Agilent 5975 Series MSD Operation Manual Agilent Technologies
Notices © Agilent Technologies, Inc. 2012 Warranty No part of this manual may be reproduced in any form or by any means (including electronic storage and retrieval or translation into a foreign language) without prior agreement and written consent from Agilent Technologies, Inc. as governed by United States and international copyright laws. The material contained in this document is provided “as is,” and is subject to being changed, without notice, in future editions.
About This Manual This manual contains information for operating and maintaining the Agilent 5975 Series Gas Chromatograph/Mass Selective Detector (GC/MSD) system. 1 “Introduction” Chapter 1 describes general information about the 5975 Series MSDs, including a hardware description, general safety warnings, and hydrogen safety information.
Online User Information Now your Agilent instrument documentation is in one place, at your fingertips. The Instrument Utilities DVD that ships with your instrument provides an extensive collection of online help, videos, and books for the Agilent 7890A GC, 7820A GC, 6890N GC, 6850 GC, 5975T LTM GC/MS, 7693A ALS, and the 7683B ALS.
Contents 1 Introduction 5975 MSD Version Abbreviations Used 10 11 The 5975 Series MSD 13 CI MSD Hardware Description Important Safety Warnings 15 17 Hydrogen Safety 19 GC precautions 19 Safety and Regulatory Certifications Cleaning/Recycling the Product Liquid Spillage 27 27 Moving or Storing the MSD 2 24 27 Installing GC Columns Columns 30 To reconfigure a 6850 GC column on its basket To prepare a capillary column for installation 32 37 To install a capillary column in a split/splitless in
Operating the MSD from the LCP Modes of operation 51 51 LCP Status Messages 53 ChemStation Loading 53 Executing tune 53 Instrument Available 53 Loading Method 53 Loading MSD Firmware 53 Loading OS 54 Complete 54 Method Loaded 54 MS locked by 54 Press Sideplate 54 Run: Acquiring 54 To view system status during startup 54 LCP Menus 55 The EI GC/MSD Interface 58 Before You Turn On the MSD Pu
To measure column flow linear velocity To confirm column flow To tune the MSD 73 74 75 To verify system performance 76 High-Mass Testing (5975 Series MSDs) To remove the MSD covers To vent the MSD 77 80 82 To open the analyzer chamber 84 To close the analyzer chamber 87 To pump down the MSD 91 To move or store the MSD 93 To set the interface temperature from the GC 4 95 Operating in Chemical Ionization (CI) Mode General Guidelines 98 The CI GC/MSD Interface To Operate the CI MSD 99 10
To perform a PCI autotune (methane only) 118 To perform an NCI autotune (methane reagent gas) To verify PCI performance 122 To verify NCI performance 123 To monitor high vacuum pressure 5 124 General Maintenance Before Starting 128 Maintaining the Vacuum System 6 133 CI Maintenance General Information 140 To Set Up Your MSD for CI Operation A 120 141 Chemical Ionization Theory Chemical Ionization Overview Positive CI Theory Negative CI Theory 5975 Series MSD Operation Manual 146 148 155
Agilent 5975 Series MSD Operation Manual 1 Introduction 5975 MSD Version 10 Abbreviations Used 11 The 5975 Series MSD 13 CI MSD Hardware Description 15 Important Safety Warnings 17 Many internal parts of the MSD carry dangerous voltages 17 Electrostatic discharge is a threat to MSD electronics 17 Many parts are dangerously hot 18 The oil pan under the standard foreline pump can be a fire hazard 18 Hydrogen Safety 19 Dangers unique to GC/MSD operation 20 Hydrogen accumulation in an MSD 20 Precautions 22 Saf
1 Introduction 5975 MSD Version 5975 Series MSDs are equipped with a diffusion pump or one of two turbomolecular (turbo) pumps. The serial number label displays a product number (Table 1) that indicates what kind of MSD you have.
Introduction 1 Abbreviations Used The abbreviations in Table 2 are used in discussing this product. They are collected here for convenience.
1 Introduction Table 2 12 Abbreviations (continued) Abbreviation Definition MSD Mass Selective Detector NCI Negative CI OFN Octafluoronaphthalene (calibrant) PCI Positive CI PFDTD Perfluoro-5,8-dimethyl-3,6,9-trioxydodecane (calibrant) PFHT 2,4,6-tris(perfluoroheptyl)-1,3,5-triazine (calibrant) PFTBA Perfluorotributylamine (calibrant) Quad Quadrupole mass filter RF Radio frequency RFPA Radio frequency power amplifier Torr Unit of pressure, 1 mm Hg Turbo Turbomolecular (pump) 5
Introduction 1 The 5975 Series MSD The 5975 Series MSD is a stand-alone capillary GC detector for use with an Agilent Series Gas Chromatograph (Table 3).
1 Introduction The gauge is required for chemical ionization (CI) operation. Table 3 5975 series MSD models and features Model 14 Feature G3170A G3175A G3171A G3176A G3172A G3174A High vacuum pump Diffusion Standard turbo Performance turbo Performance turbo Optimal He column flow mL/min 1 1 1 to 2 1 to 2 Maximum recommended gas flow mL/min* 1.5 2.0 4.0 4 Maximum gas flow, mL/min† 2 2.4 6.5 6.5 Max column id 0.25 mm (30 m) 0.32 mm (30 m) 0.53 mm (30 m) 0.
Introduction 1 CI MSD Hardware Description Figure 1 is an overview of a typical 5975 GC/MSD system. ALS 7890A GC CI gas flow module Local control panel 5975 Series MSD MSD power switch GC power switch Figure 1 5975 Series GC/MSD system The CI hardware allows the 5975 Series MSD to produce high-quality, classical CI spectra, which include molecular adduct ions. A variety of reagent gases can be used.
1 Introduction In this manual, the term “CI MSD” refers to the G3174A MSD and upgraded G3172A MSDs. It also applies, unless otherwise specified, to the flow modules for these instruments. The 5975 Series CI system adds to the 5975 Series MSD: • EI/CI GC/MSD interface • CI ion source and interface tip seal • Reagent gas flow control module • Bipolar HED power supply for PCI and NCI operation A methane/isobutane gas purifier is provided and is required.
Introduction 1 Important Safety Warnings There are several important safety notices to always keep in mind when using the MSD. Many internal parts of the MSD carry dangerous voltages If the MSD is connected to a power source, even if the power switch is off, potentially dangerous voltages exist on: • The wiring between the MSD power cord and the AC power supply, the AC power supply itself, and the wiring from the AC power supply to the power switch.
1 Introduction Many parts are dangerously hot Many parts of the GC/MSD operate at temperatures high enough to cause serious burns. These parts include but are not limited to: • The inlets • The oven and its contents • The detector • The column nuts attaching the column to an inlet or detector • The valve box • The foreline pump 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 temperature.
1 Introduction Hydrogen Safety WARN I NG The use of hydrogen as a GC carrier gas is potentially dangerous. WARN I NG When using hydrogen (H2) as the carrier gas or fuel gas, be aware that hydrogen gas can flow into the GC oven and create an explosion hazard. Therefore, be sure that the supply is turned off until all connections are made and ensure that the inlet and detector column fittings are either connected to a column or capped at all times when hydrogen gas is supplied to the instrument.
1 Introduction Dangers unique to GC/MSD operation Hydrogen presents a number of dangers. Some are general, others are unique to GC or GC/MSD operation. Dangers include, but are not limited to: • Combustion of leaking hydrogen. • Combustion due to rapid expansion of hydrogen from a high-pressure cylinder. • Accumulation of hydrogen in the GC oven and subsequent combustion (see your GC documentation and the label on the top edge of the GC oven door).
Introduction Table 4 1 Hydrogen accumulation mechanisms (continued) Mechanism Results Mass spectrometer automated shutoff valves closed Some mass spectrometers are equipped with automated diffusion pump shutoff valves. In these instruments, deliberate operator action or various failures can cause the shutoff valves to close. Shutoff valve closure does not shut off the flow of carrier gas. As a result, hydrogen may slowly accumulate in the mass spectrometer.
1 Introduction WARN I NG Once hydrogen has accumulated in a mass spectrometer, extreme caution must be used when removing it. Incorrect startup of a mass spectrometer filled with hydrogen can cause an explosion. WARN I NG After a power failure, the mass spectrometer may start up and begin the pumpdown process by itself. This does not guarantee that all hydrogen has been removed from the system or that the explosion hazard has been removed.
Introduction 1 Operating precautions • Turn off the hydrogen at its source every time you shut down the GC or MSD. • Turn off the hydrogen at its source every time you vent the MSD (do not heat the capillary column without carrier gas flow). • Turn off the hydrogen at its source every time shutoff valves in an MSD are closed (do not heat the capillary column without carrier gas flow). • Turn off the hydrogen at its source if a power failure occurs.
1 Introduction Safety and Regulatory Certifications The 5975 Series MSD conforms to the following safety standards: • Canadian Standards Association (CSA): CAN/CSA-C222 No.
Introduction 1 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 violates safety standards of design and the intended use of the instrument. Agilent Technologies assumes no liability for the customer’s failure to comply with these requirements. See accompanying instructions for more information. Indicates a hot surface. Indicates hazardous voltages.
1 Introduction Electromagnetic compatibility This device complies with the requirements of CISPR 11. Operation is subject to the following two conditions: • This device may not cause harmful interference. • This device must accept any interference received, including interference that may cause undesired operation.
Introduction 1 Cleaning/Recycling the Product To clean the unit, disconnect the power and wipe down with a damp, lint-free cloth. For recycling, contact your local Agilent sales office. Liquid Spillage Do not spill liquids on the MSD. Moving or Storing the MSD The best way to keep your MSD functioning properly is to keep it pumped down and hot, with carrier gas flow. If you plan to move or store your MSD, a few additional precautions are required.
1 28 Introduction 5975 Series MSD Operation Manual
Agilent 5975 Series MSD Operation Manual 2 Installing GC Columns Columns 30 Conditioning columns 30 Conditioning ferrules 31 Tips and hints 31 To reconfigure a 6850 GC column on its basket 32 To prepare a capillary column for installation 37 To install a capillary column in a split/splitless inlet 39 To condition a capillary column 41 To install a capillary column in the GC/MSD interface 43 Before you can operate your GC/MSD system, you must select, install, and condition a GC column.
2 Installing GC Columns Columns Many types of GC columns can be used with the MSD but there are some restrictions. During tuning or data acquisition the rate of column flow into the MSD should not exceed the maximum recommended flow. Therefore, there are limits to column length and flow. Exceeding recommended flow will result in degradation of mass spectral and sensitivity performance. Remember that column flows vary greatly with oven temperature.
2 Installing GC Columns A small portion of the capillary column stationary phase is often carried away by the carrier gas. This is called column bleed. Column bleed deposits traces of the stationary phase in the MSD ion source. This decreases MSD sensitivity and makes cleaning the ion source necessary. Column bleed is most common in new or poorly crosslinked columns. It is much worse if there are traces of oxygen in the carrier gas when the column is heated.
2 Installing GC Columns To reconfigure a 6850 GC column on its basket Before installing a 6850, first reconfigure it to better position the column ends for installation in the GC MSD interface. 1 Lay the column (19091S-433E found in the GC ship kit) on a clean surface with the column label facing the user in the 12 o’clock position.
2 Installing GC Columns 2 Remove the septum cap from the column OUTLET side and uncoil 2 column loops. See Figure 3. 1 o’clock cross-member 3 o’clock cross-member Figure 3 Column with 2 uncoiled loops 3 Attach three column clips (part number G2630-20890) to the column cage as follows: • Attach one clip onto the back of the 1 o’clock cross-member piece of the column cage. • Attach two clips onto the front of the 3 o’clock cross-member piece of the column cage.
2 Installing GC Columns See Figure 4. Column clip (1 o’clock postion) Column clips (3 o’clock position) Column outlet Figure 4 Column with column clips attached 4 Feed the outlet side of the column through the 1 o’clock positioned clip so that the column outlet is pointing toward the front of the column cage. See Figure 5. CA U T I O N 34 Be careful not to scratch the column coating.
Installing GC Columns 2 To column outlet Column clip (1 o’clock position) Column clips (3 o’clock position) Figure 5 Column fed through 1 o’clock position 5 Next, feed the outlet side of the column through the 3 o’clock positioned clips so that the column outlet is pointing toward the back of the column cage. Make sure that the part of the column that is between the two clips does NOT extend above the column label. See Figure 6. CA U T I O N Be careful not to scratch the column coating.
2 Installing GC Columns Column clip (1 o’clock postion) Column clips (3 o’clock position) To column outlet (at least 50 cm) Figure 6 Column fed through 3 o’clock position There should be approximately 50 cm of column extending beyond the 3 o’clock positioned clip. 6 Carefully rewind the remainder of the column outlet end around the column cage.
Installing GC Columns 2 To prepare a capillary column for installation Materials needed • Capillary column • Column cutter, ceramic (5181-8836) or diamond (5183-4620) • Ferrules • 0.27-mm id, for 0.10-mm id columns (5062-3518) • 0.37-mm id, for 0.20-mm id columns (5062-3516) • 0.40-mm id, for 0.25-mm id columns (5181-3323) • 0.5-mm id, for 0.32-mm id columns (5062-3514) • 0.8-mm id, for 0.
2 Installing GC Columns Capillary column Column cutter Ferrule, taper up Inlet column nut Septum Figure 7 Preparing a capillary column for installation 2 Use the column cutter to score the column 2 cm from the end. 3 Break off the end of the column. Hold the column against the column cutter with your thumb. Break the column against the edge of the column cutter. 4 Inspect the end for jagged edges or burrs. If the break is not clean and even, repeat steps 2 and 3.
Installing GC Columns 2 To install a capillary column in a split/splitless inlet Materials needed • Gloves, clean • Large (8650-0030) • Small (8650-0029) • Metric ruler • Wrench, open-end, 1/4-inch and 5/16-inch (8710-0510) To install columns in other types of inlets, refer to your Gas Chromatograph User Information. Procedure 1 Prepare the column for installation ( “To prepare a capillary column for installation” on page 37).
2 Installing GC Columns 3 Slide the septum to place the nut and ferrule in the correct position. 4 Insert the column in the inlet. 5 Slide the nut up the column to the inlet base and finger-tighten the nut. 6 Adjust the column position so the septum is even with the bottom of the column nut. 7 Tighten the column nut an additional 1/4 to 1/2 turn. The column should not slide with a gentle tug. 8 Start carrier gas flow. 9 Verify flow by submerging the free end of the column in isopropanol. Look for bubbles.
Installing GC Columns 2 To condition a capillary column Materials needed • Carrier gas, (99.9995% pure or better) • Wrench, open-end, 1/4-inch and 5/16-inch (8710-0510) WARN I NG Do not condition your capillary column with hydrogen. Hydrogen accumulation in the GC oven can result in an explosion. If you plan to use hydrogen as your carrier gas, first condition the column with ultrapure (99.999% or better) inert gas such as helium, nitrogen, or argon.
2 Installing GC Columns See also For more information about installing a capillary column, refer to the application note Optimizing Splitless Injections on Your GC for High Performance MS Analysis, publication number 5988-9944EN.
2 Installing GC Columns To install a capillary column in the GC/MSD interface Agilent 7890A and 7820A, and 6890 GCs Materials needed • Column cutter, ceramic (5181-8836) or diamond (5183-4620) • Ferrules • 0.3-mm id, for 0.10-mm id columns (5062-3507) • 0.4-mm id, for 0.20- and 0.25-mm id columns (5062-3508) • 0.5-mm id, for 0.32-mm id columns (5062-3506) • 0.8-mm id, for 0.
2 Installing GC Columns Column Interface column nut GC/MSD interface (GC end) Analyzer chamber GC/MSD interface (MSD end) 1 to 2 mm MSD Figure 9 GC Oven Installing a capillary column in the GC/MSD interface 5 Slide the column into the GC/MSD interface (Figure 9) until you can pull it out through the analyzer chamber. 6 Break 1 cm off the end of the column (page 32). Do not let any column fragments fall into the analyzer chamber. They could damage the high vacuum pump.
2 Installing GC Columns 9 Hand-tighten the nut. Make sure the position of the column does not change as you tighten the nut. Reinstall the spring-loaded tip seal if it was removed earlier. 10 Check the GC oven to be sure that the column does not touch the oven walls. 11 Tighten the nut 1/4 to 1/2 turn. Check the tightness after one or two heat cycles. 6850 GC 1 Carefully unwind the outlet end of the GC column until the 3 o’clock clip is reached.
2 Installing GC Columns 22–28 cm from 3 o’clock clip to GC/MSD interface nut Figure 10 Oven door opened and closed 7 Loosen the interface nut and push the column an additional 3–5 cm into the analyzer chamber. 8 Make a clean cut of the column so that now only 3–5 cm protrudes into the analyzer chamber. 9 Clean the outside of the free end of the column with a lint-free cloth moistened with methanol.
Installing GC Columns 2 Column Interface column nut GC/MSD interface (GC end) Analyzer chamber GC/MSD interface (MSD end) 1 to 2 mm MSD Figure 11 GC Oven MSD - GC column connection 11 Repeat step 6 to assure column integrity. 12 Tighten the interface nut an additional 1/4 to 1/2 turn with a 1/4-inch open-end wrench. Check the tightness after one or two heat cycles. 13 Turn the GC on. 14 Verify that the inlet temperature is set to 25 °C.
2 Installing GC Columns 17 Reinstall the MSD analyzer cover.
Agilent 5975 Series MSD Operation Manual 3 Operating in Electron Impact (EI) Mode Operating the MSD from the Data System 51 Operating the MSD from the LCP 51 LCP Status Messages 53 LCP Menus 55 The EI GC/MSD Interface 58 Before You Turn On the MSD 60 Pumping Down 61 Controlling Temperatures 61 Controlling Column Flow 62 Venting the MSD 63 To view MSD analyzer temperature and vacuum status 64 To set monitors for MSD temperature and vacuum status 66 To set the MSD analyzer temperatures 67 To set the GC/MSD i
3 Operating in Electron Impact (EI) Mode How to perform some basic operating procedures for the MSD. CA U T I O N 50 The software and firmware are revised periodically. If the steps in these procedures do not match your MSD ChemStation software, refer to the manuals and online help supplied with the software for more information.
3 Operating in Electron Impact (EI) Mode Operating the MSD from the Data System The software performs tasks such as pumping down, monitoring pressures, setting temperatures, tuning, and preparing to vent. These tasks are described in this chapter. Data acquisition and data analysis are described in the manuals and online help supplied with the MSD ChemStation software.
3 Operating in Electron Impact (EI) Mode Use one or more of the following keys as appropriate to respond to prompts or select options: Use [Up] to increase the displayed value or to scroll up (such as in a message list). Use [Down] to decrease the displayed value or to scroll down (such as in a message list). Use [Yes/Select] to accept the current value. Use [No/Cancel] to return to the Status mode.
3 Operating in Electron Impact (EI) Mode LCP Status Messages The following messages may be displayed on the LCP to inform you of the status of the MSD system. If the LCP is currently in Menu mode, cycle through the menus to return to Status mode. NOTE No messages will be displayed if an online instrument session is not currently running on the GC/MSD ChemStation. ChemStation Loading The Agilent MSD Productivity ChemStation software is starting up.
3 Operating in Electron Impact (EI) Mode Loading OS The operating system of the instrument controller is being initialized. Complete The run and subsequent data processing are done. The same message appears even if the run was terminated prematurely. Method Loaded Method parameters were sent to the MSD. MS locked by MS parameters can only be changed from the GC/MSD ChemStation.
Operating in Electron Impact (EI) Mode 3 LCP Menus To access a particular menu option, press [Menu] until the desired menu appears, then press [Item] until the desired menu item appears. Table 6 through Table 11 list the menus and selections. NOTE Many menu items, especially on the ChemStation, MS Parameters, and Maintenance menus, have no effect when the instrument is acquiring data. Table 6 ChemStation menu Action Description Run Method Displays the current method name and starts an analysis.
3 Operating in Electron Impact (EI) Mode Table 7 Action Description Prepare to vent Reminds you to shut down the GC then prepares the instrument for venting when [Yes/Select] is pressed. Pumpdown Initiates a pumpdown sequence. Table 8 NOTE MS Parameters menu Action Description High Vacuum Pressure Only with Micro-Ion vacuum gauge installed. Turbo Pump Speed Displays the turbo pump speed. Foreline Pressure Displays the foreline pressure.
Operating in Electron Impact (EI) Mode Table 9 Network menu (continued) Action Description Ping ChemStation Checks communication with the GC/MSD ChemStation. Ping GC Checks communication with the GC. MS Controller MAC Displays the MAC address of the SmartCard in the MSD. Table 10 Version menu Action Description Control firmware Displays the MSD firmware version. Operating system Displays the GC/MSD ChemStation operating system version. Front panel Displays the version of the LCP.
3 Operating in Electron Impact (EI) Mode The EI GC/MSD Interface The GC/MSD interface (Figure 12) is a heated conduit into the MSD for the capillary column. It is bolted onto the right side of the analyzer chamber, with an O-ring seal. It has a protective cover which should be left in place. One end of the GC/MSD interface passes through the side of the gas chromatograph and extends into the GC oven. This end is threaded to allow connection of the column with a nut and ferrule.
Operating in Electron Impact (EI) Mode 3 Heater sleeve Insulation Column Ionization chamber MSD Analyzer chamber GC oven Heater/Sensor assembly Column end protrudes 1 to 2 mm into the ionization chamber.
3 Operating in Electron Impact (EI) Mode Before You Turn On the MSD Verify the following before you turn on or attempt to operate the MSD. • The vent valve must be closed (the knob turned all the way clockwise). • All other vacuum seals and fittings must be in place and fastened correctly. (The the front side plate screw should not be tightened, unless hazardous carrier or reagent gasses are being used. • The MSD is connected to a grounded power source. • The GC/MSD interface extends into the GC oven.
3 Operating in Electron Impact (EI) Mode Pumping Down The data system or local control panel helps you pump down the MSD. The process is mostly automated. Once you close the vent valve and turn on the main power switch (while pressing on the sideplate), the MSD pumps down by itself. The data system software monitors and displays system status during pumpdown. When the pressure is low enough, the program turns on the ion source and mass filter heaters and prompts you to turn on the GC/MSD interface heater.
3 Operating in Electron Impact (EI) Mode Controlling Column Flow Carrier gas flow is controlled by head pressure in the GC. For a given head pressure, column flow will decrease as the GC oven temperature increases. With electronic pneumatic control (EPC) and the column mode set to Constant Flow, the same column flow is maintained regardless of temperature. The MSD can be used to measure actual column flow.
3 Operating in Electron Impact (EI) Mode Venting the MSD A program in the data system guides you through the venting process. It turns off the GC and MSD heaters and diffusion pump heater or the turbo pump at the correct time. It also lets you monitor temperatures in the MSD and indicates when to vent the MSD. The MSD will be damaged by incorrect venting. A diffusion pump will backstream vaporized pump fluid onto the analyzer if the MDS is vented before the diffusion pump has fully cooled.
3 Operating in Electron Impact (EI) Mode To view MSD analyzer temperature and vacuum status You can also use the Local Control Panel to perform this task. See the G1701EA GC/MSD ChemStation Getting Started manual for more information. Procedure 1 In Instrument Control view, select Edit Tune Parameters from the Instrument menu (Figure 13). Figure 13 Tune parameters 2 Select the tune file you plan to use with your method from the Load MS Tune File dialog box.
Operating in Electron Impact (EI) Mode 3 Unless you have just begun the pumpdown process, the foreline pressure should be less than 300 mTorr, or the turbo pump should be running at least 80% speed. MSD heaters remain off as long as the diffusion pump is cold or the turbo pump is operating at less than 80%. Normally, the foreline pressure will be below 100 mTorr, or the turbo pump speed will be at 100%.
3 Operating in Electron Impact (EI) Mode To set monitors for MSD temperature and vacuum status A monitor displays the current value of a single instrument parameter. They can be added to the standard instrument control window. Monitors can be set to change color if the actual parameter varies beyond a user-determined limit from its setpoint. Procedure 1 Select MS Monitors from the Instrument menu. 2 In the Edit MS Monitors box, under Type, select Zone. 3 Under Parameter, select MS Source and click Add.
Operating in Electron Impact (EI) Mode 3 To set the MSD analyzer temperatures Setpoints for the MSD ion source and mass filter (quad) temperatures are stored in the current tune (*.u) file. When a method is loaded, the setpoints in the tune file associated with that method are downloaded automatically. Procedure 1 In Instrument Control view, select Edit Tune Parameters from the Instrument menu. 2 Select Temperatures from the MoreParams menu (Figure 15).
3 Operating in Electron Impact (EI) Mode 4 To close the screen, click: • Apply to send the new temperature setpoints to the MSD. • OK to change the currently loaded tune file but not download anything to the MSD (use Apply). • Cancel to exit the panel without changing the currently loaded tune file or downloading anything to the MSD. 5 When the Save MS Tune File dialog box appears, either click OK to save your changes to the same file or type a new file name and click OK.
Operating in Electron Impact (EI) Mode 3 To set the GC/MSD interface temperature from the ChemStation You can also use the Local Control Panel to perform this task. See “Operating the MSD from the LCP” . Procedure 1 Select View>Instrument Control. 2 Select Instrument>GC Edit Parameters. 3 Click the Aux icon to edit the interface temperature (Figure 16). Figure 16 Setting the interface temperature 4 Check the heater On and type the setpoint in the Value °C column. The typical setpoint is 280 °C.
3 Operating in Electron Impact (EI) Mode CA U T I O N Never exceed the maximum temperature for your column. 5 Click Apply to download setpoints or click OK to download setpoints and close the window. 6 To make the new settings part of the method, select Save from the Method menu. CA U T I O N 70 Make sure that the carrier gas is turned on and the column has been purged of air before heating the GC/MSD interface or the GC oven.
3 Operating in Electron Impact (EI) Mode To monitor high vacuum pressure Pressure monitoring requires an optional G3397A Micro-Ion vacuum gauge. Materials needed • Micro-Ion vacuum gauge (G3397A) WARN I NG If you are using hydrogen as a carrier gas, do not turn on the Micro-Ion vacuum gauge if there is any possibility that hydrogen has accumulated in the analyzer chamber. Read “Hydrogen Safety” before operating the MSD with hydrogen carrier gas. Procedure 1 Start up and pump down the MSD (page 91).
3 Operating in Electron Impact (EI) Mode Table 13 Micro-Ion Vacuum Gauge Reading Column flow rate, mL/min Gauge reading, Torr Performance turbo pump Gauge reading, Torr Standard turbo pump Gauge reading, Torr Diffusion pump Foreline reading, Torr Diffusion pump 0.5 3.18E–06 1.3E–05 2.18E–05 34.7 0.7 4.42E–06 1.83E–05 2.59E–05 39.4 1 6.26E–06 2.61E–05 3.66E–05 52.86 1.2 7.33E–06 3.11E–05 4.46E–05 60.866 2 1.24E–05 5.25E–05 7.33E–05 91.784 3 1.86E–05 8.01E–05 1.
Operating in Electron Impact (EI) Mode 3 To measure column flow linear velocity With capillary columns, such as those used with the MSD, linear velocity is often measured rather than volumetric flow rate. Procedure 1 Set Data Acquisition for splitless manual injection and selected ion monitoring (SIM) of 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.
3 Operating in Electron Impact (EI) Mode To confirm column flow Volumetric flow can be calculated from the column head pressure if the column dimensions are known. Procedure 1 In the Instrument Control view, select Instrument>GC Edit Parameters. 2 Click the Columns icon (Figure 17 shows an example). 3 Select the appropriate column. .
3 Operating in Electron Impact (EI) Mode To tune the MSD You can also use the Local Control Panel to run the autotune that is currently loaded in the PC memory. See “Operating the MSD from the LCP” . Procedure 1 In the Instrument Control View, verify the correct tune file is loaded. For most applications, ATUNE.U (Autotune) gives good results. STUNE.U (Standard Tune) is not recommended as it may reduce sensitivity. Consider Gain autotune (GAIN.U + HiSense.U).
3 Operating in Electron Impact (EI) Mode To verify system performance Materials needed • 1 pg/µL (0.001 ppm) OFN sample (5188-5348) Verify the tune performance 1 Verify that the system has been pumping down for at least 60 minutes. 2 Set the GC oven temperature to 150 °C and the column flow to 1.0 mL/min. 3 In the Instrument Control view, select Checkout Tune from the Checkout menu. The software will perform an autotune and print the report.
3 Operating in Electron Impact (EI) Mode High-Mass Testing (5975 Series MSDs) Setup conditions 1 Obtain a sample of PFHT (5188-5357). 2 Load tune file ATUNE.U then auto tune the MSD. 3 Resolve the PFHT.M method under x\5975\PFHT.M where x is instrument number being used. 4 Update and save the method. High-mass checkout 1 Load sample into a vial and place in position 2. 2 Select High Mass Check from the Checkout menu. 3 Follow the instructions on screen.
3 Operating in Electron Impact (EI) Mode Results Figure 18 78 PFHT high mass report 5975 Series MSD Operation Manual
3 Operating in Electron Impact (EI) Mode Results will indicate the recommended amount to adjust AMU offset for high-mass. If your results are within 5 units of the targeted amount, there is no need to make adjustments. Adjustments 1 Verify ATUNE.U has been loaded. 2 Select Edit Tune Parameters from the Instrument menu via Instrument Control. 3 Click on MoreParams and select DynamicRamping Params... a Select AMU offset from the drop down box.
3 Operating in Electron Impact (EI) Mode To remove the MSD covers Materials needed • Screwdriver, Torx T-15 (8710-1622) If you need to remove one of the MSD covers, follow these procedures (Figure 19): WARN I NG 80 To remove the analyzer top cover Remove the five screws and lift the cover off. To remove the analyzer window cover 1 Press down on the rounded area on the top of the window. 2 Lift the window forward and off the MSD. Do not remove any other covers.
Operating in Electron Impact (EI) Mode 3 Analyzer window cover Latch Analyzer cover Left side cover Figure 19 Removing covers CA U T I O N Do not use excessive force or the plastic tabs that hold the cover to the mainframe will break off.
3 Operating in Electron Impact (EI) Mode To vent the MSD Procedure 1 Select Vent from the Vacuum menu in the software. Follow the instructions presented. 2 Set the GC/MSD interface heater and the GC oven temperatures to ambient (room temperature). WARN I NG If you are using hydrogen as a carrier gas, the carrier gas flow must be off before turning off the MSD power. If the foreline pump is off, hydrogen will accumulate in the MSD and an explosion may occur.
Operating in Electron Impact (EI) Mode 3 5 Remove the analyzer window cover (page 80) Vent valve knob Figure 20 YES NO Venting the MSD 6 Turn the vent valve knob (Figure 20) counterclockwise only 3/4 turns or until you hear the hissing sound of air flowing into the analyzer chamber. Do not turn the knob too far or the O-ring may fall out of its groove. Be sure to retighten the knob before pumping down. WARN I NG Allow the analyzer to cool to near room temperature before touching it.
3 Operating in Electron Impact (EI) Mode To open the analyzer chamber Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Wrist strap, antistatic • Small (9300-0969) • Medium (9300-1257) • Large (9300-0970) CA U T I O N Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components. Wear a grounded antistatic wrist strap and take other antistatic precautions (see page 131) before you open the analyzer chamber.
Operating in Electron Impact (EI) Mode 3 WARN I NG The analyzer, 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. CA U T I O N Always wear clean gloves to prevent contamination when working in the analyzer chamber.
3 Operating in Electron Impact (EI) Mode Thumbscrews Side plate Analyzer cover CHAMBER CLOSED Detector Side plate Feedthrough board Ion source CHAMBER OPEN Analyzer Figure 21 86 The analyzer chamber 5975 Series MSD Operation Manual
3 Operating in Electron Impact (EI) Mode To close the analyzer chamber Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) Procedure 1 Make sure all the internal analyzer electrical leads are correctly attached. Wiring is the same for both the EI and CI sources. The wiring is described in Table 14 and illustrated in Figure 22 and Figure 23. The term “Board” in the table refers to the feedthrough board located next to the ion source.
3 Operating in Electron Impact (EI) Mode QUADRUPOLE HTR RTS ENTR LENS ION FOC White wires to filament 1 Blue wire to entrance lens Orange wire to ion focus lens FILAMENT - 1 Red wire to repeller REP FILAMENT - 2 Black wires to filament 2 Ion source heater wires (green) Ion source sensor wires (white) RTS HTR SOURCE Figure 22 88 Feedthrough board wiring 5975 Series MSD Operation Manual
Operating in Electron Impact (EI) Mode 3 FB = Feedthrough Board Repeller (red wire from FB) Filament 1 (white wires from FB) Ion source heater wires Ion source sensor wires Filament 2 (black wires from FB) Ion focus lens (orange wire from FB) Entrance lens (blue wire from FB) Figure 23 Ion source wiring 2 Check the side plate O-ring. Make sure the O-ring has a very light coat of Apiezon L high vacuum grease. If the O-ring is very dry, it may not seal well.
3 Operating in Electron Impact (EI) Mode 3 Close the side plate. 4 Reconnect the side board control cable and source power cable to the side board. 5 Make sure the vent valve is closed. 6 Pump down the MSD (page 91). 7 If you are operating in CI mode or if hydrogen or other flammable or toxic substance is used for carrier gas, gently hand tighten the front side plate thumbscrew.
3 Operating in Electron Impact (EI) Mode To pump down the MSD You can also use the Local Control Panel to perform this task. See “Operating the MSD from the LCP” . WARN I NG Make sure your MSD meets all the conditions listed in the introduction to this chapter (page 60) before starting up and pumping down the MSD. Failure to do so can result in personal injury. WARN I NG If you are using hydrogen as a carrier gas, do not start carrier gas flow until the MSD has been pumped down.
3 Operating in Electron Impact (EI) Mode 8 Once communication with the PC has been established, click OK. Figure 24 CA U T I O N Pumping down Within 10 to 15 minutes the diffusion pump should be hot, or the turbo pump speed should be up to 80% (Figure 24). The pump speed should eventually reach 95%. If these conditions are not met, the MSD electronics will shut off the foreline pump. In order to recover from this condition, you must power cycle the MSD.
Operating in Electron Impact (EI) Mode 3 To move or store the MSD Materials needed • Ferrule, blank (5181-3308) • Interface column nut (05988-20066) • Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510) Procedure 1 Vent the MSD (page 82). 2 Remove the column and install a blank ferrule and interface nut. 3 Tighten the vent valve. 4 Move the MSD away from the GC (see the 5975 Series MSD Troubleshooting and Maintenance Manual). 5 Unplug the GC/MSD interface heater cable from the GC.
3 Operating in Electron Impact (EI) Mode Front thumbscrew Rear thumbscrew Figure 25 Side plate thumbscrews The MSD can now be stored or moved. The foreline pump cannot be disconnected; it must be moved with the MSD. Make sure the MSD remains upright and is never tipped on its side or inverted. CA U T I O N 94 The MSD must remain upright at all times. If you need to ship your MSD to another location, contact your Agilent Technologies service representative for advice about packing and shipping.
Operating in Electron Impact (EI) Mode 3 To set the interface temperature from the GC If desired, the interface temperature can be set directly at the GC. For the Agilent 7890A and 6890, set the Aux #2 temperature. For the 6850, use the optional handheld controller to set the thermal aux temperature. Refer to the GC User documentation for details. CA U T I O N Never exceed the maximum temperature of your column.
3 96 Operating in Electron Impact (EI) Mode 5975 Series MSD Operation Manual
Agilent 5975 Series MSD Operation Manual 4 Operating in Chemical Ionization (CI) Mode General Guidelines 98 The CI GC/MSD Interface 99 To Operate the CI MSD 101 To switch from the EI source to the CI source 102 To pump down the CI MSD 103 To set up the software for CI operation 104 To operate the reagent gas flow control module 106 To set up methane reagent gas flow 109 To use other reagent gases 111 To switch from the CI source to the EI source 115 CI Autotune 116 To perform a PCI autotune (methane only)
4 Operating in Chemical Ionization (CI) Mode General Guidelines • Always use the highest purity methane (and other reagent gases, if applicable.) Methane must be at least 99.9995% pure. • Always verify the MSD is performing well in EI mode before switching to CI. See “To verify system performance” . • Make sure the CI ion source and GC/MSD interface tip seal are installed. • Make sure the reagent gas plumbing has no air leaks. This is determined in PCI mode, checking for m/z 32 after the methane pretune.
4 Operating in Chemical Ionization (CI) Mode The CI GC/MSD Interface The CI GC/MSD interface (Figure 26) is a heated conduit into the MSD for the capillary column. It is bolted onto the right side of the analyzer chamber, with an O-ring seal and has a protective cover which should be left in place. One end of the interface passes through the side of the GC and extends into the oven. It is threaded to allow connection of the column with a nut and ferrule.
4 Operating in Chemical Ionization (CI) Mode WARN I NG The GC/MSD interface operates at high temperatures. If you touch it when it is hot, it will burn you. Spring-loaded seal MSD GC oven Reagent gas in Column end protrudes 1 to 2 mm into the ionization chamber.
Operating in Chemical Ionization (CI) Mode 4 To Operate the CI MSD Operating your MSD in the CI mode is slightly more complicated than operating in the EI mode. After tuning, gas flow, source temperature (Table 15), and electron energy may need to be optimized for your specific analyte.
4 Operating in Chemical Ionization (CI) Mode To switch from the EI source to the CI source CA U T I O N Always verify MSD performance in EI before switching to CI operation. Always set up the CI MSD in PCI first, even if you are going to run NCI. Procedure 1 Vent the MSD. See page 82. 2 Open the analyzer. 3 Remove the EI ion source. See page 134. CA U T I O N Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components.
Operating in Chemical Ionization (CI) Mode 4 To pump down the CI MSD You can also use the Local Control Panel to perform this task. See “Operating the MSD from the LCP” . Procedure 1 Follow the instructions for the EI MSD. See “To pump down the MSD” . After the software prompts you to turn on the interface heater and GC oven, perform the following steps. 2 Check the vacuum gauge, if present, to verify that the pressure is decreasing. 3 Press Shutoff Valve to close the gas supply and shutoff valves.
4 Operating in Chemical Ionization (CI) Mode To set up the software for CI operation Procedure 1 Switch to the Tune and Vacuum Control view. 2 Select Load Tune Values from the File menu. 3 Select the tune file PCICH4.U. 4 If CI autotune has never been run for this tune file, the software will prompt you through a series of dialog boxes. Accept the default values unless you have a very good reason for changing anything. The tune values have a dramatic effect on MSD performance.
4 Operating in Chemical Ionization (CI) Mode Table 16 Default Tune Control Limits, used by CI autotune only Reagent gas Methane Isobutane Ammonia Ion polarity Positive Negative Positive Negative Positive Negative Abundance target 1x106 1x106 N/A 1x106 N/A 1x106 Peakwidth target 0.6 0.6 N/A 0.6 N/A 0.
4 Operating in Chemical Ionization (CI) Mode To operate the reagent gas flow control module Reagent gas flows are controlled in software (Figure 27). Figure 27 CI flow control The Valve Settings have the following effects: Gas A (or B) Valve The present gas flow, if any, is turned off. The system evacuates the gas lines for 6 minutes, then turns on the selected gas (A or B). This is to reduce cross-mixing of the gases in the lines.
4 Operating in Chemical Ionization (CI) Mode The flow control module The CI reagent gas flow control module (Figure 28 and Table 17) regulates the flow of reagent gas into the CI GC/MSD interface. The flow module consists of a mass flow controller (MFC), gas select valves, CI calibration valve, shutoff valve, control electronics, and plumbing. The back panel provides Swagelok inlet fittings for methane (CH4) and one OTHER reagent gas. The software refers to them as Gas A and Gas B, respectively.
4 Operating in Chemical Ionization (CI) Mode Table 17 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 On setpoint On 100% On 100% On 100% Off 0% Shutoff valve Open Open Open Open Open Closed The Open and Closed states are shown in the monitors as 1 and 0 respe
4 Operating in Chemical Ionization (CI) Mode To set up methane reagent gas flow The reagent gas flow must be adjusted for maximum stability before tuning the CI system. Do the initial setup with methane in positive chemical ionization (PCI) mode. No flow adjustment procedure is available for NCI, as no negative reagent ions are formed.
4 Operating in Chemical Ionization (CI) Mode CA U T I O N Figure 29 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 will need to vent the MSD and clean the ion source. Reagent ion scans 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.
Operating in Chemical Ionization (CI) Mode 4 To use other reagent gases This section describes the use of isobutane or ammonia as the reagent gas. You should be familiar with operating the CI-equipped 5975 Series MSD with methane reagent gas before attempting to use other reagent gases. CA U T I O N Do not use nitrous oxide as a reagent gas. It radically shortens the life span of the filament.
4 Operating in Chemical Ionization (CI) Mode Table 18 Reagent gases Reagent gas/mode Reagent ion masses PFDTD Calibrant ions Flow adj ions: Ratio EI/PCI/NCI MSD Performance turbo pump Recommended flow: 20% PCI 40% NCI Methane/PCI 17, 29, 41* 41, 267, 599 28/27: 1.5 – 5.0 185, 351, 449 N/A † Methane/NCI 17, 35, 235 Isobutane/PCI 39, 43, 57 N/A 57/43: 5.0 – 30.0 Isobutane/NCI 17, 35, 235 185, 351, 449 N/A Ammonia/PCI 18, 35, 52 N/A 35/18: 0.1 – 1.
4 Operating in Chemical Ionization (CI) Mode Ammonia CI Ammonia (NH3) is commonly used for chemical ionization when less fragmentation is desired in the chemical ionization spectrum. This is because the proton affinity of ammonia is higher than that of methane; hence less energy is transferred in the ionization reaction.
4 Operating in Chemical Ionization (CI) Mode CA U T I O N Use of ammonia affects the maintenance requirements of the MSD. See “CI Maintenance” for more information. CA U T I O N The pressure of the ammonia supply must be less than 5 psig. Higher pressures can result in ammonia condensing from a gas to a liquid. Always keep the ammonia tank in an upright position, below the level of the flow module. Coil the ammonia supply tubing into several vertical loops by wrapping the tubing around a can or bottle.
4 Operating in Chemical Ionization (CI) Mode To switch from the CI source to the EI source Procedure 1 From the Tune and Vacuum Control view, vent the MSD. See page 82. The software will prompt you for the appropriate actions. 2 Open the analyzer. 3 Remove the CI interface tip seal. See page 143. 4 Remove the CI ion source. See page 142. 5 Install the EI ion source. See page 136. 6 Place the CI ion source and interface tip seal in the ion source storage box. 7 Pump down the MSD. See page 91.
4 Operating in Chemical Ionization (CI) Mode CI Autotune After the reagent gas flow is adjusted, the lenses and electronics of the MSD should be tuned (Table 19). 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.
Operating in Chemical Ionization (CI) Mode Table 19 4 Reagent gas settings Reagent gas Methane Isobutane Ammonia EI Ion polarity Positive Negative Positive Negative Positive Negative N/A Emission 150 A 50 A 150 A 50 A 150 A 50 A 35 A Electron energy 150 eV 150 eV 150 eV 150 eV 150 eV 150 eV 70 eV Filament 1 1 1 1 1 1 1 or 2 Repeller 3V 3V 3V 3V 3V 3V 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
4 Operating in Chemical Ionization (CI) Mode To perform a PCI autotune (methane only) CA U T I O N Always verify MSD performance in EI before switching to CI operation. See page 76. Always set up the CI MSD in PCI first, even if you are going to run NCI. Procedure 1 Verify that the MSD performs correctly in EI mode first. See page 76. 2 Load the PCICH4.U tune file (or an existing tune file for the reagent gas you are using).
Operating in Chemical Ionization (CI) Mode Figure 30 4 PCI autotune 5975 Series MSD Operation Manual 119
4 Operating in Chemical Ionization (CI) Mode To perform an NCI autotune (methane reagent gas) CA U T I O N Always verify MSD performance in EI before switching to CI operation. See page 76. Always set up the CI MSD in PCI with methane as the reagent gas first, even if you are going to be using a different reagent gas or going to run NCI. Procedure 1 From the Tune and Vacuum Control view, load NCICH4.U (or an existing tune file for the reagent gas you are using).
Operating in Chemical Ionization (CI) Mode Figure 31 4 NCI autotune 5975 Series MSD Operation Manual 121
4 Operating in Chemical Ionization (CI) Mode To verify PCI performance Materials needed • Benzophenone, 100 pg/L (8500-5440) CA U T I O N Always verify MSD performance in EI before switching to CI operation. See page 76. Always set up the CI MSD in PCI first, even if you are going to run NCI. Procedure 1 Verify that the MSD performs correctly in E1 mode. 2 Verify that the PCICH4.U tune file is loaded. 3 Select Gas A and set flow to 20%. 4 In Tune and Vacuum Control view, perform CI setup.
4 Operating in Chemical Ionization (CI) Mode To verify NCI performance This procedure is for EI/PCI/NCI MSDs only. Materials needed • Octafluoronaphthalene (OFN), 100 fg/µL (5188-5347) CA U T I O N Always verify MSD performance in EI before switching to CI operation. See page 76. Always set up the CI MSD in PCI first, even if you are going to run NCI. Procedure 1 Verify that the MSD performs correctly in EI mode. 2 Load the NCICH4.U tune file, and accept the temperature setpoints.
4 Operating in Chemical Ionization (CI) Mode To monitor high vacuum pressure WARN I NG If you are using hydrogen as a carrier gas, do not turn on the Micro-Ion vacuum gauge if there is any possibility that hydrogen has accumulated in the manifold. Read “Hydrogen Safety” before operating the MSD with hydrogen carrier gas. Procedure 1 Start up and pump down the MSD. See page 103. 2 In the Tune and Vacuum Control view select Turn Vacuum Gauge on/off from the Vacuum menu.
Operating in Chemical Ionization (CI) Mode 4 Typical pressure readings Use the G3397A Micro-Ion vacuum gauge. Note that the mass flow controller 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 (Table 20). They were taken with the following set of conditions.
4 126 Operating in Chemical Ionization (CI) Mode 5975 Series MSD Operation Manual
Agilent 5975 Series MSD Operation Manual 5 General Maintenance Before Starting 128 Maintaining the Vacuum System 133 Agilent Technologies 127
5 General Maintenance Before Starting You can perform much of the maintenance required by your MSD. For your safety, read all of the information in this introduction before performing any maintenance tasks. Scheduled maintenance Common maintenance tasks are listed in Table 21. Performing these tasks when scheduled can reduce operating problems, prolong system life, and reduce overall operating costs. Keep a record of system performance (tune reports) and maintenance operations performed.
5 General Maintenance Tools, spare parts, and supplies Some of the required tools, spare parts, and supplies are included in the GC shipping kit, MSD shipping kit, or MSD tool kit. You must supply others yourself. Each maintenance procedure includes a list of the materials required for that procedure.
5 General Maintenance Dangerous temperatures Many parts in the MSD operate at, or reach, temperatures high enough to cause serious burns. These parts include, but are not limited to: • GC/MSD interface • Analyzer parts • Vacuum pumps WARN I NG Never touch these parts while your MSD is on. After the MSD is turned off, give these parts enough time to cool before handling them. WARN I NG The GC/MSD interface heater is powered by a thermal zone on the GC.
5 General Maintenance pumps, install a hose to take the exhaust from the foreline pump outdoors or into a fume hood vented to the outdoors. For the standard foreline pump, this requires removing the oil trap. Be sure to comply with your local air quality regulations. WARN I NG The oil trap supplied with the standard foreline pump stops only foreline pump oil. It does not trap or filter out toxic chemicals. If you are using toxic solvents or analyzing toxic chemicals, remove the oil trap.
5 General Maintenance 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. CA U T I O N To be effective, an antistatic wrist strap must fit snugly (not tight). A loose strap provides little or no protection. Antistatic precautions are not 100% effective. Handle electronic circuit boards as little as possible and then only by the edges.
5 General Maintenance Maintaining the Vacuum System Periodic maintenance As listed earlier in Table 21, some maintenance tasks for the vacuum system must be performed periodically.
5 General Maintenance To remove the EI ion source Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Pliers, long-nose (8710-1094) Procedure 1 Vent the MSD. See page 82. 2 Open the analyzer chamber. See page 84. Make sure you use an antistatic wrist strap and take other antistatic precautions before touching analyzer components. 3 Disconnect the seven wires from the ion source. Do not bend the wires any more than necessary (Figure 32 and Table 22).
General Maintenance 5 4 Trace the wires for the ion source heater and temperature sensor to the feedthrough board. Disconnect them there. 5 Remove the thumbscrews that hold the ion source in place. 6 Pull the ion source out of the source radiator. WARN I NG The analyzer operates at high temperatures. Do not touch any part until you are sure it is cool.
5 General Maintenance To reinstall the EI ion source Materials needed • Gloves, clean, lint-free • Large (8650-0030) • Small (8650-0029) • Pliers, long-nose (8710-1094) Procedure 1 Slide the ion source into the source radiator (Figure 33). 2 Install and hand tighten the source thumbscrews. Do not overtighten the thumbscrews. 3 Connect the ion source wires as shown in “To close the analyzer chamber” . Close the analyzer chamber.
General Maintenance 5 4 Pump down the MSD. See page 91.
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Agilent 5975 Series MSD Operation Manual 6 CI Maintenance General Information 140 Ion source cleaning 140 Ammonia 140 To Set Up Your MSD for CI Operation 141 Guidelines 141 To install the CI ion source 142 To install the CI interface tip seal 143 This chapter describes maintenance procedures and requirements that are unique to 5975 Series MSDs equipped with the Chemical Ionization hardware.
6 CI Maintenance General Information Ion source cleaning The main effect of operating the MSD in CI mode is the need for more frequent ion source cleaning. In CI operation, the ion source chamber is subject to more rapid contamination than in EI operation because of the higher source pressures required for CI. WARN I NG Always perform any maintenance procedures using hazardous solvents under a fume hood. Be sure to operate the MSD in a well-ventilated room.
6 CI Maintenance 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, verify that the GC/MSD system is performing correctly. See “To verify system performance” . • Make sure the reagent gas inlet line(s) are equipped with gas purifiers (not applicable for ammonia). • Use extra-high purity reagent gases; 99.
6 CI Maintenance To install the CI ion source CA U T I O N Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components. Wear a grounded antistatic wrist strap and take other antistatic precautions before you open the analyzer chamber. Procedure 1 Vent the MSD and open the analyzer. See page 84. 2 Remove the EI ion source. See page 134. 3 Remove the CI ion source from its storage box and insert the ion source into the radiator.
6 CI Maintenance To install the CI interface tip seal Materials needed • Interface tip seal (G1099-60412) The interface tip seal must be in place for CI operation. It is necessary to achieve adequate ion source pressure for CI. CA U T I O N Electrostatic discharges to analyzer components are conducted to the side board where they can damage sensitive components. Wear a grounded antistatic wrist strap and take other antistatic precautions before you open the analyzer chamber.
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Agilent 5975 Series MSD Operation Manual A Chemical Ionization Theory Chemical Ionization Overview 146 Positive CI Theory 148 Negative CI Theory 155 Agilent Technologies 145
A Chemical Ionization Theory Chemical Ionization Overview Chemical ionization (CI) is a technique for creating ions used in mass spectrometric analyses. There are significant differences between CI and electron ionization (EI). This section describes the most common chemical ionization mechanisms. In EI, relatively high-energy electrons (70 eV) collide with molecules of the sample to be analyzed. These collisions produce (primarily) positive ions.
A Chemical Ionization Theory contaminated ion source. Water contamination is most common immediately after new reagent gas tubing or reagent gas cylinders are connected. This contamination will often decrease if the reagent gas is allowed to flow for a few hours, purging the system. References on chemical ionization A. G. Harrison, Chemical Ionization Mass Spectrometry, 2nd Edition, CRC Press, INC. Boca Raton, FL (1992) ISBN 0-8493-4254-6. W. B. Knighton, L. J. Sears, E. P.
A Chemical Ionization Theory Positive CI Theory Positive CI (PCI) occurs with the same analyzer voltage polarities as EI. For PCI, the reagent gas is ionized by collision with emitted electrons. The reagent gas ions react chemically with sample molecules (as proton donors) to form sample ions. PCI ion formation is more “gentle” than electron ionization, producing less fragmentation.
Chemical Ionization Theory Figure 35 A Methyl stearate (MW = 298): EI, methane PCI, and ammonia PCI 5975 Series MSD Operation Manual 149
A Chemical Ionization Theory Proton transfer Proton transfer can be expressed as BH+ + M MH+ + B where the reagent gas B has undergone ionization resulting in protonation. If the proton affinity of the analyte (sample) M is greater than that of the reagent gas, then the protonated reagent gas will transfer its proton to the analyte forming a positively charged analyte ion.
Chemical Ionization Theory Table 23 Reagent gas proton affinities Species Proton affinity kcal/mole Reactant ion formed H2 100 H3+ (m/z 3) CH4 127 C2H4 160 H2O 165 CH5+ (m/z 17) C2H5+ (m/z 29) H O+ (m/z 19) H2S 170 H3S+ (m/z 35) CH3OH 182 CH3OH2+ (m/z 33) t-C4H10 195 t-C4H9+ (m/z 57) NH3 207 NH4+ (m/z 18) Table 24 A 3 Proton affinities of selected organic compounds for PCI Molecule Proton affinity (kcal/mole) Molecule Proton affinity (kcal/mole) Acetaldehyde 185 Methyl
A Chemical Ionization Theory Table 24 Proton affinities of selected organic compounds for PCI (continued) Molecule 152 Proton affinity (kcal/mole) Molecule Proton affinity (kcal/mole) Isopropyl alcohol 190 Xylene 187 Methanol 182 5975 Series MSD Operation Manual
A Chemical Ionization Theory Hydride abstraction In the formation of reagent ions, various reactant ions can be formed that have high hydride-ion (H–) affinities. If the hydride-ion affinity of a reactant ion is higher than the hydride-ion affinity of the ion formed by the analyte's loss of H–, then the thermodynamics are favorable for this chemical ionization process. Examples include the hydride abstraction of alkanes in methane chemical ionization.
A Chemical Ionization Theory intense [M+NH4]+ ion observed at M+18 m/z, either through condensation or association. If this resulting ion is unstable, subsequent fragmentation may be observed. The neutral loss of H2O or NH3, observed as a subsequent loss of 18 or 17 m/z, respectively, is also common. Charge exchange Charge-exchange ionization can be described by the reaction: · · X+ + M M+ + X where X+ is the ionized reagent gas and M is the analyte of interest.
A Chemical Ionization Theory Negative CI Theory Negative chemical ionization (NCI) is performed with analyzer voltage polarities reversed to select negative ions. There are several chemical mechanisms for NCI. Not all mechanisms provide the dramatic increases in sensitivity often associated with NCI.
A Chemical Ionization Theory Figure 36 156 Endosulfan I (MW = 404): EI and methane NCI 5975 Series MSD Operation Manual
A Chemical Ionization Theory Electron capture Electron capture is the primary mechanism of interest in NCI. Electron capture (often referred to as high-pressure electron capture mass spectrometry or HPECMS) provides the high sensitivity for which NCI is known. For some samples under ideal conditions, electron capture can provide sensitivity as much as 10 to 1000 times higher than positive ionization.
A Chemical Ionization Theory Dissociative electron capture Dissociative electron capture is also known as dissociative resonance capture. It is a process similar to electron capture. The difference is that during the reaction, the sample molecule fragments or dissociates. The result is typically an anion and a neutral radical.
Chemical Ionization Theory A Ion-molecule reactions Ion-molecule reactions occur when oxygen, water, and other contaminants are present in the CI ion source. Ion-molecule reactions are two to four times slower than electron-attachment reactions and do not provide the high sensitivity associated with electron capture reactions.
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