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Agilent Technologies 5977B CI MSD, Operating Manual

The Agilent Technologies 5977B CI MSD is an advanced scientific instrument offering precise and reliable mass spectrometry analysis. To ensure optimal usage, download the comprehensive Operating Manual for free from our website. This user-friendly manual provides detailed instructions and troubleshooting insights for maximizing the capabilities of the 5977B CI MSD.

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6

Operating in CI Mode

CI Autotune

5977B Series MSD Operating Manual

145

CI Autotune

After the reagent gas flow is adjusted, the lenses and electronics of the MSD 
should be tuned. (See 

Table 11

 on page 146.) 

Perfluoro-5,8-dimethyl-3,6,9-trioxidodecane (PFDTD) is used as the calibrant. 
Instead of flooding the entire vacuum chamber, the PFDTD is introduced directly 
into the ionization chamber through the GC/MSD interface by means of the gas 
flow control module.

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.

EMV at or above 2600 V, however, indicates a problem. If your method requires 
EMV set at +400, you may not have adequate sensitivity in your data acquisition.

CAUTION

After the source is changed from EI to CI, 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.

CAUTION

Always verify MSD performance in EI before switching to CI operation. (See 

“To Verify EI System Performance” 

on page 131.) Always set up the CI MSD in 

PCI first, even if you are going to run NCI.

Summary of Contents for 5977B CI MSD

Page 1: ...Agilent 5977B Series MSD Operating Manual ...

Page 2: ...ity and fitness for a particular purpose Agilent shall not be liable for errors or for incidental or consequen tial damages in connection with the furnishing use or performance of this document or of any information con tained herein Should Agilent and the user have a separate written agree ment with warranty terms covering the material in this document that conflict with these terms the warranty ...

Page 3: ...n connect the flow path from the inlet through the guard chip bus components and column to the MS Tail assembly and maintain the column guard chip 4 Installing 7890 GC Columns Chapter 4 describes how to install a capillary column into a 7890 GC oven connect to the MSD through the GC MSD interface condition the column and calibrate the column flow 5 Operating in EI Mode Chapter 5 describes basic ta...

Page 4: ...ftware Library Insert the memory stick into a USB port and follow the prompts This can be installed by anyone who has authority to copy information onto the receiving computer 2013 Agilent Technologies Inc All rights reserved Made in USA Agilent Technologies GC GCMS Hardware User Manuals and Videos S1 Disk 2 3 To install 1 Insert disk into DVD drive 2 Follow the instructions on the screen 3 If aut...

Page 5: ...Many internal parts of the MSD carry dangerous voltages 21 Electrostatic discharge is a threat to MSD electronics 22 Many parts are dangerously hot 22 The oil pan under the foreline pump can be a fire hazard 23 Hydrogen Safety 24 GC precautions 24 Dangers unique to GC MSD operation 25 Hydrogen accumulation in an MSD 25 Precautions 26 Safety and Regulatory Certifications 28 Information 29 Symbols 2...

Page 6: ...umn 41 To Install a Capillary Column in the GC MSD Interface Using the Self Tightening Column Nut 42 To Install a Capillary Column in the GC MSD Interface Using a Standard Column Nut 47 To Install the GC MSD Interface Tip Seal 50 The GC MSD Interface for an 8890 Series GC 52 3 Installing Intuvo 9000 GC Columns Columns 56 Conditioning columns 57 Tips and hints 57 To Replace an Intuvo GC Column 59 T...

Page 7: ...elf Tightening Column Nut 84 To Install a Capillary Column in the GC MSD Interface Using a Standard Column Nut 89 To Install the GC MSD Interface Tip Seal 93 To Calibrate Column Flow Linear Velocity in a 7890 GC 95 The GC MSD Interface for a 7890B Series GC 98 5 Operating in EI Mode Operating the MSD from the DS 103 Operating the MSD from the 7890 GC Control Panel 104 Configuring the MSD through t...

Page 8: ...Instrument Control View 122 To Set the GC MSD Interface Temperature from MassHunter 124 To Monitor High Vacuum Pressure 125 To Tune the MSD in EI Mode 127 To Set the Operation Mode for the Optional JetClean System 129 To Set the JetClean Parameters for the Clean Only Mode 130 To Verify EI System Performance 131 To Perform High Mass Testing 132 To Open the MSD Covers 135 To Vent the MSD 136 To Pump...

Page 9: ...o Verify PCI Performance 163 To Verify NCI Performance 164 To Monitor CI Mode High Vacuum Pressure 165 7 General Maintenance Before Starting 168 Maintaining the Vacuum System 173 Maintaining the Analyzer 174 To Open the Analyzer Chamber 176 To Remove the EI HES 178 To Connect Disconnect Wiring to the EI HES 180 To Disassemble the EI HES 181 To Clean the EI HES 184 To Assemble the EI HES 187 To Rem...

Page 10: ...7 To Replace the Electron Multiplier Horn 218 To Close the Analyzer Chamber 220 8 CI Maintenance General Information 222 To set up your MSD for CI operation 222 To Switch from the EI HES to the CI Source 223 To Remove the EI HES Radiator 224 To Connect Disconnect Wiring to the EI HES Radiator 225 To Install the CI Source Radiator 227 To Switch from the CI Source to the EI HES 229 To Remove the CI ...

Page 11: ...g from the CI Source 236 To Connect Disconnect EI HES Model Wiring to the CI Source 237 To Disassemble the CI Source 238 To Clean the CI Source 241 To Assemble the CI Source 244 To Remove the CI Source Filament 247 To Install a CI Source Filament 249 To Install the CI Source 250 ...

Page 12: ...12 5977B Series MSD Operating Manual ...

Page 13: ...ertifications 28 Intended Use 31 Cleaning Recycling the Product 31 Accidental Liquid Spillage 31 Moving or Storing the MSD 31 To Replace the Primary Fuses 32 This chapter describes general information about the MSD including a hardware description general safety warnings and hydrogen safety information If you are using the Agilent Intuvo 9000 Gas Chromatograph with your MSD Chemical Ionization CI ...

Page 14: ... and a high efficiency source HES The optional 5977B chemical ionization CI system includes a positive chemical ionization negative chemical ionization PCI NCI ion source reagent gas flow control system CI calibration system and other required hardware features The serial number label displays a product number that indicates what type of MSD you have See Table 1 Table 1 Available MSD models Model ...

Page 15: ...fluorotriphenylphosphine calibrant Diff Diffusion DIP Direct insertion probe DS Data System EI Electron ionization EM Electron multiplier detector EMV Electron multiplier voltage EPC Electronic pneumatic control eV Electron volt GC Gas chromatograph HED High energy dynode refers to detector and its power supply HES High Efficiency Source New generation EI source constructed from inert material Ine...

Page 16: ... PFDTD Perfluoro 5 8 dimethyl 3 6 9 trioxydodecane calibrant PFHT 2 4 6 tris perfluoroheptyl 1 3 5 triazine calibrant PFTBA Perfluorotributylamine calibrant Quad Quadrupole mass filter RF Radio frequency RFPA Radio frequency power amplifier SS Stainless steel Torr Unit of pressure 1 mm Hg Turbo Turbomolecular pump WUI Web user interface XTR EI Extractor source Table 2 Abbreviations continued Abbre...

Page 17: ...rial XTR source HES CI PCI NCI source Turbo pump equipped 5977B models when used with an 8890 or 7890 GC are field upgradeable to CI PCI NCI modes The upgrade adds a CI source CI source radiator for HES systems CI flow module with an MFC plumbing and CI tuning calibration Independently MSD heated hyperbolic quadrupole mass filter Independently MSD heated ion source HED EM Independently GC heated G...

Page 18: ...Optimal He column flow mL min 1 1 to 2 Maximum recommended gas flow mL min Total gas flow into the MSD column flow plus reagent gas flow if applicable Based on helium gas use For other gases the maximum flow will vary 1 5 4 Maximum gas flow mL min Expect degradation of spectral performance and sensitivity 2 6 5 Max column id 0 25 mm 30 m 0 53 mm 30 m CI capability Turbo pump models are field upgra...

Page 19: ... were field upgraded for CI operation It also applies unless otherwise specified to the flow modules for these instruments The CI hardware upgrade allows the MSD to produce high quality classical CI spectra which include molecular adduct ions A variety of reagent gases can be used See Chapter 6 Operating in CI Mode on page 143 Figure 1 5977B Series GC MSD system shown with an Agilent 8890 GC ALS 8...

Page 20: ...G3397B is integrated in the system Its use is required for CI and it is recommended for EI also The CI system has been optimized to achieve the relatively high CI source pressure required for CI while still maintaining high vacuum in the quadrupole and detector 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 vol...

Page 21: ...cs boards in the instrument The internal wires and cables connected to these boards The wires for any heater oven detector inlet or valve box If one of the primary fuses has failed the MSD will already be off but for safety switch off the MSD and unplug the power cord It is not necessary to allow air into the analyzer chamber WARNING All these parts are shielded by covers With the covers in place ...

Page 22: ...ts GC oven and its contents including the column nuts attaching the column to a GC inlet GC MSD interface or GC detector GC detector GC valve box Foreline pump Diffusion pump Heated MSD ion source GC MSD interface and quadrupole Always cool these areas of the system to room temperature before working on them They will cool faster if you first set the temperature of the heated zone to room temperat...

Page 23: ... made of refractory ceramic fibers To avoid inhaling fiber particles we recommend the following safety procedures Ventilate your work area Wear long sleeves gloves safety glasses and a disposable dust mist respirator Dispose of the insulation in a sealed plastic bag Wash your hands with mild soap and cold water after handling the insulation WARNING Combustible materials or flammable nonflammable w...

Page 24: ... remove the large round plastic cover for the GC MSD interface located on the GC left side panel In the unlikely event of an explosion this cover may dislodge WARNING The use of hydrogen H2 as a GC carrier gas detector fuel gas or in the optional JetClean system is potentially dangerous WARNING When using hydrogen H2 as the carrier gas or fuel gas be aware that hydrogen can flow into the GC oven a...

Page 25: ...should always be either connected to a column or have a cap or plug installed WARNING The MSD cannot detect leaks in the valves for the optional JetClean system It is possible that hydrogen can leak into the MSD from this cleaning system Always turn off the JetClean system close the manual hydrogen shutoff valve to the JetClean MFC and ensure good vacuum before venting the MSD Table 4 Hydrogen acc...

Page 26: ...low of carrier gas If a GC s carrier flow is not under EPC control the flow increases to its maximum This flow may be more than some mass spectrometers can pump away resulting in the accumulation of hydrogen in the mass spectrometer If the mass spectrometer is shut off at the same time the accumulation can be fairly rapid Power failure If the power fails both the GC and mass spectrometer shut down...

Page 27: ...not heat the capillary column without carrier gas flow Turn off the hydrogen at its source if a power failure occurs If a power failure occurs while the GC MSD system is unattended even if the system has restarted by itself 1 Immediately turn off the hydrogen at its source 2 Turn off the GC 3 Turn off the MSD and allow it to cool for 1 hour 4 Eliminate all potential sources of ignition in the room...

Page 28: ...D conforms to the following regulations on Electromagnetic Compatibility EMC and Radio Frequency Interference RFI CISPR 11 EN 55011 Group 1 Class A IEC EN 61326 AUS NZ This ISM device complies with Canadian ICES 001 Cet appareil ISM est conforme a la norme NMB 001 du Canada EMC declaration for South Korea This equipment has been evaluated for its suitability for use in a commercial environment Whe...

Page 29: ...ower sources and secure the unit against unintended operation Refer servicing to qualified service personnel Substituting parts or performing any unauthorized modification to the instrument may result in a safety hazard Symbols Warnings in the manual or on the instrument must be observed during all phases of operation service and repair of this instrument Failure to comply with these precautions v...

Page 30: ...evice away from the radio or television 3 Plug the device into a different electrical outlet so that the device and the radio or television are on separate electrical circuits 4 Ensure that all peripheral devices are also certified 5 Ensure that appropriate cables are used to connect the device to peripheral equipment 6 Consult your equipment dealer Agilent Technologies or an experienced technicia...

Page 31: ...down with a damp lint free cloth For recycling contact your local Agilent sales office Accidental Liquid Spillage Do not spill liquids on the MSD If liquid is accidentally spilled on the MSD first cut the power Once the MSD is disconnected from all power sources dry all affected parts If the liquid spillage affects the electronics wait at least 24 hours depending upon the ambient humidity While wa...

Page 32: ...MSD and unplug the power cord It is not necessary to allow air into the analyzer chamber 2 Turn one of the fuse holders counterclockwise until it pops out The fuse holders are spring loaded See Figure 2 on page 33 3 Remove the old fuse from the fuse holder 4 Install a new fuse in the fuse holder 5 Reinstall the fuse holder WARNING Never replace the primary fuses while the MSD is connected to a pow...

Page 33: ... Fuses 5977B Series MSD Operating Manual 33 6 Repeat steps 3 through 5 for the other fuse Always replace both fuses 7 Reconnect the MSD power cord to the electrical outlet 8 Pumpdown the MSD Figure 2 Primary fuses Primary fuses in holders ...

Page 34: ...1 Introduction To Replace the Primary Fuses 34 5977B Series MSD Operating Manual ...

Page 35: ...ightening Column Nut 42 To Install a Capillary Column in the GC MSD Interface Using a Standard Column Nut 47 To Install the GC MSD Interface Tip Seal 50 The GC MSD Interface for an 8890 Series GC 52 Before you can operate your GC MSD system you must select install and condition a GC column This chapter shows you how to install and condition a column For correct column and flow selection you must k...

Page 36: ... the GC MSD interface is essential See To Condition a Capillary Column on page 41 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 Table 5 Gas flows Feature Gas flows High v...

Page 37: ...the 5977B Series MSDs may be different from that for previous MSDs Using the procedure from another instrument may not work and may damage the column or the MSD Always use carrier gas that is at least 99 9995 pure Because of thermal expansion new ferrules may loosen after heating and cooling a few times Check for tightness after two or three heating cycles or use the self tightening column nuts Al...

Page 38: ... 3516 0 40 mm id for 0 25 mm id columns 5181 3323 0 5 mm id for 0 32 mm id columns 5062 3514 0 8 mm id for 0 53 mm id columns 5062 3512 Inlet column nut 5181 8830 for Agilent 7890 7820 and 8890 8860 GCs Magnifying loupe Septum may be old used inlet septum To install columns in other types of inlets refer to your GC User Information WARNING The GC operates at high temperatures Do not touch any part...

Page 39: ...rrule should point away from the column nut 3 Use the column cutter to score the column 2 cm or more from the end 4 While holding the column break the column end off at the score 5 Inspect the end for jagged edges or burrs If the break is not clean and even repeat steps 3 and 4 6 Wipe the outside of the free end of the column with a lint free cloth moistened with methanol 7 Position the column so ...

Page 40: ... turn The column should not slide with a gentle tug 13 Start carrier gas flow 14 Verify flow by submerging the free end of the column in isopropanol Look for bubbles See also For more information about installing a capillary column refer to Optimizing Splitless Injections on Your GC for High Performance MS Analysis Agilent Technologies publication number 5988 9944EN Figure 4 Installing a capillary...

Page 41: ...n 4 Increase the temperature at a rate of 10 to 15 C min 5 Hold at the maximum temperature for 30 minutes 6 Set the GC oven temperature to 30 C and wait for the GC to become ready 7 Attach the column to the GC MSD interface See To Install a Capillary Column in the GC MSD Interface Using the Self Tightening Column Nut on page 42 WARNING Do not condition your capillary column with hydrogen Hydrogen ...

Page 42: ... on page 44 Not used with EI SS or Inert source Knurled tip seal retainer G3870 20547 Not used with EI SS or Inert source Tip seal spring G7005 20024 Not used with EI SS or Inert source Column cutter ceramic 5181 8836 or diamond 5183 4620 Flashlight Magnifying loupe Gloves clean Large 8650 0030 Small 8650 0029 Self Tightening column nut for GC MSD interface 5190 5233 Ferrules Vespel 0 27 mm id for...

Page 43: ...gainst the column cutter with your thumb break the column against the edge of the column cutter 8 Inspect the end for jagged edges or burrs If the break is not clean and even repeat steps 6 and 7 9 Wipe the end with alcohol CAUTION Always wear clean gloves while handling any parts that go inside the GC or the analyzer chambers WARNING The analyzer GC MSD interface and other components in the analy...

Page 44: ...e Figure 5 the column extends about 1 mm from the column guide tube For an EI HES Installation See Figure 6 the column extends 4 to 5 mm from the column guide tube Use the flashlight and magnifying loupe if necessary to see the end of the column inside the analyzer chamber Do not use your finger to feel for the column end Figure 5 Installing a capillary column in the GC MSD interface for an EI EXT...

Page 45: ...alls Figure 7 Installing a capillary column in the GC MSD interface 14 Install the spring tip seal and knurled tip seal retainer on the GC MSD interface See To Install the GC MSD Interface Tip Seal on page 50 Do not use the tip seal spring and knurled tip seal retainer with an EI SS or Inert source The interface socket on these sources does not allow the tip seal installation to fit See Figure 64 ...

Page 46: ...eal When the ion source is aligned correctly the analyzer chamber can be closed all the way with no resistance except the spring tension from the interface tip seal 16 You can align the ion source and interface tip seal by wiggling the side plate on its hinge If the door still will not close contact your Agilent Technologies service representative 17 Close the analyzer chamber door See To Close th...

Page 47: ...Tightening Column Nut on page 42 Materials needed Interface tip seal G3870 20542 See Figure 5 on page 44 and Figure 6 on page 44 Not used with EI SS or Inert source Knurled tip seal retainer G3870 20547 Not used with EI SS or Inert source Tip seal spring G7005 20024 Not used with SS or Inert EI source Column cutter ceramic 5181 8836 or diamond 5183 4620 Flashlight Magnifying loupe Gloves clean Lar...

Page 48: ...the column cutter with your thumb break the column against the edge of the column cutter 8 Inspect the end for jagged edges or burrs If the break is not clean and even repeat steps 6 and 7 9 Wipe the end with alcohol CAUTION Always wear clean gloves while handling any parts that go inside the GC or the analyzer chambers WARNING The analyzer GC MSD interface and other components in the analyzer cha...

Page 49: ...nstall the spring tip seal and knurled tip seal retainer on the GC MSD interface See To Install the GC MSD Interface Tip Seal on page 50 Do not use the tip seal spring and knurled tip seal retainer with an EI SS or Inert source The interface socket on these sources does not allow the tip seal installation to fit See Figure 64 on page 199 16 Gently check the alignment of the ion source and the inte...

Page 50: ...ify that the CI source EI XTR source or HES is installed This tip seal and its spring must not be installed when an EI SS or Inert source is installed See Figure 8 on page 51 2 Remove the interface tip seal spring and knurled nut retainer from the ion source storage box In this order slide the spring tip seal and knurled tip seal retainer over the column sleeve CAUTION Electrostatic discharges to ...

Page 51: ...sed all the way with no resistance except the spring tension from the interface tip seal 5 You can align the analyzer and interface by wiggling the side plate on its hinge If the analyzer still will not close contact your Agilent Technologies service representative Figure 8 Interface tip seal Interface tip seal Knurled tip seal retainer Tip seal base CAUTION Forcing the analyzer closed if these pa...

Page 52: ...ace passes through the side of the GC and extends into the oven This end is threaded to allow connection of the column with a nut and ferrule The other end of the interface fits into the ion source The end of the capillary column extends slightly past the end of the column guide tube and into the ionization chamber Figure 9 GC MSD interface for an 8890 GC with EI XTR HES and CI sources Ionization ...

Page 53: ...The interface temperature should be slightly higher than the maximum GC oven temperature but never higher than the maximum column temperature The GC MSD interface can be used with both EI and CI sources The EI XTR HES and CI sources require a tip seal assembly The tip seal spring and knurled tip seal retainer interfere with and must be removed when using the EI SS and Inert sources See To Install ...

Page 54: ...2 Installing 8890 GC Columns The GC MSD Interface for an 8890 Series GC 54 5977B Series MSD Operating Manual ...

Page 55: ...he GC MSD Interface Tip Seal 74 The GC MSD Interface for a 9000 Series GC 76 This chapter shows you how to install an Agilent Intuvo column connect the flow path from the inlet through the guard chip bus components and column to the MS Tail assembly and maintain the column guard chip If you are using the Agilent Intuvo 9000 Gas Chromatograph with your MSD Chemical Ionization CI is not currently su...

Page 56: ...emember that column flows vary greatly with temperature requiring measurements of the actual flow to be taken Use Table 6 to determine an acceptable column flow Table 6 Gas flows Feature Gas flows High vacuum pump Diffusion Turbo Optimal He column flow mL min 1 1 to 2 Maximum recommended gas flow mL min Total gas flow into the MSD column flow plus reagent gas flow if applicable plus JetClean H2 fl...

Page 57: ...races of oxygen in the carrier gas when the column is heated To minimize column bleed all capillary columns should be conditioned before they are installed in the GC MSD interface See To Condition an Intuvo Capillary Column on page 72 Tips and hints Always use carrier gas that is at least 99 9995 pure Always wear clean gloves when handling a component s click and run connectors Always wear clean g...

Page 58: ...rrule and the fitting Instead the Intuvo 9000 GC click and run connections use a sealing system based on contact between flat surfaces Compared to traditional ferrule seals these connections are leak free and easy to make When making these seals follow a few simple guidelines Do not touch the click and run sealing surfaces with bare skin or dirty gloves Skin oils and dirt can contaminate the flow ...

Page 59: ...rom the GC panel select Maintenance Column Perform Maintenance Install Column Start Maintenance This procedure cools the inlet detector column Guard Chip and other components in the flow path heated zones to 40 C and configures the GC Follow the on screen GC prompts 2 From MassHunter Data Acquisition Vent the MSD See To Vent the MSD on page 136 3 If you are using hydrogen or other flammable gas as...

Page 60: ...D Operating Manual 4 Open the GC front door See Figure 10 5 Open the bus door and remove it by lifting the door vertically off its hinge pins 6 Lower the oven door Figure 10 9000 GC front door bus door oven door and Intuvo torque driver Bus door Oven door Intuvo torque driver Front door ...

Page 61: ...e column SmartID key from the lower USB port 9 Using the Intuvo torque driver remove the two compression bolts that seal the column s click and run connectors to the bus and store for later use 10 Remove and store the column for later use in accordance with the column manufacturer s recommendations Figure 11 9000 GC column and related parts SmartID key Column clamps Retainer ring Compression bolts...

Page 62: ...o the single column right bus fitting See the GC manual for installing 2 columns in the GC 14 Insert the column s attached Intuvo SmartID Key into the lower USB connection shown 15 Secure the new column by rotating the 1 c tab of the 4 column clamps over the column retaining ring using the Intuvo torque driver 16 Verify that the column s click and run fittings sit flat against the gasket 17 Loosel...

Page 63: ...or detector chips All chips must be installed before installing the new gasket 3 Carefully remove the new gasket from its packaging Inspect the gasket to be sure it is not deformed The two round lobes are the sealing surfaces 4 Carefully insert the round gasket lobes into the bus click and run fitting Note that the gasket is double sided 5 Place the hole in the gasket over the alignment stud in th...

Page 64: ...ard chip 2 pk G4587 60565 Multimode inlet Intuvo guard chip 2 pk G4587 60665 Split Splitless inlet Intuvo jumper chip 2 pk G4587 60575 Multimode Inlet Intuvo jumper chip 2 pk G4587 60675 Intuvo gasket polyimide 5 pk for temperatures 350 C 5190 9072 Intuvo gasket nickel 5 pk for temperatures 350 C to 450 C 5190 9073 Intuvo torque driver stored on oven door 5190 9571 7 16 inch open end wrench Proced...

Page 65: ... See To Vent the MSD on page 136 3 Wait until the GC reaches the ready state indicating the components are cooled below 40 C and the instrument is vented before continuing the steps in this procedure 4 If you are using hydrogen or other flammable gas as a carrier gas or for the JetClean system close the manual gas supply valve to the instrument before turning off the MSD power 5 If installed remov...

Page 66: ...que driver 13 Lift the right side of the Guard Chip tab over the boss then rotate it out of the bus connection 14 Remove the left side of the Guard Chip from the inlet base 15 Install a new Guard Chip The larger end of the Guard Chip inserts into the inlet base first then the smaller end is rotated into the bus connection lifting its tab over the boss and into the bus mounting slot 16 Finger tight...

Page 67: ...the provided torque driver until you hear one click 21 Install the inlet cover 22 Install the bus door on its hinges and close it 23 Close the GC front door 24 If removed install the ALS injector CAUTION Use the Intuvo torque driver to tighten the compression bolt until you hear one click Over tightening can damage the flow path strip the fittings and cause leaks ...

Page 68: ...er stored on oven door 5190 9571 7 16 inch open end wrench Procedure 1 Vent the MSD See To Vent the MSD on page 136 When prompted set the temperature for the ion source quads inlet detector column Guard Chip 9000 GC MS Tail and other components in the flow path heated zones to 40 C 2 If you are using hydrogen or other flammable gas as a carrier gas close the manual gas supply valve to the instrume...

Page 69: ...be difficult to tighten 7 Open the GC front door 8 Open the bus door and remove it by lifting the door vertically off its hinge pins 9 Using the Intuvo torque driver remove the compression bolt that secures the 9000 GC MS Tail click and run bus connection Also remove the bolt from the empty bus connection See Figure 14 10 Open the MS tail heater assembly by loosening the thumb screw at the top of ...

Page 70: ...D interface and gently place the click and run connection into the bus connection 15 Check that the 9000 GC MS Tail click and run fitting sits flat against the gasket in the bus connection 16 Screw the 9000 GC MS Tail column nut to the transfer line threaded connector finger tight then use a inch wrench to tighten the nut an additional 20 to 30 degrees 17 Loosely install the two compression bolts ...

Page 71: ...e 74 The interface tip seal spring and knurled tip seal retainer are not used with EI SS or Inert source 25 Gently check the alignment of the ion source and the interface tip seal When the ion source is aligned correctly the front analyzer chamber can be closed all the way with no resistance except the spring tension from the interface tip seal 26 You can align the ion source and interface tip sea...

Page 72: ...conditioning See To Replace an Intuvo GC Column on page 59 2 Set a minimum velocity of 30 cm s or as recommended by the column manufacturer Allow gas to flow through the column at room temperature for 15 to 30 minutes to remove air 3 Increase the column temperature to 120 C 4 Hold at the this temperature for 30 minutes 5 Use MassHunter to run an air and water check Proceed to the next step if the ...

Page 73: ...olumn temperature to increase from 120 C to the maximum temperature limit for the column at a rate of 10 to 15 C min 7 Hold at the maximum temperature for 30 minutes The column is conditioned and ready to be used with your method CAUTION Never exceed the maximum column temperature in the GC MSD interface the GC oven or the inlet ...

Page 74: ...hat the CI source EI XTR source or HES is installed The tip seal spring and knurled tip seal retainer must not be installed when an EI SS or Inert source is installed See Figure 17 on page 75 2 Remove the interface tip seal spring and knurled nut retainer from the ion source storage box In this order slide the spring tip seal and knurled tip seal retainer over the column sleeve CAUTION Electrostat...

Page 75: ...ed all the way with no resistance except the spring tension from the interface tip seal 5 You can align the analyzer and interface by wiggling the side plate on its hinge If the analyzer still will not close contact your Agilent Technologies service representative Figure 17 GC MSD interface tip seal Interface tip seal Knurled tip seal retainer Tip seal base CAUTION Forcing the analyzer closed if t...

Page 76: ...s slightly past the end of the column guide tube and into the ionization chamber The 9000 GC MS Tail maintains temperature at several points along its length by a heated bus an MS tail heater assembly and the GC MSD Interface The 9000 GC MS Tail is heated by an electric cartridge heater The heater is powered and controlled by a heated zone of the 9000 GC The 9000 GC MS Tail temperature can be set ...

Page 77: ...nstall a Capillary Column in the GC MSD Interface Using a Standard Column Nut 89 To Install the GC MSD Interface Tip Seal 93 To Calibrate Column Flow Linear Velocity in a 7890 GC 95 The GC MSD Interface for a 7890B Series GC 98 Before you can operate your GC MSD system you must select install and condition a GC column This chapter shows you how to install and condition a column For correct column ...

Page 78: ...on page 95 for instructions on how to measure actual flow in your column Use the Flow Calculation software and Table 7 to determine whether a given column will give acceptable flow with realistic head pressure Table 7 Gas flows Feature Gas flows High vacuum pump Diffusion Turbo Optimal He column flow mL min 1 1 to 2 Maximum recommended gas flow mL min Total gas flow into the MSD column flow plus r...

Page 79: ...from the ferrules Thermal cycling ferrules to their maximum operating temperatures prior to running your application will help reduce leaks from the assembly Tips and hints The column installation procedures for the 5977B Series MSDs may be different from that for previous MSDs Using the procedure from another instrument may not work and may damage the column or the MSD Always use carrier gas that...

Page 80: ... 3516 0 40 mm id for 0 25 mm id columns 5181 3323 0 5 mm id for 0 32 mm id columns 5062 3514 0 8 mm id for 0 53 mm id columns 5062 3512 Inlet column nut 5181 8830 for Agilent 7890 7820 and 8890 8860 GCs Magnifying loupe Septum may be old used inlet septum To install columns in other types of inlets refer to your GC User Information WARNING The GC operates at high temperatures Do not touch any part...

Page 81: ...rrule should point away from the column nut 3 Use the column cutter to score the column 2 cm or more from the end 4 While holding the column break the column end off at the score 5 Inspect the end for jagged edges or burrs If the break is not clean and even repeat steps 3 and 4 6 Wipe the outside of the free end of the column with a lint free cloth moistened with methanol 7 Position the column so ...

Page 82: ...2 turn The column should not slide with a gentle tug 13 Start carrier gas flow 14 Verify flow by submerging the free end of the column in isopropanol Look for bubbles See also For more information about installing a capillary column refer to Optimizing Splitless Injections on Your GC for High Performance MS Analysis Agilent Technologies publication number 5988 9944EN Figure 20 Installing a capilla...

Page 83: ...n 4 Increase the temperature at a rate of 10 to 15 C min 5 Hold at the maximum temperature for 30 minutes 6 Set the GC oven temperature to 30 C and wait for the GC to become ready 7 Attach the column to the GC MSD interface See To Install a Capillary Column in the GC MSD Interface Using the Self Tightening Column Nut on page 84 WARNING Do not condition your capillary column with hydrogen Hydrogen ...

Page 84: ...2 on page 86 Not used with EI SS or Inert source Knurled tip seal retainer G3870 20547 Not used with EI SS or Inert source Tip seal spring G7005 20024 Not used with EI SS or Inert source Column cutter ceramic 5181 8836 or diamond 5183 4620 Flashlight Magnifying loupe Gloves clean Large 8650 0030 Small 8650 0029 Self Tightening column nut for GC MSD interface 5190 5233 Ferrules Vespel 0 27 mm id fo...

Page 85: ...g the column against the column cutter with your thumb break the column against the edge of the column cutter 8 Inspect the end for jagged edges or burrs If the break is not clean and even repeat steps 6 and 7 CAUTION Always wear clean gloves while handling any parts that go inside the GC or the analyzer chambers WARNING The analyzer GC MSD interface and other components in the analyzer chamber op...

Page 86: ...tallation See Figure 21 the column extends about 1 mm from the column guide tube For an EI HES Installation See Figure 22 the column extends 4 to 5 mm from the column guide tube Use the flashlight and magnifying loupe if necessary to see the end of the column inside the analyzer chamber Do not use your finger to feel for the column end Figure 21 Installing a capillary column in the GC MSD interfac...

Page 87: ...14 Install the spring tip seal and knurled tip seal retainer on the GC MSD interface See To Install the GC MSD Interface Tip Seal on page 93 Do not use the interface tip seal spring and knurled tip seal retainer with an EI SS or Inert source The interface socket on these sources does not allow the tip seal installation to fit See Figure 56 on page 180 Figure 23 Installing a capillary column in the...

Page 88: ...eal When the ion source is aligned correctly the analyzer chamber can be closed all the way with no resistance except the spring tension from the interface tip seal 16 You can align the ion source and interface tip seal by wiggling the side plate on its hinge If the door still will not close contact your Agilent Technologies service representative 17 Close the analyzer chamber door See To Close th...

Page 89: ...ightening Column Nut on page 84 Materials needed Interface tip seal G3870 20542 See Figure 21 on page 86 and Figure 22 on page 86 Not used with EI SS or Inert source Knurled tip seal retainer G3870 20547 Not used with EI SS or Inert source Tip seal spring G7005 20024 Not used with SS or Inert EI source Column cutter ceramic 5181 8836 or diamond 5183 4620 Flashlight Magnifying loupe Gloves clean La...

Page 90: ...olumn against the column cutter with your thumb break the column against the edge of the column cutter 8 Inspect the end for jagged edges or burrs If the break is not clean and even repeat steps 6 and 7 CAUTION Always wear clean gloves while handling any parts that go inside the GC or the analyzer chambers WARNING The analyzer GC MSD interface and other components in the analyzer chamber operate a...

Page 91: ...h the oven walls 13 Tighten the nut 1 4 to 1 2 turn 14 Check the nut s tightness after one or two heat cycles tighten additionally as appropriate 15 Install the spring tip seal and knurled tip seal retainer on the GC MSD interface See To Install the GC MSD Interface Tip Seal on page 93 Do not use the interface tip seal spring and knurled seal tip retainer with an EI SS or Inert source The interfac...

Page 92: ... Nut 92 5977B Series MSD Operating Manual 17 You can align the ion source and interface tip seal by wiggling the side plate on its hinge If the door still will not close contact your Agilent Technologies service representative 18 Close the analyzer chamber door See To Close the Analyzer Chamber on page 220 ...

Page 93: ... and HES is installed This tip seal and its spring must not be installed when an EI SS or Inert source is installed See Figure 22 on page 86 2 Remove the interface tip seal spring and knurled nut retainer from the ion source storage box In this order slide the spring tip seal and knurled tip seal retainer over the column sleeve 3 Thread the knurled tip seal retainer into the tip seal base finger t...

Page 94: ...the spring tension from the interface tip seal 5 You can align the analyzer and interface by wiggling the side plate on its hinge If the analyzer still will not close contact your Agilent Technologies service representative Figure 24 GC MSD interface tip seal Interface tip seal Knurled tip seal retainer Tip seal base CAUTION Forcing the analyzer closed if these parts are misaligned will damage the...

Page 95: ... up a real time plot to monitor m z 28 2 Press Prep Run on the GC keypad 3 Inject 1 µL of air into the GC inlet and press Start Run 4 Wait until a peak elutes at m z 28 Note the retention time 5 In the Instrument Control view select GC Parameters from the Instrument menu 6 Select the Configuration tab and then select the Columns tab 7 Select your installed column from the table 8 Click Calibrate t...

Page 96: ...ters that are different than those used in your method 11 Enter the recorded retention time in the Holdup Time field Move the cursor to another parameter s field and the calibrated column length appears 12 Click OK to save the changes and exit the dialog 13 Click OK on the Calibrate Columns dialog to save the calibration With capillary columns such as those used with the MSD linear velocity is oft...

Page 97: ...alculation for average linear velocity Average linear velocity cm s where L Length of the column in meters t Retention time in seconds Calculation for volumetric flow rate Volumetric flow rate mL min where D Internal column diameter in millimeters L Column length in meters t Retention time in minutes 100 L t 0 785 D 2 L t ...

Page 98: ...ace passes through the side of the GC and extends into the oven This end is threaded to allow connection of the column with a nut and ferrule The other end of the interface fits into the ion source The end of the capillary column extends slightly past the end of the column guide tube and into the ionization chamber Figure 26 GC MSD interface for a 7890B GC with EI XTR HES and CI sources Ionization...

Page 99: ...The interface temperature should be slightly higher than the maximum GC oven temperature but never higher than the maximum column temperature The GC MSD interface can be used with both EI and CI sources The EI XTR HES and CI sources require a tip seal assembly The tip seal spring and knurled tip seal retainer interfere with and must be removed when using the EI SS and Inert sources See To Install ...

Page 100: ...4 Installing 7890 GC Columns The GC MSD Interface for a 7890B Series GC 100 5977B Series MSD Operating Manual ...

Page 101: ...enting the MSD 116 To View MSD Temperature and Vacuum in Manual Tune 117 To Set Monitors for MSD Temperature and Vacuum Status 119 To Set Analyzer Temperatures from the Instrument Control View 122 To Set the GC MSD Interface Temperature from MassHunter 124 To Monitor High Vacuum Pressure 125 To Tune the MSD in EI Mode 127 To Set the Operation Mode for the Optional JetClean System 129 To Set the Je...

Page 102: ...ating Manual This chapter describes how to perform some basic operating procedures for the Agilent 5977B Series GC MSD using EI If you are using the Agilent Intuvo 9000 Gas Chromatograph with your MSD Chemical Ionization CI is not currently supported ...

Page 103: ...ures tuning and venting the MSD These tasks are described in this chapter Additional information is described in the manuals and online help supplied with the Agilent MassHunter GC MS Acquisition software CAUTION The software and firmware are revised periodically If the steps in these procedures do not match your Agilent MassHunter GC MS Acquisition software refer to the manuals and online help su...

Page 104: ...nting and setting temperatures right from the GC control panel Limited features are available from the GC control panel The Agilent MassHunter GC MS Acquisition software is the full featured controller for most instrument control operations MSD designated key on the GC control panel The MS Aux Det key on the 7890B GC control panel allows access to control and configuration parameters on the MSD Se...

Page 105: ... 3 Use GC keypad to enter the desired temperature 4 Press Enter to apply the changes To view MSD vacuum pressure and Turbo speed Foreline Pressure from the GC control panel 1 Press MS Aux Det to display the 5977B MSD menu 2 Press the down arrow to scroll to HiVac Pressure or Turbo Speed of full Foreline Pressure To vent the MSD from the GC control panel 1 With the MSD pumped down press MS Aux Det ...

Page 106: ...er the new IP address for the MSD then press Enter to complete the entry 3 Wait for the GC to display the new IP address Reboot the MSD or proceed to the gateway address with the down arrow 4 Press the down arrow to scroll to GW and use the GC keypad to enter the new gateway address for the LAN and press Enter to complete the entry 5 Press the down arrow to scroll to SW and use the GC keypad to en...

Page 107: ...bling BOOTP causes the server to automatically assign an IP address to the MSD 1 Press Config and then press MS Aux Det to bring up the CONFIGURE MS DETECTOR menu 2 Press the down arrow to scroll to MSD BOOTP 3 To enable BOOTP press On Yes To disable BOOTP press Off No 4 Wait for the MSD to confirm the change on the GC control panel 5 Reboot the MSD See To reboot the MSD from the GC control panel ...

Page 108: ...an Agilent 8890 7890B or 7890A model with the correct firmware To change the network settings of the MSD This procedure assumes that the operator has access to a PC located on the same LAN subnet as the MSD 1 Open the top hinged cover on the MSD for accessing the analyzer to view the eModule mini display readout 2 Press the MSD On Off switch to start the instrument When the instrument has complete...

Page 109: ...s MSD Operating Manual 109 4 Enter the IP address into a PC web browser URL to display the WUI page See Figure 28 5 Click Set Real Time Clock or Edit NetConfig and go to Edit NetConfig MSD network configuration See Figure 29 Figure 28 WUI main menu Figure 29 WUI Edit NetConfig ...

Page 110: ...alues Before clicking submit you can recover the previous settings by clicking Return to Main Menu and then returning here 8 Click Submit to upload this net configuration to the MSD A dialog opens to confirm that the network configuration process has started See Figure 30 9 Click OK to close the dialog and wait for the prompt requesting to Manually reboot of the MSD SmartCard to activate the new S...

Page 111: ...display accessible when the analyzer door cover is open allows the operator to view the LAN configuration of the instrument including its IP address subnet mask default gateway and MAC address This LAN configuration can be changed using the GC control panel or the web user interface WUI from a web browser Figure 31 eModule mini display ...

Page 112: ...of the instrument using color codes and LED on off timing See Table 8 Table 8 Front panel Instrument Status LED codes Instrument status LED code Ready Solid green Acquiring data Blinking green 2 sec Not ready Solid yellow JetClean Acquire Clean operation Blinking magenta JetClean Clean Only operation Solid magenta Ready and not connected to DS Solid blue Start up prior to FW load Blinking red 2 se...

Page 113: ...rged of any gas to remove oxygen from the system If hydrogen is used as carrier gas or JetClean system supply the carrier gas and JetClean system supply shutoff valves must be closed and the analyzer top sideplate thumbscrew must be loosely fastened The foreline pump exhaust is properly vented WARNING The exhaust from the foreline pump contains solvents and the chemicals you are analyzing If using...

Page 114: ...SD will shut down if it cannot pumpdown correctly Using the menus or MSD monitors the DS can display Motor speed for turbo pump MSDs percent spin speed Foreline pressure for diffusion pump MSDs Analyzer chamber pressure vacuum for MSDs with the optional G3397B Micro Ion Gauge Controller The 8890 and 7890B GC control panels also display this data Controlling Temperatures MSD temperatures are contro...

Page 115: ...other unretained chemical and time how long it takes to reach the MSD With this time measurement you can calculate the column flow See To Calibrate Column Flow Linear Velocity in a 7890 GC on page 95 as appropriate For an 8890 GC see the 8890 GC Operating Manual Controlling JetClean Hydrogen Flow The JetClean option uses hydrogen gas for cleaning the ion source The JetClean system MFC sends hydrog...

Page 116: ...ore you vent the MSD A temperature of 100 C is hot enough to burn skin always wear cloth gloves when handling analyzer parts WARNING If hydrogen is used as a carrier gas or JetClean system supply the carrier and JetClean system supply shutoff valves must be closed before turning off the MSD power If the foreline pump is off hydrogen will accumulate in the MSD and an explosion may occur Read Hydrog...

Page 117: ...el to perform this task See Operating the MSD from the 7890 GC Control Panel on page 104 For an 8890 GC see the 8890 GC Operating Manual Procedure 1 In Instrument Control view select Edit Tune Parameters from the Instrument menu to display the Manual Tune dialog 2 Click the Values tab to view the MSD Temperatures and Vacuum See Figure 32 and Figure 33 on page 118 Figure 32 Manual tune values tab ...

Page 118: ... or the turbo pump is 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 on at the end of the pumpdown cycle and turn off at the beginning of the vent cycle The reported setpoints will not change during...

Page 119: ...color if the actual parameter varies beyond a user determined limit from its setpoint Procedure 1 In Instrument Control view select Edit Monitors from the Instrument menu to display the Select Monitors dialog See Figure 34 2 In the Available Monitors column select a monitor and click Add to move the selection to the Selected Monitors column Repeat for additional monitors 3 Click OK The new monitor...

Page 120: ... To Set Monitors for MSD Temperature and Vacuum Status 120 5977B Series MSD Operating Manual 4 Select Window Arrange Monitors or click and drag each monitor to the desired position See Figure 35 Figure 35 Arranging monitors ...

Page 121: ...pen that monitor s dialog for setting alarms See Figure 36 a Select the Set Alarm check box b Set the Warning Level Alarm Level and Below Minimum to appropriate values c Enter descriptive text in the Monitor Label field if the default label is not appropriate d Click OK to finish the monitor s alarm configuration 6 To make the new settings part of the method save the Method Figure 36 Monitor s ala...

Page 122: ... select MS Temperatures from the Instrument menu See Figure 37 2 Enter the MS Source and MS Quad mass filter temperatures in the Setpoint and Limit fields See Table 9 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 different from that of an adjacent zone Figure 37 MS te...

Page 123: ...ure parameters to the currently loaded tune file and download these parameters to the MSD click Apply 4 Click Close to exit the dialog If changes were made to any parameters the Save MS Tune File dialog displays Click OK to save your changes to the same file or type a new file name and click OK Click Cancel to discard the edit made to any parameter ...

Page 124: ...t On to turn on the heater and type the setpoint in the Value C column The typical setpoint is 280 C 4 Click Apply to download setpoints or click OK to download setpoints and close the window 5 To make the new settings part of the method select Save from the Method menu Figure 38 8890 GC edit parameters window CAUTION Ensure that the carrier gas is turned on and the column has been purged of air b...

Page 125: ...ge 139 3 In the Tune and Vacuum Control view select Turn Vacuum Gauge on off from the Vacuum menu 4 Select Manual Tune from the Parameters menu to display the Manual Tune dialog 5 Select the Values tab to view the HiVac reading See Figure 39 WARNING If you are using hydrogen as a carrier gas or for the JetClean system the hydrogen gas flow must be off before turning off the MSD power If the foreli...

Page 126: ... GC MS Acquisition software for information on troubleshooting air leaks and other vacuum problems In the Instrument Control view you can set up an MSD Monitor for displaying this vacuum reading The vacuum can also be read on the 8890 or 7890 Series GC control panel or from the Manual Tune screen Table 10 Ion vacuum gauge reading Column flow rate mL min Optional gauge reading Torr Turbo pump Gauge...

Page 127: ...file select MS Tune File from the Instrument menu to display the Select Tune File dialog The Settings area displays the important parameters for a selected tune file The tune file must match the type of ion source in the analyzer If you are using an EI source select a tune file created for an EI source 4 Click the MS Tune icon to display the Select Tune Type dialog See Figure 40 5 Select Tune MSD ...

Page 128: ...from the Checkout menu in Instrument Control view To view history of tune results in the Instrument Control view select Checkout View Previous Tunes To manually tune your MSD or to perform special autotunes from the View menu select Tune and Vacuum Control view See the manuals and online help provided with your Agilent MassHunter GC MS Acquisition software for additional information about tuning ...

Page 129: ...l JetClean System Procedure 1 In Instrument Control view click the MS Parameters icon 2 In the Single Quadrupole MS Method Editor navigation panel select the JetClean tab See Figure 41 3 From the Operation dropdown menu select a mode For detailed information on the JetClean system see the JetClean Operating manual Figure 41 Selecting the JetClean Operation mode ...

Page 130: ...rs for the Clean Only Mode Procedure 1 In Instrument Control view click the MS Parameters icon 2 In the Single Quadrupole MS Method Editor select the JetClean tab See Figure 42 3 From the Operation dropdown menu select Clean Only 4 Enter the parameters supplied by your method developer 5 Save the method Figure 42 JetClean set to Clean Only mode ...

Page 131: ...d then select Evaluate Tune from the Checkout menu The software will evaluate the last autotune and print a System Verification Tune report Verify the sensitivity performance 1 Set up to inject 1 µL of the checkout sample shown in the Materials needed for your source type above either with the ALS or manually 2 In the Instrument Control view select Sensitivity Check from the Checkout menu The syst...

Page 132: ... MSD See To Tune the MSD in EI Mode on page 127 2 Resolve the PFHT M method under MassHunter MSD x methods checkout PFHT M where x is the instrument number being used 3 Update and save the method 4 Load the PFHT calibration sample into a vial and place in position 2 5 In Instrument Control view select High Mass Check from the Checkout menu 6 Follow the instructions on screen 7 The run is completed...

Page 133: ...5 Operating in EI Mode To Perform High Mass Testing 5977B Series MSD Operating Manual 133 Figure 43 PFHT high mass report ...

Page 134: ... then click the Amu Offset sub tab 4 Select the Enable This Lens checkbox 5 Enter the recommend dynamic offset Voltage V and click OK 6 Click Save to save this dynamic Amu Offset for the high mass You can overwrite the existing autotune file to include high mass adjustment or save this file to a new name for example ATUNEHIGH U When an autotune is performed it will overwrite this dynamic Amu Offse...

Page 135: ...lightly forward and lift it off the MSD See Figure 44 Pull the handle on the side of the MSD to the left and down to release the magnetic latch and open the cover The cover is held in place by its hinges See Figure 44 CAUTION Do not use excessive force or the plastic tabs that hold the cover to the mainframe will break off Figure 44 5977B MSD covers Analyzer window cover Handle Analyzer cover WARN...

Page 136: ...OMM communication between the GC and MSD in Instrument Control view select GC Parameters from the Instrument menu to display the GC Edit Parameters dialog Select Oven and set the oven temperature to room temperature Also select Aux Heaters MSD Transfer line and Inlets and set those temperatures to room temperature Click OK to close the dialog and send this temperature to the GC WARNING If hydrogen...

Page 137: ... supports DCOMM MassHunter will load the Fast Vent method to turn off the GC oven and interface heaters the source and quad heaters and the turbo pump If your system does not support DCOMM or if DCOMM has been disabled when prompted set the GC MSD interface heater and the GC oven temperatures to ambient room temperature 5 Turn off the MSD by pressing the power switch See Figure 1 on page 19 6 Unpl...

Page 138: ...he hissing sound of air flowing into the analyzer chamber See Figure 46 Do not turn the knob too far or the O ring may fall out of its groove WARNING Neveropentheventvalvewithoutfirstclosingthehydrogensupplylinetoallpossible sourcesofhydrogenentrytotheanalyzer Thisrequiresclosingthehydrogenshutoff valvetothecarriergas flowmoduleandtheshutoffvalveto theJetClean system supplyifeitherofthese hydrogen...

Page 139: ...he MSD on page 113 Failure to do so can result in personal injury WARNING Never open the vent valve without first closing the hydrogen supply line to all possible sources of hydrogen entry to the analyzer This requires closing the hydrogen shutoff valve to the carrier gas flow module and the shutoff valve to the JetClean system supply if either of these hydrogen sources exist on the instrument Rea...

Page 140: ...ont of the MSD 7 Press lightly on the side board to ensure a correct seal Press on the metal box on the side board 8 Close the vent valve when it makes a hissing sound See Figure 47 The foreline 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 v...

Page 141: ...n the ion source and mass filter quad heaters The temperature setpoints are stored in the current autotune u file 13 After the message Okay to run appears wait 2 hours for the MSD to reach thermal equilibrium Data acquired before the MSD has reached thermal equilibrium may not be reproducible 14 If using the JetClean system prepare the hydrogen system for use Refer to the JetClean system Operating...

Page 142: ...5 Operating in EI Mode To Pumpdown the MSD 142 5977B Series MSD Operating Manual ...

Page 143: ... Verify NCI Performance 164 To Monitor CI Mode High Vacuum Pressure 165 This chapter provides information and instructions for operating the 5977B Series CI MSDs in CI mode Most of the information in the preceding chapter is also relevant Most of the material is related to methane CI but one section discusses the use of other reagent gases The software contains instructions for setting the reagent...

Page 144: ...pure Always verify the MSD is performing well in EI mode before switching to CI See To Verify EI System Performance on page 131 Ensure the CI source and GC MSD interface tip seal are installed Ensure the reagent gas plumbing has no air leaks This is determined in PCI mode checking for m z 32 after the methane pretune Ensure the reagent gas inlet line is equipped with gas purifiers not applicable f...

Page 145: ...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 EMV at or above 2600 V however indicates a problem If your method requires EMV set at 400 you may not have adequate sensitivity in your data acquisition CAUTION After the source is changed from ...

Page 146: ...V 70 eV Filament 1 1 1 1 1 1 1 or 2 Repeller 3 V 3 V 3 V 3 V 3 V 3 V 30 V Ion focus 130 V 130 V 130 V 130 V 130 V 130 V 90 V Entrance lens offset 20 V 20 V 20 V 20 V 20 V 20 V 25 V EM volts 1200 1400 1200 1400 1200 1400 1300 Shutoff valve Open Open Open Open Open Open Closed Gas select 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 ...

Page 147: ...ratio in the methane flow adjust panel Determine if a gross air leak is present by monitoring the ions at m z 19 protonated water and 32 Confirm that the MSD 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 It is difficult to diagnose an air leak and difficult to tell whethe...

Page 148: ...alog click the Values tab to monitor that the pressure is decreasing Hi Vac gauge option installed 3 In the Manual Tune dialog click the CI Gas tab then in the Valve Settings area close Gas Valve A Gas Valve B and the ShutOff Valve 4 Verify that PCICH4 U is loaded top left in Manual Tune dialog and click the Values tab to accept the temperature setpoints Always start up and verify system performan...

Page 149: ...ee Table 13 for default values for the Tune Control Limits box These limits are used by Autotune only They should not be confused with the parameters set in Edit MS Parameters or with those appearing on the tune report Notes for Table 13 N A Not available There are no PFDTD ions formed in PCI with any reagent gas but methane hence CI autotune is not available with these configurations CAUTION Alwa...

Page 150: ...ce Higher signal abundance also gives higher noise abundance This is adjusted for data acquisition by setting the EMV in the method Peakwidth target Higher peakwidth values give better sensitivity lower values give better resolution Maximum emission current Optimum emission current maximum for NCI is very compound specific and must be selected empirically Optimum emission current for pesticides fo...

Page 151: ...ttings for controlling the CI gas flow See Figure 49 CAUTION After the system has been switched from EI to CI mode or vented for any other reason the MSD must be baked out for at least 2 hours before tuning CAUTION Continuing with CI autotune if the MSD has an air leak or large amounts of water will result in severe ion source contamination If this happens you need to vent the MSD and clean the io...

Page 152: ... the shutoff valve is closed The CI flow control module The CI reagent gas flow control module regulates the flow of reagent gas into the CI GC MSD interface The flow module consists of a MFC gas select valves CI calibration valve shutoff valve control electronics and plumbing See Figure 50 and Table 14 on page 153 The back panel provides Swagelok inlet fittings for methane CH4 and one OTHER reage...

Page 153: ...ly Gas A select valve Gas B select valve MFC Calibration valve Restrictor Calibration vial Shutoff valve GC MSD interface GC column CI source Table 14 Flow control module state diagram Result Gas A flow Gas B flow Purge with Gas A Purge with Gas B Pump out flow module Standby vented or EI mode Gas A Open Closed Open Closed Closed Closed Gas B Closed Open Closed Open Closed Closed MFC On setpoint O...

Page 154: ... Source on page 250 4 Pump out the system See To Pumpdown the MSD in CI Mode on page 148 5 Wait until the pressure is near the previously recorded pressure for the EI autotune See To Monitor CI Mode High Vacuum Pressure on page 165 6 Select Bake out MSD from the Manual Tune view in the Execute menu to display the Specify Bake Out parameters dialog Set a minimum time of 2 hours adjust the other par...

Page 155: ... CI mode with an air leak will rapidly contaminate the ion source The peak at m z 19 protonated water is less than 50 of the peak at m z 17 9 When prompted click OK to perform the methane Flow Adjust Methane pretune 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 ...

Page 156: ...life span of the filament CAUTION Not all setup operations can be performed in all modes with all reagent gases See Table 15 for details Table 15 Reagent gases Reagent gas mode Reagent ion masses PFDTD Calibrant ions Flow adj ions Ratio EI PCI NCI MSD Turbo pump Recommended flow 20 PCI 40 NCI Methane PCI 17 29 41 41 267 599 28 27 1 5 5 0 Methane NCI 17 35 235 185 351 449 N A Isobutane PCI 39 43 57...

Page 157: ...t proton affinities ammonia CI 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 corresponding to NH4 NH4 NH3 and NH4 NH3 2 To adjust your MSD for isobutane or ammonia CI use the following procedure Procedure 1 Perform a standard PCI autotune with methane and PFDTD See To Perfor...

Page 158: ...Troubleshooting and Maintenance Manual 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 CI while minimizing its negative effects Carbon Dioxide CI Carbon dioxide is often used as a reagent gas for CI It has obvious advantages of availability and safety CAUTION Use of ammonia affects the maintenance requir...

Page 159: ...Gas Flow on page 154 5 Under the Tune menu click CI Autotune There are no tune performance criteria If autotune completes it passes See Figure 52 on page 160 If the tune sets the EMV at or above 2 600 V however you may not be able to acquire data successfully if your method sets EMV to 400 or higher The autotune report contains information about air and water in the system See PCI autotune report ...

Page 160: ...6 Operating in CI Mode To Perform a PCI Autotune Methane Only 160 5977B Series MSD Operating Manual Figure 52 PCI autotune report ...

Page 161: ... the existing values 3 Under the Tune menu click CI Autotune There are no tune performance criteria If autotune completes it passes See Figure 53 on page 162 If the tune sets the EMV at or above 2 600 V however you may not be able to acquire data successfully if your method sets EMV to 400 or higher CAUTION Always verify MSD performance in EI before switching to CI operation See To Verify EI Syste...

Page 162: ...6 Operating in CI Mode To Perform an NCI Autotune Methane Reagent Gas 162 5977B Series MSD Operating Manual Figure 53 NCI autotune ...

Page 163: ...rform CI setup See To Perform a PCI Autotune Methane Only on page 159 5 Run CI Autotune See CI Autotune on page 145 6 Run the PCI sensitivity method BENZ_PCI M using 1 µL of 100 pg µL benzophenone 7 Verify that the system conforms to the published sensitivity specification Please refer to the Agilent Web site at www agilent com chem for specifications CAUTION Always verify MSD performance in EI be...

Page 164: ...w run CI Autotune See To Perform an NCI Autotune Methane Reagent Gas on page 161 Note that there are no criteria for a passing Autotune in CI If the Autotune completes it passes 5 Run the NCI sensitivity method OFN_NCI M using 2 µL of 100 fg µL OFN 6 Verify that the system conforms to the published sensitivity specification Please refer to the Agilent Web site at www agilent com chem for specifica...

Page 165: ...essures for various helium carrier gas flows are approximate and vary from instrument to instrument See Table 16 on page 166 Typical pressure readings Use the G3397B Micro Ion vacuum gauge Note that the MFC is calibrated for methane and the vacuum gauge is calibrated for nitrogen so these measurements are not accurate but are intended as a guide to typical observed readings See Table 16 on page 16...

Page 166: ...t 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 Table 16 MFC settings and typical pressure readings MFC Pressure Torr Methane Ammonia EI PCI NCI MSD Turbo pump EI PCI NCI MSD Turbo pump 10 5 5 10 5 5 0 10 5 15 8 0 10 5 7 0 10 5 20 1 0 10 4 8 5 10 5 25 1 2 10 4 1 0 10 4 30 1 5 1 4 1 2 10 4 35 2 0 10 4 1 5 10 4 40 2 5 ...

Page 167: ... the EI XTR SS or Inert Source 196 To Connect Disconnect Wiring from the EI XTR SS and Inert Sources 197 To Disassemble the EI SS or EI Inert Source 198 To Disassemble the EI XTR Source 201 To Clean an EI XTR SS or Inert Source 204 To Assemble an EI SS or Inert Source 209 To Assemble the EI XTR Source 212 To Replace a Filament in an EI XTR SS or Inert Source 215 To Install the EI XTR SS or Inert S...

Page 168: ...ery 6 months Replace the foreline pump oil Every 3 months for CI MSDs using ammonia reagent gas Every 6 months Replace the diffusion pump fluid Every year Change the dry foreline pump tip seal Every year Check the dry foreline pump As needed Tune the MSD As needed Change the foreline pump exhaust filter As needed Clean the ion source As needed Check the carrier gas trap s on the GC and MSD As need...

Page 169: ...ers the instrument and the power switch When the power switch is on potentially dangerous voltages exist on Electronic circuit boards Toroidal transformer Wires and cables between these boards Wires and cables between these boards and the connectors on the back panel of the MSD Some connectors on the back panel for example the foreline power receptacle Normally all of these parts are shielded by s...

Page 170: ...e exhaust from the foreline pump will contain traces of the carrier gas and your samples Exhaust from the standard foreline pump also contains tiny droplets of foreline pump oil An oil trap is supplied with the standard 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 this oil trap For ...

Page 171: ...he 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 ca...

Page 172: ...a conductive metal part of the assembly being worked on but not to electronic components exposed wires or traces or pins on connectors Take extra precautions such as a grounded antistatic mat if you must work on components or assemblies that have been removed from the MSD This includes the analyzer CAUTION To be effective an antistatic wrist strap must fit snugly not tight A loose strap provides l...

Page 173: ...ine pump seals once a year Failure to perform these tasks as scheduled can result in decreased instrument performance It can also result in damage to your instrument Other procedures Tasks such as replacing a foreline vacuum gauge or Micro Ion vacuum gauge should be performed only when needed Refer to the Agilent 5977B Series MSD Troubleshooting and Maintenance manual and the online help in Agilen...

Page 174: ...ssHunter GC MS Acquisition software provides more extensive information Precautions Cleanliness Keep components clean during analyzer maintenance Analyzer maintenance involves opening the analyzer chamber and removing parts from the analyzer During analyzer maintenance procedures take care to avoid contaminating the analyzer or the interior of the analyzer chamber Wear clean gloves during all anal...

Page 175: ...ver be disturbed In the event of extreme contamination it can be cleaned but such cleaning should only be done by a trained Agilent Technologies service representative The HED ceramic insulator must never be touched More information is available If you need more information about the locations or functions of analyzer components refer to the Agilent 5977B Series MSD Troubleshooting and Maintenance...

Page 176: ... Open the MSD Covers on page 135 3 Loosen the analyzer side plate thumbscrews if they are fastened See Figure 54 on page 177 CAUTION Electrostatic discharges to analyzer components are conducted to the quad driver board where they can damage sensitive components Wear a grounded antistatic wrist strap and take other antistatic precautions See Electrostatic discharge on page 171 before you open the ...

Page 177: ... fastened if hydrogen or other flammable or toxic substances are used for carrier gas or during CI operation 4 Gently swing the side plate out CAUTION In the next step if you feel resistance stop Do not try to force the side plate open Verify that the MSD is vented Verify that both the front and rear side plate screws are completely loose Figure 54 The analyzer chamber for an Inert model MSD Ceram...

Page 178: ...nnect the wires from the EI HES See Figure 55 on page 179 Do not bend the wires any more than necessary See To Connect Disconnect Wiring to the EI HES on page 180 WARNING The analyzers GC MSD interface and other components in the analyzer chamber operate at very high temperatures Do not touch any part until you are sure it is cool CAUTION Always wear clean gloves to prevent contamination when work...

Page 179: ... the ion source out of the source radiator The source contacts have spring loaded pins so some force must be applied to pull the source out Figure 55 The analyzer chamber for the HES MSD Ceramic source board Ion source Thumbscrew Source heater and temperature sensor wires Source radiator Source finger grip Thumbscrew ...

Page 180: ...rge 8650 0030 Small 8650 0029 Pliers long nose 8710 1094 Tweezers 8710 2460 Procedure 1 Use tweezers or needle nose pliers to connect disconnect the ceramic board wire leads red white black and gray at the source connectors See Figure 56 Figure 56 Wiring to be connected disconnected during source installation or removal Repeller Filament common Filament 1 Filament 2 Ceramic source board ...

Page 181: ...nt block by lifting the source body up off of the filament block while holding the filament block so that the dual filament will not fall and become damaged 4 Use a T6 Torx screwdriver to remove the two screws securing the source mount to the source body 5 Remove the source mount from the lens body 6 Remove the repeller and ring heater sensor assembly from the source body 7 Separate the repeller f...

Page 182: ...ses from the lens insulator casing Putting excessive stress on this casing can break or crack it If this happens do not attempt to operate with a defective lens insulator it must be replaced Figure 57 Exploded parts view of the EI HES 1 2 8 16 17 15 9 4 3 11 10 6 5 7 13 12 14 8 12 Table 18 Parts list for EI HES Figure 57 Item number Item description Part number 1 Source finger grip G7002 20008 2 F...

Page 183: ...4 screw x 12 mm long gold plated screw G7002 20083 9 Source body G7002 20084 10 Post extractor lens 2 3 G7004 20090 11 Post extractor lens 1 4 G7004 20004 12 M2 x 6 mm gold plated screw G7002 20109 13 Locking ring lens insulator G7002 20126 14 High efficiency dual filament G7002 60001 15 Ring heater sensor assembly G7002 60043 16 Source mount 1 5 mm G7002 60053 17 Repeller assembly G7002 67057 Not...

Page 184: ... free Large 8650 0030 Small 8650 0029 Solvents Methanol reagent grade Methylene chloride reagent grade Acetone reagent grade Ultrasonic bath Procedure 1 Disassemble the EI HES See To Disassemble the EI HES on page 181 2 Collect the following parts to be cleaned See Figure 58 on page 185 Filament mount Source mount does not get abrasively or ultrasonically cleaned Repeller Source body Extractor len...

Page 185: ...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 Figure 58 EI HES parts to be cleaned Source body Repeller Entrance lens 1 Ion focus lens 2 Post extractor lens 2 3 Post extractor lens 1 4 Extractor lens 5 CAUTION The filaments source heater assembly insulators source mounting plate and fil...

Page 186: ... rinsed away before ultrasonic cleaning If the methanol becomes cloudy or contains visible particles rinse again 6 Separate the parts that were abrasively cleaned from the parts that were not abrasively cleaned 7 Ultrasonically clean the parts each group separately for 15 minutes in each of the following solvents Methylene chloride reagent grade Acetone reagent grade Methanol reagent grade 8 Place...

Page 187: ... the end groove in the lens insulator and rotate the lens until you feel the ball seat into the circular recess b Insert the next 4 lenses in numerical order into the lens insulator The lens chamber open end always faces the entrance lens 1 Rotate each lens until you feel the ball seat into the circular recess It is easier to insert lens 5 on an angle because the lens stack at this point makes the...

Page 188: ...he full opening extending to the end of the source body Verify that the ceramic is sitting flush at the end of the source body 4 Using the T6 Torx driver install and secure the gold plated setscrew and lock ring lens insulator that holds the lens assembly in place See Figure 60 on page 189 Figure 59 Assembled EI HES lens stack Grooves aligned CAUTION The ceramic insulator must be positioned flat a...

Page 189: ...e source mount to the source body 9 On the side of the filament block opposite the finger grip orient the dual filament ceramic holder so that it lines up with the flat of the filament block Fully insert the three filament leads into the filament block 10 Inset the filament block into the source holder and use a T6 Torx screwdriver to secure it to the holder with the gold plated screw The filament...

Page 190: ... Item number Item description Part number 1 Source finger grip G7002 20008 2 Filament block G7002 20019 3 Extractor lens 5 with 3 mm opening G7004 20061 4 Ceramic insulator for extractor G7002 20064 5 Entrance lens assembly Extended HES 1 G7004 20065 6 Ion focus lens 2 G7004 20068 7 Lens insulator holder G7002 20074 8 M2 x 0 4 screw x 12 mm long gold plated screw G7002 20083 9 Source body G7002 20...

Page 191: ...ractor lens 1 4 G7004 20004 12 M2 x 6 mm gold plated screw G7002 20109 13 Locking ring lens insulator G7002 20126 14 High efficiency dual filament G7002 60001 15 Ring heater sensor assembly G7002 60043 16 Source mount 1 5 mm G7002 60053 17 Repeller assembly G7002 67057 Not shown HES assembly G7004 67056 Table 19 Parts list for EI HES Figure 61 continued Item number Item description Part number ...

Page 192: ...mber on page 176 3 Remove the ion source and place it on a clean cloth on your work surface See To Remove the EI HES on page 178 4 Remove the screw securing the filament block to the source mount See Figure 62 CAUTION Always wear clean gloves to prevent contamination when working in the analyzer chamber WARNING The analyzer GC MSD interface and other components in the analyzer chamber operate at v...

Page 193: ...ck to remove the filament block from the source 6 Remove the dual filament from the filament block by lifting the source body up off of the filament block while holding the filament block so that the dual filament will not fall and become damaged CAUTION Use extra caution when removing the dual filament as it is extremely brittle ...

Page 194: ...ve the old filament See To Remove the EI HES filaments on page 192 2 Insert the 3 pins on the dual filament through the rear of the filament block See Figure 62 on page 192 3 Place the filament block in the source mount 4 Use a T6 Torx screwdriver to tighten the screw securing the filament block to the source mount 5 Reinstall the ion source See To Install the EI HES on page 195 6 Close the analyz...

Page 195: ...l resistance is felt 2 Snap the source into place so that the source mount tabs are flush against the source mount attachment surface of radiator Some force is required to overcome the resistance of the spring loaded pins for the electrical contacts 3 Connect the EI HES wires See To Connect Disconnect Wiring to the EI HES on page 180 4 Install and hand tighten the source thumbscrews Do not overtig...

Page 196: ...nnect Disconnect Wiring from the EI XTR SS and Inert Sources on page 197 4 Remove the thumbscrews that hold the ion source in place See Figure 70 on page 217 5 Pull the ion source out of the source radiator WARNING The analyzers GC MSD interface and other components in the analyzer chamber operate at very high temperatures Do not touch any part until you are sure it is cool CAUTION Always wear cle...

Page 197: ...Pliers long nose 8710 1094 Tweezers 8710 2460 Procedure 1 Use tweezers or needle nose pliers to connect disconnect the ceramic source board wire leads at the source connectors See Figure 63 2 Use tweezers or needle nose pliers to connect disconnect the source heater wire leads at the ceramic source board Figure 63 Wiring for the EI XTR Source Extractor lens Source heater Repeller Filament 1 Source...

Page 198: ...emove the filaments from the source 3 Loosen the two gold plated screws from the source heater block assembly and separate the repeller assembly from the source body The repeller assembly includes the source heater block assembly repeller and related parts 4 Remove the repeller nut and washers then remove the repeller from the source heater block assembly 5 Remove the repeller insulators and the r...

Page 199: ...le 20 Parts list for the EI SS or Inert source Figure 64 Item number Item description Part number SS Part number Inert 1 Gold plated set screw G1999 20022 G1999 20022 2 Gold plated screw G3870 20021 G3870 20021 3 Interface socket G1099 20136 G1099 20136 4 Source body G1099 20130 G2589 20043 5 Drawout cylinder G1072 20008 G1072 20008 6 Drawout plate 05971 20134 G2589 20100 7 4 turn filament G7005 6...

Page 200: ... 05971 20143 12 Repeller insulator G1099 20133 G1099 20133 13 Repeller G3870 60172 G3870 60173 14 Flat washer 3050 0627 3050 0627 15 Belleville spring washer 3050 1301 3050 1301 16 Repeller nut 0535 0071 0535 0071 17 Source heater block assembly G3870 60180 G3870 60179 18 Repeller block insert G3870 20135 G3870 20135 Table 20 Parts list for the EI SS or Inert source Figure 64 continued Item number...

Page 201: ... the two gold plated screws and separating the filaments from the source 3 Loosen the two gold plated screws on the source heater block assembly and separate the repeller assembly from the source body The repeller assembly includes the source heater block assembly repeller and related parts 4 Remove the gold plated setscrews from the side of the source body 5 Pull the entrance lens and ion focus l...

Page 202: ...bling the EI XTR source Table 21 Parts list for EI XTR source Figure 65 Item Description Part number 1 Setscrews G3870 20446 2 Screws G3870 20021 3 Source body G3870 20440 4 Extractor lens G3870 20444 5 Extractor lens insulator G3870 20445 6 Filaments G7005 60061 7 Spring washer 3050 1301 7 Flat washer 3050 0982 ...

Page 203: ...us lens 05971 20143 11 Repeller insulator G1099 20113 12 Repeller G3870 60171 13 Flat washer 3050 0891 14 Belleville spring washer 3050 1301 15 Repeller nut 0535 0071 16 Source heater block assembly G3870 60177 17 Repeller block insert G3870 20135 Not shown EI XTR source assembly G7003 67720 Table 21 Parts list for EI XTR source Figure 65 continued Item Description Part number ...

Page 204: ...n lint free Large 8650 0030 Small 8650 0029 Solvents Acetone reagent grade Methanol reagent grade Methylene chloride reagent grade Ultrasonic bath Preparation 1 Disassemble the ion source See To Disassemble the EI SS or EI Inert Source on page 198 or To Disassemble the EI XTR Source on page 201 2 Collect the following parts to be cleaned for an EI SS or Inert source See Figure 66 on page 206 Repel...

Page 205: ...er Repeller block insert Source body Extractor lens Ion focus lens Entrance lens These are the parts that contact the sample or ion beam The other parts normally should not require cleaning CAUTION If 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 ...

Page 206: ...ource parts to be cleaned Ion focus lens Entrance lens Drawout cylinder Interface socket Source body EI SS or EI Inert source parts to be cleaned EI XTR source parts to be cleaned Repeller Repeller block insert Entrance lens Ion focus lens Extractor lens Source body Repeller block insert Drawout plate Repeller ...

Page 207: ...thanol becomes cloudy or contains visible particles rinse again three times 4 Separate the parts that were abrasively cleaned from the parts that were not abrasively cleaned 5 Ultrasonically clean the parts each group separately for 15 minutes For dirty parts use all three solvents in the order shown cleaning 15 minutes with each of the following solvents Methylene chloride reagent grade Acetone r...

Page 208: ...ert Source 208 5977B Series MSD Operating Manual 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 on a dirty surface Set them only on clean lint free cloths ...

Page 209: ...epeller block insert c Install the repeller through the repeller insulators then put the flat washer followed by the belleville spring washer onto the end of the repeller shaft and secure finger tight with the repeller nut 2 Insert the drawout plate and the drawout cylinder into the source body 3 Assemble the ion focus lens entrance lens and lens insulators 4 Slide these assembled parts into the s...

Page 210: ... 1 2 8 15 15 15 15 14 14 14 2 2 16 16 16 8 12 12 12 10 2 8 8 7 17 18 3 8 8 7 12 13 4 6 5 11 9 Table 22 Parts list for the EI standard or EI Inert source Figure 67 Item number Item description Part number SSL Part number Inert 1 Gold plated set screw G1999 20022 G1999 20022 2 Gold plated screw G3870 20021 G3870 20021 3 Interface socket G1099 20136 G1099 20136 4 Source body G1099 20130 G2589 20043 5...

Page 211: ...170 20126 G3170 20126 11 Ion focus lens 05971 20143 05971 20143 12 Repeller insulator G1099 20133 G1099 20133 13 Repeller G3870 60172 G3870 60173 14 Flat washer 3050 0627 3050 0627 15 Belleville spring washer 3050 1301 3050 1301 16 Repeller nut 0535 0071 0535 0071 17 Source heater block assembly G3870 60180 G3870 60179 18 Repeller block insert G3870 20135 G3870 20135 Table 22 Parts list for the EI...

Page 212: ...trance lens into the source body with the ion focus lens against the extractor lens 5 Install the two gold plated setscrews that holds the lenses in place 6 Assemble the repeller assembly a Install the repeller block insert into the source heater block assembly b Install the repeller insulators into the source heater block assembly and repeller block insert c Install the repeller through the repel...

Page 213: ...ng the EI XTR source Table 23 Parts list for EI XTR source Figure 68 Item Description Part number 1 Setscrews G3870 20446 2 Screws G3870 20021 3 Source body G3870 20440 4 Extractor lens G3870 20444 5 Extractor lens insulator G3870 20445 6 Filaments G7005 60061 7 Spring washer 3050 1301 7 Flat washer 3050 0982 ...

Page 214: ...s lens 05971 20143 11 Repeller insulator G1099 20113 12 Repeller G3870 60171 13 Flat washer 3050 0891 14 Belleville spring washer 3050 1301 15 Repeller nut 0535 0071 16 Source heater block assembly G3870 60177 17 Repeller block insert G3870 20135 Not shown EI XTR source assembly G7003 67720 Table 23 Parts list for EI XTR source Figure 68 continued Item Description Part number ...

Page 215: ...driver 1 5 mm 8710 1570 Procedure 1 Vent the MSD See Venting the MSD on page 116 2 Open the analyzer chamber See To Open the Analyzer Chamber on page 176 3 Remove the ion source See To Remove the EI XTR SS or Inert Source on page 196 4 Remove the gold plated screw and washer from the filament See Figure 69 on page 216 5 Slide the filament assembly off the ion source assembly WARNING The analyzer o...

Page 216: ... See To Pumpdown the MSD on page 139 11 Autotune the MSD See To Tune the MSD in EI Mode on page 127 12 In the Manual Tune dialog the Filament parameter allows you to enter 1 or 2 for the filament number Whichever number was present during the previous autotune enter the other filament number 13 Autotune the MSD again 14 Enter the filament number that gave the best results If you decide to use the ...

Page 217: ...nto the source radiator See Figure 70 2 Insert and hand tighten the source thumbscrews Do not overtighten the thumbscrews See Figure 70 3 Connect the ion source wires See To Connect Disconnect Wiring from the EI XTR SS and Inert Sources on page 197 4 Close the analyzer chamber See To Close the Analyzer Chamber on page 220 Figure 70 Installing the EI source Ceramic source board Ion source Thumbscre...

Page 218: ... Pliers long nose 8710 1094 Procedure 1 Vent the MSD See To Vent the MSD on page 136 2 Open the analyzer chamber See To Open the Analyzer Chamber on page 176 3 Open the retaining clip See Figure 71 on page 219 Lift the arm of the clip up and swing the clip away from the electron multiplier horn 4 Slide the blue signal wire from the connector in the sideplate 5 Remove the electron multiplier horn S...

Page 219: ...ies MSD Operating Manual 219 8 Close the retaining clip 9 Close the analyzer chamber See To Close the Analyzer Chamber on page 220 Figure 71 Replacing the EM horn on a Series 2 Detector Figure 72 Electron multiplier horn Retaining Electron multiplier horn Blue signal wire ...

Page 220: ...Swing the analyzer side plate closed 3 Ensure the vent valve is closed 4 If hydrogen or other flammable or toxic substance is used for carrier gas gently hand tighten the top thumbscrew on the analyzer side plate 5 Pumpdown the MSD See To Pumpdown the MSD on page 139 6 Once the MSD has pumped down close the left analyzer cover and replace the window cover 7 Tune the MSD CAUTION Do not force the an...

Page 221: ...m the CI Source to an EI XTR SS or Inert Source 234 To Remove the CI Source 235 To Connect Disconnect non HES Model Wiring from the CI Source 236 To Connect Disconnect EI HES Model Wiring to the CI Source 237 To Disassemble the CI Source 238 To Clean the CI Source 241 To Assemble the CI Source 244 To Remove the CI Source Filament 247 To Install a CI Source Filament 249 To Install the CI Source 250...

Page 222: ...ethane after using ammonia Be sure to install the ammonia with the tank in an upright position This will help prevent liquid ammonia from getting into the flow module To set up your MSD for CI operation Setting up your MSD for operation in CI mode requires special care to avoid contamination and air leaks Guidelines Before venting in EI mode for the installation of the CI source verify that the GC...

Page 223: ...radiator in the storage container 8 Remove the CI source radiator from the storage container 9 Install the CI source radiator See To Install the CI Source Radiator on page 227 10 Remove the CI source from the storage container 11 Install the CI source This requires shortening the column so that it protrudes from the transfer line by 1 to 2 mm See To Install the CI Source on page 250 12 Pumpdown th...

Page 224: ...ator on page 225 3 Use a T10 Torx screwdriver to loosen the 2 screws that secure the radiator to the analyzer and place the radiator in its storage container WARNING The analyzers GC MSD interface and other components in the analyzer chamber operate at very high temperatures Do not touch any part until you are sure it is cool CAUTION Always wear clean gloves to prevent contamination when working i...

Page 225: ...650 0030 Small 8650 0029 Pliers long nose 8710 1094 Tweezers 8710 2460 Procedure 1 Use tweezers or needle nose pliers to connect disconnect the green ground wire and the 5 lens wires from the radiator Do not bend the wires any more than necessary See Figure 73 2 Use tweezers or needle nose pliers to connect disconnect the 2 purple source heater wires and the 2 gray RTD wires from the ceramic sourc...

Page 226: ...igure 73 Wiring between the ceramic source board feedthrough connector and the EI HES radiator The number in parenthesis is the number engraved on the lens Entrance lens 1 Ion focus lens 2 Post extractor lens 2 3 Post extractor lens 1 4 Extractor lens 5 Ground wire Heater wires RTD wires Ceramic source board ...

Page 227: ...re it using the two retained screws with a number T10 Torx screwdriver WARNING The analyzers GC MSD interface and other components in the analyzer chamber operate at very high temperatures Do not touch any part until you are sure it is cool CAUTION Always wear clean gloves to prevent contamination when working in the analyzer chamber CAUTION Make sure you use an antistatic wrist strap and take oth...

Page 228: ...CI Maintenance To Install the CI Source Radiator 228 5977B Series MSD Operating Manual 2 Connect the green ground wire to the radiator See Figure 74 Figure 74 CI Source radiator Green ground wire Radiator ...

Page 229: ...the ferrule 10 Install the column into the GC MSD interface extending 4 to 5 mm past the analyzer end of the transfer line See To Install a Capillary Column in the GC MSD Interface Using the Self Tightening Column Nut on page 42 or To Install a Capillary Column in the GC MSD Interface Using a Standard Column Nut on page 47 11 Remove the EI HES radiator from the storage container 12 Install the EI ...

Page 230: ...ING The analyzers GC MSD interface and other components in the analyzer chamber operate at very high temperatures Do not touch any part until you are sure it is cool CAUTION Always wear clean gloves to prevent contamination when working in the analyzer chamber CAUTION Make sure you use an antistatic wrist strap and take other antistatic precautions before touching analyzer components CAUTION When ...

Page 231: ...ee To Remove the CI Source on page 235 2 Disconnect the green ground wire from the radiator See Figure 75 3 Use a T 10 Torx screwdriver to loosen the two retained screws that secure the radiator to the analyzer and place the radiator in its storage container Figure 75 CI Source radiator Green ground wire Radiator ...

Page 232: ... M3 x 12 gold plated screws part number G7002 20110 2 Use tweezers to connect the wires from the EI HES radiator See To Connect Disconnect Wiring to the EI HES Radiator on page 225 WARNING The analyzers GC MSD interface and other components in the analyzer chamber operate at very high temperatures Do not touch any part until you are sure it is cool CAUTION Always wear clean gloves to prevent conta...

Page 233: ...urce See To Install the CI Source on page 250 6 Install the CI Extractor interface tip seal if it is not already installed p n G3870 20542 See To Install the GC MSD Interface Tip Seal on page 50 7 Close the analyzer See To Close the Analyzer Chamber on page 220 8 Pumpdown the MSD See To Pumpdown the MSD in CI Mode on page 148 CAUTION Always verify MSD performance in EI before switching to CI opera...

Page 234: ...f installing an EI XTR source locate the brown extractor wire from storage and connect it to the extractor lens and the source board 6 Place the CI source in the ion source storage box 7 If installing an EI SS or Inert source remove the interface tip seal spring and knurled tip seal retainer and put them in the CI storage container 8 Pumpdown the MSD See To Pumpdown the MSD on page 139 CAUTION Alw...

Page 235: ...ce on page 237 Trace the wires for the ion source heater and temperature sensor to the ceramic source board and disconnect them there See To Connect Disconnect EI HES Model Wiring to the CI Source on page 237 4 Remove the two large thumbscrews that hold the ion source in place 5 Pull the ion source out of the source radiator and place it in its storage container WARNING The analyzers GC MSD interf...

Page 236: ...650 0029 Pliers long nose 8710 1094 Tweezers 8710 2460 Procedure 1 Use pliers to connect disconnect the ceramic board wire leads at the source connectors See Figure 76 2 Use pliers to connect disconnect the source heater wire leads at the ceramic source board See Figure 76 Figure 76 Wiring between the ceramic source board and the source Filament 1 Repeller Dummy filament Entrance lens Ion focus So...

Page 237: ...nose 8710 1094 Tweezers 8710 2460 Procedure 1 Use pliers to connect disconnect the ceramic board wire leads red white black and gray at the source connectors See Figure 77 2 Use pliers to connect disconnect the source heater wire leads at the ceramic source board See Figure 77 Figure 77 Wiring between the ceramic source board and the source Filament 1 Repeller Dummy filament Entrance lens Ion focu...

Page 238: ... Table 24 on page 239 while using this procedure 1 Remove the CI source See To Remove the CI Source on page 235 2 Remove the filaments See To Remove the CI Source Filament on page 247 3 Separate the source heater assembly from the source body The source heater assembly includes the source heater repeller and related parts 4 Disassemble the repeller assembly by removing the ceramic insulator from t...

Page 239: ...14 Table 24 Parts list for CI source Figure 78 Item Description Part number 1 Set screw G1999 20022 2 Filament screw G1999 20021 3 CI repeller insulator G1999 20433 4 CI lens insulator G3170 20540 5 CI drawout cylinder G1999 20444 6 CI drawout plate G1999 20446 7 CI source heater block assembly G3870 60415 8 Entrance lens G3170 20126 9 CI source body G3170 20430 ...

Page 240: ...ent G1999 60454 14 Washer spring curved 2 2 mm ID 4 5 mm OD Qty 2 3050 1374 15 Flat washer 3050 9082 Not shown Package GC MS source Clamshell G7002 80008 Not shown Bracket GC MS source Clamshell G7002 00008 Not shown CI source assembly G7002 67404 Not shown CI source assembly without tip seal G7077 67404 Table 24 Parts list for CI source Figure 78 continued Item Description Part number ...

Page 241: ...rge 8650 0030 Small 8650 0029 Solvents Acetone reagent grade Methanol reagent grade Methylene chloride reagent grade Ultrasonic bath Preparation 1 Disassemble the CI source See To Disassemble the CI Source on page 238 2 Collect the following parts to be cleaned for a CI source See Figure 79 on page 242 Repeller Source body Drawout plate Drawout cylinder Ion focus lens Entrance lens These are the p...

Page 242: ...e discolorations where electrons from the filaments enter the source body 3 Rinse away all abrasive residue with reagent grade methanol Ensure all abrasive residue is rinsed before ultrasonic cleaning If the methanol becomes cloudy or contains visible particles rinse again three times 4 Separate the parts that were abrasively cleaned from the parts that were not abrasively cleaned CAUTION If the C...

Page 243: ...cleaning with methanol is sufficient 6 Place the parts in a clean beaker Loosely cover the beaker with clean aluminum foil dull side down 7 Dry the cleaned parts in an oven at 100 C for five to six minutes WARNING Al All of these solvents are hazardous Work in a fume hood and take all appropriate precautions WARNING Let Let the parts cool before you handle them NOTE Take care to avoid contaminatin...

Page 244: ...hile using this procedure 1 Assemble the ion focus lens entrance lens and lens insulator 2 Slide the drawout plate and the drawout cylinder into the source body 3 Slide the parts assembled in step 1 into the source body 4 Install the setscrew that holds the lenses in place 5 Attach the ceramic disk to the repeller and place on top of the source body 6 Place the heater block assembly on top of the ...

Page 245: ...list for CI source Figure 80 Item Description Part number 1 Set screw G1999 20022 2 Filament screw G1999 20021 3 CI repeller insulator G1999 20433 4 CI lens insulator G3170 20540 5 CI drawout cylinder G1999 20444 6 CI drawout plate G1999 20446 7 CI source heater block assembly G3870 60415 8 Entrance lens G3170 20126 9 CI source body G3170 20430 10 Ion focus lens G1999 20443 ...

Page 246: ...4 Washer spring curved 2 2 mm ID 4 5 mm OD Qty 2 3050 1374 15 Flat washer 3050 9082 Not shown Package GC MS source Clamshell G7002 80008 Not shown Bracket GC MS source Clamshell G7002 00008 Not shown CI source assembly G7002 67404 Not shown CI source assembly without tip seal G7077 67404 Table 25 Parts list for CI source Figure 80 continued Item Description Part number ...

Page 247: ...er chamber See To Open the Analyzer Chamber on page 176 3 Remove the CI source See To Remove the CI Source on page 235 4 Remove the screw holding the filament to the CI source body See Figure 81 5 Slide the filament off the CI source assembly See Figure 81 CAUTION Always wear clean gloves to prevent contamination when working in the analyzer chamber WARNING The analyzer GC MSD interface and other ...

Page 248: ...8 CI Maintenance To Remove the CI Source Filament 248 5977B Series MSD Operating Manual Figure 81 Changing the CI source filament Screw Filament CI source body ...

Page 249: ... To Remove the CI Source Filament on page 247 2 Place the new filament into its position on the ion source body See Figure 81 on page 248 3 Secure the filament to the ion source body with the screw See Figure 81 on page 248 4 After installing the filament verify that it is not grounded to source body 5 Reinstall the CI source See To Install the CI Source on page 250 or General Information on page ...

Page 250: ...2 4 Install the thumbscrews See Figure 82 5 Connect the wiring to the CI source See To Connect Disconnect non HES Model Wiring from the CI Source on page 236 or To Connect Disconnect EI HES Model Wiring to the CI Source on page 237 CAUTION Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components Wear a grounded antistatic wrist stra...

Page 251: ...he CI Source 5977B Series MSD Operating Manual 251 6 Close the analyzer door See To Close the Analyzer Chamber on page 220 7 Pumpdown the MSD See To Pumpdown the MSD in CI Mode on page 148 8 Tune the MSD See CI Autotune on page 145 ...

Page 252: ...8 CI Maintenance To Install the CI Source 252 5977B Series MSD Operating Manual ...

Page 253: ......

Page 254: ...www agilent com Agilent Technologies Inc 2019 First edition January 2019 G7077 90034 G7077 90034 ...

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