socket Source body Set scr ew Repeller Repeller insulator a Filament ARS Source heater assembly Repeller insulator Washe r Re
240. rier gas the carrier gas flow must be off before turning off the MSD power If the foreline pump is off hydrogen will accumulate in the MSD and an explosion may occur Read the Hydrogen Carrier Gas Safety Guide 5955 5398 before operating the MSD with hydrogen carrier gas Be sure the GC oven and the GC MSD interface are cool before turning off carrier gas flow Reconnect the HIVAC POWER cable Remove the analyzer cover page 52 Turn the vent valve knob counterclockwise to admit air into the analyzer chamber Do not remove the knob Be sure to retighten the knob before pumping down To open the analyzer chamber page 56 68 To operate the CI MSD 70 To switch from EI to CI operating mode 72 To set up the software for CI operation 73 To set up methane reagent gas flow 76 CI autotune 78 To perform a positive CI autotune methane only 80 To perform a negative CI autotune any reagent gas 82 To verify positive CI performance 84 To verify negative CI performance 85 To operate the reagent gas flow control module 74 To monitor high vacuum pressure 86 To use other reagent gases 88 To switch from CI to EI operating mode 92 Operating the CI MSD NOTE Operating the MSD in CI mode This chapter provides information and instructions about operating the 5973N CI MSDs in CI mode Most of the material is related to methane chemical ionization but one section discusses the use of other reagent gases Sequ
241. s washer and repeller nut The resulting assembly is called the repeller assembly Do not overtighten the repeller nut or the ceramic repeller insulators will break when the source heats up The nut should only be finger tight Connect the repeller assembly to the source body Reinstall the filaments Reinstall the ion source in the source radiator See page 216 Do not forget to reconnect the wires from the feedthrough board to the ion source Do not forget to reconnect the heater and temperature sensor wires to the feedthrough board Close the analyzer chamber See page 58 Pump down the MSD See page 60 224 6 Maintaining the MSD To reinstall the heater and sensor in the ion source Source body Repeller Repeller insulator Filament Repeller insulator Washer Repeller nut Filament Source heater assembly 225 Materials needed 6 Maintaining the MSD To remove the heater and sensor from the mass filter CAUTION To remove the heater and sensor from the mass filter Gloves clean lint free large 8650 0030 small 8650 0029 Hex ball driver 1 5 mm 8710 1570 Hex ball driver 2 0 mm 8710 1804 Vent the MSD See page 54 Open the analyzer chamber See page 56 Disconnect the mass filter heater and temperature sensor wires from the feedthrough board Remove the mass filter heater assembly from the mass filter radiator Do no
242. s are not met the MSD electronics will shut off the foreline pump In order to recover from this condition you must power cycle the MSD If the MSD does not pump down correctly see the manual or online help for information on troubleshooting air leaks and other vacuum problems When prompted turn on the GC MSD interface heater and GC oven Click OK when you have done so The software will turn on the ion source and mass filter quad heaters The tem perature setpoints are stored in the current autotune u file 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 After the message Okay to run appears wait two hours for the MSD to reach thermal equilibrium Data acquired before the MSD has reached thermal equilibrium may not be reproducible Reinstall the MSD top cover The top cover was removed during the vent procedure 61 Software changes See also 2 Operating the MSD To pump down the CI MSD To pump down the CI MSD 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 You can also use the Control Panel to perform this task See the 5973N Control Panel Quick Reference Guide for more information Follow the instructions in the previous module See To pump down the MSD on page 60
243. s make up the vacuum system Analyzer chamber Side plate analyzer door and front and rear end plates Vacuum seals Foreline rough pump High vacuum pump vapor diffusion or turbomolecular pump Calibration valve s and vent valve Vacuum control electronics Vacuum gauges and gauge control electronics Each of these is discussed in more detail in the following material 262 8 Vacuum System Calibration valve Vent valve Front side plate thumbscrew Analyzer chamber Side plate E RES Eero ae Side plate hinge i Mo i Triode gauge tube 1 aa Rear side plate thumbscrew i ete gt High vacuum pump clamps AE TT At iy Foreline pump Foreline hose High vacuum pump High vacuum cooling fan 263 8 Vacuum System Diffusion pump MSD vacuum system Diffusion pump MSD vacuum system The diffusion pump requires baffling to prevent vapor from migrating into the ana lyzer chamber Foreline pressure is monitored by the foreline gauge The ac board controls the diffusion pump heater Calibration valve Diffusion pump Diffusion pump baffle adapter anifold cooling fins Diffusion pump analyzer
244. s to take against 205 238 EM See also Detector See Electron multiplier EM voltage 313 Emergency venting the MSD in case of 68 Emission current 302 if there is none 117 EMVolts at or above 2600V in NCI autotune 82 End plate O rings 270 390 Index Endosulfan EI and NCI spectra 382 Entrance lens 304 Error messages difficulty in mass filter electronics 112 difficulty with the EM supply 112 difficulty with the fan 113 difficulty with the HED supply 113 difficulty with the high vacuum pump 113 foreline pressure has exceeded 300 mTorr 114 internal MS communication fault 114 latched 112 lens supply fault 114 log amplifier ADC error 114 no peaks found 114 temperature control disabled 115 temperature control fault 115 the high vacuum pump is not ready 116 the system is in standby 116 the system is in vent state 117 there is no emission current 117 there is not enough signal to begin tune 117 translating error numbers into messages 112 ESD See Electrostatic discharge Excessive noise or low signal to noise ratio in CI MSD 140 Exhaust oil trap for foreline pump 166 272 venting the foreline pump 34 F Face seals 270 Fan for high vacuum pump 276 280 cleaning 177 incorrect operation of 113 replacing 194 Ferrules conditioning 21 part numbers 362 Ferrules inlet part numbers 22 Ferrules interface part numbers 30 Filaments 302 care 303 electron energy 302 emission current 302
245. ssembly G1099 60107 Heater sleeve G1099 20210 replace the old sleeve if it is damaged Screwdriver Torx T 15 8710 1622 Hex driver 1 5 mm 8710 1570 Slide the new heater and temperature sensor into the heater sleeve Reinstall the setscrew Slide the heater sleeve onto the GC MSD interface Align the heater sleeve so the screws are on top Tighten the screws evenly Slide the insulation onto the GC MSD interface There is a shallow groove along the inner surface of the insulation This groove must line up with the heads of the screws in the heater sleeve If it does not you can crack or otherwise damage the insulation Reinstall the GC MSD interface cover Make sure the wires from the heater and sensor pass through the cutout in the interface cover Reconnect the MSD to the GC See page 179 Make sure you reconnect the GC MSD interface cable to the GC Make sure you reinstall the capillary column Pump down the MSD See page 60 Turn on the GC Re establish appropriate temperature setpoints for the GC MSD interface and GC oven 236 6 Maintaining the MSD To reinstall the GC MSD interface heater and sensor Heater sleeve Heater sleeve screw Heater sleeve screw Set screw Temperature sensor Heater Interface welded assembly Insulation Cover 237 WARNING WARNING 6 Maintaining the MSD Maintaining the electronics Th
246. symptoms 98 102 difficulty in mass filter electronics 112 difficulty with the EM supply 112 difficulty with the fan 113 difficulty with the HED supply 113 difficulty with the high vacuum pump 113 error messages 112 117 excessive noise or low signal to noise ratio in CI MSD 140 foreline pressure has exceeded 300 mTorr 114 foreline pressure is too high 107 foreline pressure is too low 108 foreline pump is not operating 97 gauge controller displays 9 9 9 and then goes blank 108 GC does not turn on 96 GC MSD interface will not heat up 111 general symptoms 96 97 high abundances at m z 18 28 32 44 or at m z 14 and 16 104 high analyzer chamber pressure with reagent gas flow 130 high background 103 high electron multiplier voltage in CI MSD 147 high mass sensitivity is poor 106 internal MS communication fault 114 ion source will not heat up 110 isotopes missing or ratios are incorrect 103 large peak at m z 19 in CI MSD 141 lens supply fault 114 log amplifier ADC error 114 mass filter quad heater will not heat up 111 mass spectral symptoms 103 106 MSD does not turn on 96 MSD is on but foreline pump is not running 97 no or low PFDTD signal but reagent ions are normal 138 no or low reagent gas signal 135 no peaks 98 114 no peaks in CI MSD 133 peak at m z 32 in CI MSD 142 peak widths are inconsistent 104 peak widths are unstable in CI MSD 149 peaks are front
247. system software contains a program that monitors and displays system status during pumpdown When the pressure is low enough the program turns on the ion source and mass filter heaters It also prompts you to turn on the GC MSD interface heater 5973N MSDs will shutdown if they cannot pump down correctly Pressure in the MSD can be monitored two ways The diffusion pump MSD is equipped with a gauge that measures foreline pressure Foreline pressure can be monitored only through the data system The turbo pump MSD does not have a foreline gauge Instead the data system displays turbo pump motor speed Each MSD is equipped with a triode ionization gauge tube If your MSD is also equipped with an 59864B Gauge Controller the triode gauge can measure the pressure in the analyzer chamber The high vacuum pressure measured by the triode gauge cannot be monitored through the data system It is displayed on the gauge controller 35 2 Operating the MSD MSD temperatures are controlled through the data system The MSD has independent heaters and temperature sensors for the ion source and quadrupole mass filter You can adjust the setpoints and view these temperatures from the data system or from the control panel The GC MSD interface heater is powered and controlled by the Thermal Aux 2 heated zone of the 6890 Plus GC The GC MSD interface tempera ture can be set and monitored from the data system or from the GC keypad Column flow is c
248. t is not connected properly Try the other filament e Filament has failed Try the other filament e MSD electronics are not working correctly There is not enough signal to begin tune e Corrupted tune file e Poor mass axis calibration e Amu gain or offset is too high e Calibration vial is empty or almost empty e Excessive pressure in the analyzer chamber e Air leak e Electron multiplier voltage is too low e Signal cable is not connected e Electrical leads to the detector are not connected correctly e Electrical leads to the ion source are not connected correctly e Filament shorted to the source body 117 4 Troubleshooting the MSD Air leaks Air leaks Air leaks are a problem for any instrument that requires a vacuum to operate Leaks are generally caused by vacuum seals that are damaged or not fastened cor rectly Symptoms of leaks include e Higher than normal analyzer chamber pressure or foreline pressure e Higher than normal background e Peaks characteristic of air m z 18 28 32 and 44 or m z 14 and 16 e Poor sensitivity e 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 e Injection port septum e Injection port column nut e Broken or cracked capillary column Leaks can occur in many more places in the MSD e GC MSD interface colu
249. t touch the mass filter contact leads This could cause ESD damage to the side board 226 6 Maintaining the MSD To remove the heater and sensor from the mass filter Mass filter contact lead do not touch Mass filter radiator Mass filter heater assembly Pa Feedthrough board Mass filter contact lead do not touch 227 Materials needed 6 Maintaining the MSD To reinstall the heater and sensor in the mass filter CAUTION To reinstall the heater and sensor in the mass filter Gloves clean lint free large 8650 0030 small 8650 0029 Hex ball driver 1 5 mm 8710 1570 Hex ball driver 2 0 mm 8710 1804 Mass filter heater assembly G1099 60172 Unpack the new mass filter heater assembly The heater temperature sensor and heater block are already assembled Install the heater assembly on top of the mass filter radiator Connect the heater and temperature sensor wires to the feedthrough board Close the analyzer chamber See page 58 Pump down the MSD See page 60 Do not touch the mass filter contact leads This could cause ESD damage to the side board 228 6 Maintaining the MSD To reinstall the heater and sensor in the mass filter Mass filter contact lead do not touch Mass filter radiator Mass filter heater assembly Pa Feedthrough board Mass filter contact lead do not touch
250. tandard turbo pump Fan turbo pump position 3160 1037 351 12 Parts Analyzer Analyzer This table lists the replacement parts for the analyzer Analyzer screws and the individual ion source parts are listed the next tables Table 16 Analyzer parts Description Part number Analyzer complete tested with side board G1099 69228 detector complete G1099 80001 electron multiplier horn 05971 80103 feedthrough board G1099 60425 HED feedthrough G1099 80012 O ring viton for HED feedthrough 0905 0490 ion source complete G1099 69106 magnet assembly 05971 60160 mass filter cable kit G1099 60130 mass filter contacts 4 required G1099 60142 mass filter ceramic support detector end G1099 20124 mass filter ceramic support source end G1099 20123 mass filter heater assembly G1099 60172 mass filter radiator G1099 20121 mounting bracket detector end G1099 00002 mounting bracket source end G1099 00001 pins for source and detector end mounting brackets G1099 20137 side plate includes thumbscrews G1099 60021 source radiator G1099 20122 352 Table 17 12 Parts Analyzer Analyzer screws Description Part number Heater sensor quadrupole set screw 0515 1446 lon source thumbscrew G1099 20138 Magnet mounting screws 0515 1046 Screw to attach magnet bracket to source radiator 0515 1602 Screws to attach source radiator and detector to quadrupole radiator 0515 1052 Screws for mass filter contact assembly and
251. te the side plate O ring CAUTION CAUTION To lubricate the side plate O ring Cloths clean 05980 60051 Gloves clean lint free large 8650 0030 small 8650 0029 Grease Apiezon L high vacuum 6040 0289 The side plate O ring needs a thin coat of grease to ensure a good vacuum seal If the side plate O ring appears dry or does not seal correctly lubricate it using this procedure A good test is to wipe off the side plate with methanol then close the analyzer chamber If the O ring has enough grease on it it will leave a faint trace on the side plate Vacuum seals other than the side plate O ring and vent valve O ring do not need to be lubricated Lubricating other seals can interfere with their correct function Vent the MSD See page 54 Open the analyzer chamber See page 56 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 Do not use anything except the recommended vacuum grease Excess grease can trap alr and dirt Grease on surfaces of the O ring other than the exposed surface can trap air resulting in air spikes during operation Use a clean lint free cloth or glove to wipe away excess grease If the O ring looks shiny there is too much grease on it Close the analyzer chamber See page 58 Pump down the MSD See page 60 200 6 Maintaining the MSD To lubricate the side plate O ring Side plate O ring
252. tes a problem Check the level and condition of the fluid Make sure pump is cool and power cycle MSD to reset 277 See Also 8 Vacuum System Diffusion pump and fan You can check the condition and level of the diffusion pump fluid through the win dow sight glass near the base of the front of the pump If the level drops below the appropriate marker there are separate ranges for hot and cold conditions or if the fluid turns dark brown or black replace the fluid Otherwise replace the fluid once a year Diffusion pump fluid that is exposed to air at operating temperature will break down and turn dark brown or black This reaction is called cracking Cracked pump fluid gives two symptoms higher manifold pressure and high background with a large peak at m z 446 Maintaining the vacuum system 159 Troubleshooting 5973N MSD in the online help for information on trouble shooting air leaks and other vacuum problems 278 8 Vacuum System Diffusion pump and fan Diffusion pump outlet Inlet Cooling fins Too hot sensor Too cold sensor Fluid level window Diffusion pump heater cable Cold fluid level marker Hot fluid level marker 279 See Also 8 Vacuum System Turbomolecular pump and fan Turbomolecular pump and fan The turbo pump in the MSD is clamped directly to the bottom of the analyzer chamber The turbo pump has a
253. the MSD To view MSD analyzer temperature and vacuum status 38 To set monitors for MSD temperature and vacuum status 40 To set the MSD analyzer temperatures 42 To set the GC MSD interface temperature from the PC 44 To monitor high vacuum pressure 46 To measure column flow linear velocity 48 To calculate column flow 49 To tune the MSD 50 To verify system performance 51 To remove the MSD covers 52 To vent the MSD 54 To open the analyzer chamber 56 To close the analyzer chamber 58 To pump down the MSD 60 To pump down the CI MSD 62 To connect the gauge controller 63 To move or store the MSD 65 To set the interface temperature from a 6890 Plus GC 67 To vent the MSD without the ChemStation 68 Chapter 3 Chapter 4 Contents Operating the CI MSD To switch from EI to CI operating mode 72 To set up the software for CI operation 73 To operate the reagent gas flow control module 74 To set up methane reagent gas flow 76 CI autotune 78 To perform a positive CI autotune methane only 80 To perform a negative CI autotune any reagent gas 82 To verify positive CI performance 84 To verify negative CI performance 85 To monitor high vacuum pressure 86 Typical pressure readings 87 To use other reagent gases 88 Isobutane CI 90 Ammonia CI 90 Carbon dioxide NCI 91 To switch from CI to EI operating mode 92 Troubleshooting the MSD General symptoms 96 GC does not turn on 96 MSD does not turn o
254. the entrance lens offset generally increases the abundance of ions at low masses without sub stantially decreasing the abundance of high mass ions Entrance lens gain Entrance lens gain EntLens controls the variable voltage applied to the entrance lens It determines how many volts are applied for each amu It can be varied from 0 to 128 mV amu A typical range is 0 to 40 mV amu 304 Interface socket Source body Set screw Repeller Repeller insulator Filament Source heater assembly Repeller insulator Washer Repeller nut Filament on focus lens Drawout cylinder Drawout plate Lens insulator one of a pair Entrance lens 10 Analyzer lon source 305 10 Analyzer Cl ion source CI ion source The Cl 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 There is a dummy filament to provide connections for the other wires The holes 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 Cl interface tip The seal for the interface tip ensures a leak tight seal and electrical isolation between the Cl interface a
255. the mass spectra generated typically have lower abundance of the molecular ion As with electron capture the products of dissociative electron capture are not always stable The reverse reaction sometimes occurs This reverse reaction is sometimes called an associative detachment reaction The equation for the reverse reaction is M xX gt MX e Ion pair formation Ion pair formation is superficially similar to dissociative electron capture The ion pair formation reaction is represented by the equation B a a a MX e henna gt M X e As with dissociative electron capture the sample molecule fragments Unlike dis sociative electron capture however the electron is not captured by the fragments Instead the sample molecule fragments in such a way that the electrons are dis tributed unevenly and positive and negative ions are generated 385 Appendix A Chemical lonization Theory Negative Cl theory Ion molecule reactions Ion molecule reactions occur when oxygen water and other contaminants are present in the CI ion source Ion molecule reactions are 2 4 times slower than electron attachment reactions and do not provide the high sensitivity associated with electron capture reactions Ion molecule reactions can be described by the general equation M X gt MX where X is most often a halogen or hydroxyl group that has been created by ion ization of contaminants by electrons from the filament Ion molecule reactions co
256. the pressure in the MSD is above approxi mately 8 x 10 Torr The gauge controller will display all 9s and then go blank The triode gauge tube can measure pressures between approximately 8 x 10 and 3 x 10 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 from instrument to instrument 86 3 Operating the Cl MSD To monitor high vacuum pressure Typical pressure readings Use the 59864B high vacuum gauge controller Note that the mass flow controller is calibrated for methane and the high vacuum gauge controller is calibrated for nitrogen so these measurements are not accurate but are intended as a guide to typical observed readings They were taken with the following set of conditions Note that these are typical PCI temperatures Source temperature 250 C Quad temperature 150 C Interface temperature 320 C Helium carrier gas flow 1ml min MFC Pressure Torr Methane Ammonia EI PCI NCI MSD EI PCI MSD EI PCI NCI MSD EI PCI MSD Performance Standard Performance Standard turbo pump turbo pump Not turbo pump turbo pump 10 55x105 20x107 50x105 15x107 15 8 0x10 25x107 70x10 20x107 20 10x10 30x107 85x10 30x107 25 1 2x10 Notrecommended 1 0x107 Notrec
257. the pump oil This will greatly increase the life of the pump Only perform this procedure if the pump is at normal operating temperature The water in the air can cause condensation of the ammonia at the ballast valve if the pump is cold Ballast control Open the ballast valve on the foreline pump all the way several turns counterclockwise The sound of the pump will get much louder Leave the ballast valve open for one hour You can continue to run samples while the pump is ballasting Close the ballast valve Leaving the ballast valve open all the time will result in loss of pump oil and damage to the pump Always purge the flow module with methane after flowing ammonia The use of ammonia reagent gas also requires that the foreline pump oil be changed every 2 3 months instead of the usual six months 254 Materials needed 7 CI Maintenance To replace the methane isobutane gas purifier CAUTION WARNING To replace the methane isobutane gas purifier Methane isobutane gas purifier G1999 80410 Front ferrule for 1 8 inch tubing 65180 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 This frequency may vary depending on purity of the gas and care taken in uncapping and installing the gas purifier A large leak upstream from the gas purifier can quickly exhaust the reduced met
258. this does not work well for the reagent gas flow system it takes as long as 15 minutes for the peak to reach the ion source if the leak is at the inlet to the flow module 126 Schematic of CI flaw control module CI Troubleshooting Air leaks Gas A O ae Methane supply Gar sale Isolation valve A Mass GS Flow i Controller Gas select valve B Gas B rare ter gas ane OnE supply D Amber interface i Restrictor PFDTD vial GC column Flow 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 El 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 gt setpoint On 100 On 100 On 100 Off 0 Isolation valve Open Open Open Open Open Closed 127 5 Cl Troubleshooting Pressure related symptoms overview 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 contro
259. tion valve with restrictor with less restriction than that in the performance turbo MSD this is to allow the correct diffusion of 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 com pounds can be used for manual tuning CI calibration valve The CI tuning compound is perfluoro 5 8 dimethy1 3 6 9 trioxidodecane PFDTD The CI calibration valve is part of the reagent gas flow control module It is controlled by the ChemStation software and opens automatically during Cl autotune or manual tuning allowing PFDTD to diffuse through the GC MSD inter face and into the ion source Vent valve The vent valve knob screws into a threaded port in the front end plate An O ring is compressed between the knob and the end plate to form a seal The threaded end of the knob has an air passage inside it allowing air to flow into the manifold when the knob is partially unscrewed If you turn the knob too far the O ring can come out of its slot 283 8 Vacuum System Calibration valves and vent valve EI calibration valve Vent valve knob Calibration vial EI calibration valve Vent valve knob O ring Yu Air passage Valve closed Valve open Valve open too far
260. to tilt it up slightly Remove the fill cap Place a container under the drain plug Remove the drain plug Allow the pump oil to drain out The oil drains faster if it is still warm The old pump oil may contain toxic chemicals Treat it as hazardous waste Refill the foreline pump See page 164 162 6 Maintaining the MSD To drain the foreline pump 163 ASAVAYAN YY Fill cap Pump motor h 7 Drain plug Materials needed See also 6 Maintaining the MSD To refill the foreline pump To refill the foreline pump Foreline pump oil 6040 0834 approximately 0 28 liters required Funnel Gloves oil and solvent resistant Screwdriver flat blade large 8730 0002 Drain plug O ring Gif required 0905 1515 A video demonstration of this procedure is on the 5973N MSD Maintenance CD ROM Drain the foreline pump See page 162 Reinstall the drain plug If the old O ring appears worn or damaged replace it Remove the propping object from under the pump motor 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 liters of oil Wait a few minutes for the oil to settle If the oil level drops add oil to bring the oil level to near the upper line Reinstall the fill cap If necessary slide the foreline pump back under the analyzer
261. trument shutdown There are three parameters that affect the filaments filament selection Filament filament emission Emission current and electron energy EleEnergy Filament selection The filament selection parameter Filament allows you to select which filament in the ion source is active Sometimes one filament will give better performance than the other To select the better of the two filaments run two autotunes one with each filament Use the fil ament that gives the best results Emission current The filament emission current Emission is variable between 0 and 315 uA but should be set to the software default for normal operation Electron energy The electron energy EleEnergy is the amount of energy on the ionizing electrons The electron energy is determined by the bias voltage 70 V dc bias on the fila ment causes emitted electrons to possess 70 eV electron volts This value is adjustable between 5 to 241 V dc but for normal operation set this parameter to 70 302 10 Analyzer lon source Filament care Like the filaments in incandescent light bulbs the ion source filaments will eventu ally burn out Certain practices will reduce the chance of early failure e Ifyou have an optional 59864B Gauge Controller use it to verify that the system has an adequate vacuum before turning on the analyzer especially after any maintenance has been performed e Ifyou are controlling your MSD from the
262. uisition by setting the EMV in the method c There are no PFDTD ions formed in PCI with any reagent gas but methane hence CI autotune is not available with these configurations d Higher peakwidth values give better sensitivity lower values give better resolution e Optimum emission current maximum for NCI is very compound specific and must be selected empirically Opti mum emission current for pesticides for example may be about 200uA 73 3 Operating the CI MSD To operate the reagent gas flow control module To operate the reagent gas flow control module For a video demonstration of the gas flow control module see the 5973N MSD Maintenance CD ROM 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 El 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 setting On setpoint On setpoint On 100 On 100 On 100 Off 0 Isolation valve Open Open Open Open Open Closed 74 3 Operating the Cl MSD To operate the reagent gas flow control module Flow control knob mass flo
263. uld prevent the GC from operating Gauge controller displays 9 9 9 and then goes blank This indicates the pressure in the analyzer chamber is above 8 x 10 Torr e Solvent peak from an on column injection e MSD has not had enough time to pump down e Excessive foreline pressure e Bad connection or bad cable between the triode gauge and gauge controller e Diffusion pump fluid level is low or fluid is contaminated e Triode gauge tube has failed e Line voltage too low e Turbomolecular pump is not working correctly 108 4 Troubleshooting the MSD Pressure symptoms Power indicator on the gauge controller does not light e Unplugged gauge controller power cord e Incorrect or inadequate line voltage at the electrical outlet e Failed gauge controller fuse 109 4 Troubleshooting the MSD Temperature symptoms Temperature symptoms The MSD has three heated zones e Jon source Source in the MSD ChemStation software e Mass filter Quad in the MSD ChemStation software e GC MSD interface Thermal Aux 2 in the MSD ChemStation software Each of these heated zones has a heater cartridge and temperature sensor The ion source and mass filter are powered and controlled by the MSD The GC MSD interface is powered and controlled by the GC Ion source will not heat up e High vacuum pump is off or has not reached normal operating conditions e Incorrect temperature setpoint e lon source has not had enough time to reach temp
264. une view run Cl Autotune See page 85 Note that there are no criteria for a passing Autotune in CI If the Autotune com pletes it passes Run the NCI sensitivity method OFN_NCI M using 1 ul of 1pg ul OFN Verify that the system conforms to the published sensitivity specification The 5973Network Series Mass Selective Detector Specifications 5968 7358E 85 Materials needed 3 Operating the CI MSD To monitor high vacuum pressure WARNING WARNING To monitor high vacuum pressure Gauge controller 59864B Triode gauge cable 8120 6573 Never connect or disconnect the cable from the triode gauge tube while the MSD is under vacuum Risk of implosion and injury due to broken glass exists If you are using hydrogen as a carrier gas do not turn on the triode gauge tube if there is any possibility that hydrogen has accumulated in the manifold The triode gauge filament can ignite hydrogen Read the Hydrogen Carrier Gas Safety Guide 5955 5398 before operating the MSD with hydrogen carrier gas Connect the gauge controller to the triode gauge tube See page 63 Start up and pump down the MSD See page 60 Switch on the power switch on the back of the gauge controller Press and release the GAUGE button After a few seconds the pressure should be displayed Pressure is displayed in the format X X X where X is the base 10 exponent Units are Torr The gauge controller will not turn on if
265. urbo pump 282 Calibration valves and vent valve 283 Calibration valves 283 EI calibration valve 283 CI calibration valve 283 Vent valve 283 Triode gauge tube 285 Gauge controller 287 16 Chapter 9 Chapter 10 Contents GC MSD Interfaces and CI Flow Control EI GC MSD interface 291 EI CI GC MSD interface CI interface 292 Reagent gas flow control module 293 Analyzer Ion source 300 Ion source body 300 Filaments 302 Magnet 303 Repeller 303 Drawout plate and cylinder 304 Ion focus 304 Entrance lens 304 Cl ion source 306 Quadrupole mass filter 308 AMU gain 308 AMU offset 309 219 width 309 DC polarity 310 Mass axis gain 310 Mass axis offset 310 Quadrupole maintenance 311 Detector 312 Detector focus lens 312 High energy dynode 312 Electron multiplier horn 312 Analyzer heaters and radiators 314 17 Chapter 11 Chapter 12 Appendix A Contents Electronics Control panel and power switch 320 Side board 322 Electronics module 323 Main board 324 Signal amplifier board 325 AC board 326 LAN MSD control card 330 Power supplies 331 Back panel and connectors 332 Interfacing to external devices 334 Parts Electronics 339 Vacuum system 344 Analyzer 352 EI GC MSD interface 358 Consumables and maintenance supplies 360 CI Parts 364 Chemical Ionization Theory Chemical ionization overview 374 References on chemical ionization 375 P
266. usion pump e Air intakes to the cooling fan are blocked e Laboratory temperature is too high generally above 35 C e High vacuum signal cable is disconnected or not working correctly e Diffusion pump temperature sensor is not working correctly e MSD electronics are not working correctly 113 4 Troubleshooting the MSD Error messages Turbomolecular pump e Large vacuum leak is preventing the turbo pump from reaching 50 of full speed e Foreline pump is not working correctly e Turbo pump is not working correctly e Turbo pump controller is not working correctly e MSD electronics are not working correctly Foreline pressure has exceeded 300 mTorr Only diffusion pump equipped MSDs have a foreline pressure gauge e Excessive carrier gas flow typically gt 5 ml min e Excessive solvent volume injected e Large vacuum leak e Severely degraded foreline pump oil e Collapsed or kinked foreline hose e Foreline pump is not working correctly e Foreline gauge is not working correctly Internal MS communication fault e MSD electronics are not working correctly Lens supply fault e Electrical short in the analyzer e MSD electronics are not working correctly Log amplifier ADC error e MSD electronics are not working correctly No peaks found e Emission current was set to 0 e Electron multiplier voltage is too low e Amu gain or offset is too high e Poor mass axis calibration 114 4 Troubleshooting the MSD Error m
267. ve is open e Foreline pump oil level is low or oil is contaminated e Foreline hose is constricted e Foreline gauge is not working correctly e Foreline pump is not working correctly Analyzer chamber pressure is too high EI operating mode If the pressure you observe is above 1 0 x 10 Torr or if the pressure you observe for a given column flow has increased over time check the following e Column carrier gas flow is too high e Air leak e Foreline pump is not working correctly see Foreline pressure is too high e Diffusion pump fluid level is low or fluid is contaminated e Turbomolecular pump is not working correctly 107 4 Troubleshooting the MSD Pressure symptoms Foreline pressure is too low If the pressures you observe are below 20 mTorr check for the following e Column carrier gas flow is too low e Column plugged or crushed by an overtightened nut e Empty or insufficient carrier gas supply e Bent or pinched carrier gas tubing e Foreline gauge is not working correctly These could create a fault condition in the GC that would prevent the GC from operating Analyzer chamber pressure is too low If the pressures you observe are below 1 x 10 Torr check for the following e Column carrier gas flow is too low e Column plugged or crushed by overtightened nut e Empty or insufficient carrier gas supply e Bent or pinched carrier gas tubing These could create a fault condition in the GC that wo
268. ve off of the GC MSD interface It may be necessary to gently pry open the slot in the heater sleeve to loosen the heater sleeve from the interface Loosen the setscrew and remove the heater and temperature sensor from the heater sleeve Heat and oxidation often result in a heater or less frequently a temperature sen sor being welded inside the heater sleeve The holes for the heater and sensor pass all the way through the heater sleeve A rod can be inserted to drive the stuck part out However to function correctly the heater and sensor must have perfect contact with their holes If a heater or sensor is difficult to remove the holes will probably be damaged enough that the heater sleeve should be replaced Polishing the holes is not an acceptable solution since it will enlarge the holes Installing a new heater and sensor in a damaged heater sleeve will result in poor performance of the heated zone and could reduce the lifetime of the new parts 234 6 Maintaining the MSD To remove the GC MSD interface heater and sensor Heater sleeve Heater sleeve screw Heater sleeve screw Set screw Temperature sensor Heater Interface welded assembly Insulation Cover 235 Materials needed 6 Maintaining the MSD To reinstall the GC MSD interface heater and sensor CAUTION To reinstall the GC MSD interface heater and sensor GC MSD interface heater a
269. w control knob Flow control display 75 3 Operating the CI MSD To set up methane reagent gas flow CAUTION 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 Adjusting the methane reagent gas flow is a three step process setting the flow control pre tuning on the reagent gas ions and adjusting the flow for stable reagent ion ratios for methane m z 28 27 Your data system will prompt you through the flow adjustment procedure After the system has been switched from El to Cl mode or vented for any other reason the MSD must be baked out for at least 2 hours before tuning Press the Gas A button Verify that only the Gas A light is on Adjust the flow to 20 for PCI NCI MSDs or 10 for PCI MSDs Check the vacuum gauge controller to verify correct pressure See page 86 Select Methane Pretune from the Setup menu The methane pretune tunes the instrument for optimum monitoring of the ratio of methane reagent ions m z 28 27 Examine the displayed profile scan of the reagent ions e 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 ai
270. w these procedures Analyzer cover Grasp the front of the analyzer cover and lift up enough to unlatch the five front tabs Reach back and grasp the back edge of the analyzer cover Pull forward to disengage the rear spring latch It may take a firm pull to disengage the latch To reinstall the analyzer cover reverse these steps Lower MSD cover Remove the analyzer cover Remove the 3 screws that hold the lower MSD cover in place Pull the cover left slightly to disengage the two right side tabs and then pull it straight forward To reinstall the lower MSD cover reverse these steps Do not remove any covers other than the upper and lower MSD covers Dangerous voltages are present under other covers 52 2 Operating the MSD To remove the MSD covers a Analyzer cover Latch tabs Lower cover Slots for tabs CAUTION Do not use excessive force or the plastic tabs that hold the cover to the mainframe will break off 53 Firmware changes 2 Operating the MSD To vent the MSD WARNING WARNING CAUTION WARNING To vent the MSD The firmware is revised periodically If the steps in this procedure do not match your MSD control panel refer to the manuals and online help supplied with the software or the 5973N MSD Control Panel Quick Reference for more informa tion If your system is equipped with a gauge controller
271. your local air quality regulations The oil trap stops only foreline pump oil It does not trap or filter out toxic chemicals If you are using toxic solvents or analyzing toxic chemicals remove the oil trap Do not use the trap if you have a CI MSD Install a hose to take the foreline pump exhaust outside or to a fume hood The fluids in the diffusion pump and foreline pump also collect traces of the samples being analyzed All used pump fluid should be considered hazard ous and handled accordingly Dispose of used fluid correctly as specified by your local regulations When replacing pump fluid use appropriate chemical resistant gloves and safety glasses Avoid all contact with the fluid 157 CAUTION CAUTION 6 Maintaining the MSD Electrostatic discharge is a threat to the MSD electronics during maintenance All of the printed circuit boards in the MSD contain components that can be damaged 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 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 When you work on or near printed circuit boards or when you work on c

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