Page 1 Agilent 5975 Series MSD Operation Manual for MassHunter Agilent Technologies...
Page 2 Do not proceed beyond a WARNING notice until the indicated conditions are fully understood and met. 5975 Series MSD Operation Manual...
Page 3 This manual contains information for operating and maintaining the Agilent 5975 Series Gas Chromatograph/Mass Selective Detector (GC/MSD) system. “Introduction” Chapter 1 describes general information about the 5975 Series MSDs, including a hardware description, general safety warnings, and hydrogen safety information. “Installing GC Columns”...
Page 4 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, 5975 Series MSD, 7693A ALS, and the 7683B ALS. Included are localized versions of the information you need most, such as: •...
Page 5: Table Of Contents
To Condition a Capillary Column To Install a Capillary Column in the GC/MSD Interface Agilent 7890A and 7820A, and 6890 GCs 6850 GC Operating in Electron Impact (EI) Mode Operating the MSD from the Data System 5975 Series MSD Operation Manual for MassHunter...
Page 6 To View MSD Temperature and Vacuum in Manual Tune To Set Monitors for MSD Temperature and Vacuum Status To Set Analyzer Temperatures from the Instrument Control View To Set the GC/MSD Interface Temperature from MassHunter To Monitor High Vacuum Pressure 5975 Series MSD Operation Manual for MassHunter...
Page 7 To Calibrate Column Flow Linear Velocity To Tune the MSD in EI Mode To Verify System Performance To Perform High-Mass Testing (5975 Series MSDs) To Remove the MSD Covers To Vent the MSD To Open the Analyzer Chamber To Close the Analyzer Chamber...
Page 8 To Install the CI Ion Source To Install the CI Interface Tip Seal To Remove the CI Source To Disassemble the CI Source To Clean the CI Source To Assemble the CI Source 5975 Series MSD Operation Manual for MassHunter...
Page 9: Series Msd Operation Manual For Masshunter
To Replace a Filament in a CI Source Chemical Ionization Theory Chemical Ionization Overview Positive CI Theory Negative CI Theory 5975 Series MSD Operation Manual for MassHunter...
Page 10 5975 Series MSD Operation Manual for MassHunter...
Page 11 Agilent 5975 Series MSD 5975 Series MSD Operation Manual for MassHunter Introduction 5975 MSD Version Abbreviations Used The 5975 Series MSD CI MSD Hardware Description Important Safety Warnings Many internal parts of the MSD carry dangerous voltages Electrostatic discharge is a threat to MSD electronics...
Page 12: Introduction
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. Table 1...
Page 13: Abbreviations Used
Electron volt Gas chromatograph High-energy dynode (refers to detector and its power supply) Inside diameter Local Area Network Local control panel (on the MSD) Low thermal mass Mass to charge ratio Mass flow controller 5975 Series MSD Operation Manual for MassHunter...
Page 14 Octafluoronaphthalene (calibrant) 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 Radio frequency RFPA Radio frequency power amplifier Torr Unit of pressure, 1 mm Hg Turbo Turbomolecular (pump) 5975 Series MSD Operation Manual for MassHunter...
Page 15: The 5975 Series Msd
Introduction 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). The MSD features: • Local Control Panel (LCP) for locally monitoring and operating the MSD •...
Page 16 (30 m) CI capability ‡ capability (3rd party) Total gas flow into the MSD: column flow plus reagent gas flow (if applicable). † Expect degradation of spectral performance and sensitivity. ‡ Direct insertion probe. 5975 Series MSD Operation Manual for MassHunter...
Page 17: Ci Msd Hardware Description
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. 5975 Series MSD Operation Manual for MassHunter...
Page 18 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 •...
Page 19: Important Safety Warnings
Do not touch any of the boards unless it is absolutely necessary. If you must handle them, wear a grounded wrist strap and take other antistatic precautions. Wear a grounded wrist strap any time you must remove the MSD right side cover. 5975 Series MSD Operation Manual for MassHunter...
Page 20: Many Parts Are Dangerously Hot
Combustible materials (or flammable/non-flammable wicking material) placed WARNING under, over, or around the foreline (roughing) pump constitutes a fire hazard. Keep the pan clean, but do not leave absorbent material such as paper towels in it. 5975 Series MSD Operation Manual for MassHunter...
Page 21: Hydrogen Safety
When using hydrogen as a carrier gas, remove the large round plastic cover for the MSD transfer line located on the GC left side panel. In the unlikely event of an explosion, this cover may dislodge. 5975 Series MSD Operation Manual for MassHunter...
Page 22: Dangers Unique To Gc/Msd Operation
It can also be shut down accidentally by an internal or external failure. A mass spectrometer shutdown does not shut off the flow of carrier gas. As a result, hydrogen may slowly accumulate in the mass spectrometer. 5975 Series MSD Operation Manual for MassHunter...
Page 23 As described previously, in some GCs a power failure may cause the carrier gas flow to be set to maximum. As a result, hydrogen may accumulate in the mass spectrometer. 5975 Series MSD Operation Manual for MassHunter...
Page 24: Precautions
WARNING personal injury in the event of an explosion. You must remove the plastic cover over the glass window on the front of a 5975 MSD. In the unlikely event of an explosion, this cover may dislodge. General laboratory precautions •...
Page 25 Environmental Health and Safety (EHS) requirements. Always check for leaks after changing a tank or servicing the gas lines. Always make sure the vent line is vented into a fume hood. 5975 Series MSD Operation Manual for MassHunter...
Page 26: Safety And Regulatory Certifications
• AUS/NZ This ISM device complies with Canadian ICES-001. Cet appareil ISM est conforme a la norme NMB—001 du Canada. The 5975 Series MSD is designed and manufactured under a quality system registered to ISO 9001. Information The Agilent Technologies 5975 Series MSD meets the following IEC (International Electro-technical Commission) classifications: Equipment Class I, Laboratory Equipment, Installation Category II, Pollution Degree 2.
Page 27: Symbols
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.
Page 28: Electromagnetic Compatibility
4 Make sure that all peripheral devices are also certified. 5 Make sure that appropriate cables are used to connect the device to peripheral equipment. 6 Consult your equipment dealer, Agilent Technologies, or an experienced technician for assistance. 7 Changes or modifications not expressly approved by Agilent Technologies could void the user’s authority to operate the equipment.
Page 29: Cleaning/Recycling The Product
If you plan to move or store your MSD, a few additional precautions are required. The MSD must remain upright at all times; this requires special caution when moving. The MSD should not be left vented to atmosphere for long periods. 5975 Series MSD Operation Manual for MassHunter...
Page 30 Introduction 5975 Series MSD Operation Manual for MassHunter...
Page 31 Agilent 5975 Series MSD Operation Manual for MassHunter Installing GC Columns Columns Conditioning columns Conditioning ferrules Tips and hints To Reconfigure a 6850 GC Column on its Basket To Prepare a Capillary Column for Installation To Install a Capillary Column in a Split/Splitless Inlet...
Page 32: Columns
Total gas flow into the MSD = column flow + reagent gas flow (if applicable) † Expect degradation of spectral performance and sensitivity. Conditioning columns  Conditioning a column before it is connected to the GC/MSD interface is essential. 5975 Series MSD Operation Manual for MassHunter...
Page 33: Conditioning Ferrules
Tips and hints • The column installation procedures for the 5975 Series MSDs is different from that for previous MSDs. Using the procedure from another instrument may not work and may damage the column or the MSD.
Page 34: Installing Gc Columns
(closer to the fan) of the column cage holder. See Figure Column inlet 6850 column nut Column outlet Figure 2 Column 5975 Series MSD Operation Manual for MassHunter...
Page 35 Attach two clips onto the front of the 3 o’clock cross-member piece of the column cage. These clips will help provide appropriate orientation of column ends for their insertion into the GC inlet and MSD interface. 5975 Series MSD Operation Manual for MassHunter...
Page 36 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 Be careful not to scratch the column coating. CA UT IO N 5975 Series MSD Operation Manual for MassHunter...
Page 37 Make sure that the part of the column that is between the two clips does NOT extend above the column label. See Figure Be careful not to scratch the column coating. CA UT IO N 5975 Series MSD Operation Manual for MassHunter...
Page 38 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. 5975 Series MSD Operation Manual for MassHunter...
Page 39: To Prepare A Capillary Column For Installation
• Septum (may be old, used inlet septum) Procedure 1 Slide a septum, column nut, and conditioned ferrule onto the free end of the column (Figure 7). The tapered end of the ferrule should point away from the column nut. 5975 Series MSD Operation Manual for MassHunter...
Page 40 4 Inspect the end for jagged edges or burrs. If the break is not clean and even, repeat steps 2 and 3. 5 Wipe the outside of the free end of the column with a lint-free cloth moistened with methanol. 5975 Series MSD Operation Manual for MassHunter...
Page 41: To Install A Capillary Column In A Split/Splitless Inlet
2 Position the column so it extends 4 to 6 mm past the end of the ferrule (Figure Insulation cup Reducing nut Capillary column 4 to 6 mm Ferrule (inside nut) Inlet column nut Septum Figure 8 Installing a capillary column for a split/splitless inlet 5975 Series MSD Operation Manual for MassHunter...
Page 42 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. 5975 Series MSD Operation Manual for MassHunter...
Page 43: To Condition A Capillary Column
CA UT IO N GC oven, or the inlet. 5 Hold this temperature. Allow the carrier gas to flow for several hours. 6 Return the GC oven temperature to a low standby temperature. 5975 Series MSD Operation Manual for MassHunter...
Page 44 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. 5975 Series MSD Operation Manual for MassHunter...
Page 45: To Install A Capillary Column In The Gc/Msd Interface
• Safety glasses • Wrench, open-end, 1/4-inch and 5/16-inch (8710-0510) Note that the column installation procedure for the 5975 Series MSDs is different from CA UT IO N that for most previous MSDs. Using the procedure from another instrument may result in poor sensitivity and possible damage to the MSD.
Page 46 8 Adjust the column so it projects 1 to 2 mm past the end of the interface. Use the flashlight and hand lens if necessary to see the end of the column inside the analyzer chamber. Do not use your finger to feel for the column end. 5975 Series MSD Operation Manual for MassHunter...
Page 47: 6850 Gc
5 Hand tighten the interface nut. 6 Carefully close the oven door while observing to see that the column does not develop sharp bends or touch the oven walls/floor. Try this procedure several times. 5975 Series MSD Operation Manual for MassHunter...
Page 48 10 Adjust the column so that it protrudes 1 to 2 mm into the analyzer chamber past the end of the GC/MSD interface, and hand tighten the nut. See Figure Make sure the position of the column does not change as you retighten the nut. 5975 Series MSD Operation Manual for MassHunter...
Page 49 Press on the side plate of the MSD to achieve a good seal. Verify that the foreline pump and front fan turn on and that the foreline pump stops gurgling within 60 seconds. 5975 Series MSD Operation Manual for MassHunter...
Page 50 Installing GC Columns 17 Reinstall the MSD analyzer cover. 5975 Series MSD Operation Manual for MassHunter...
Page 51: 3 Operating In Electron Impact (Ei) Mode
To Calibrate Column Flow Linear Velocity To Calibrate Column Flow Linear Velocity To Tune the MSD in EI Mode To Verify System Performance To Perform High-Mass Testing (5975 Series MSDs) To Remove the MSD Covers To Vent the MSD To Open the Analyzer Chamber...
Page 52: Operating In Electron Impact (Ei) Mode
The software and firmware are revised periodically. If the steps in these procedures do CA UT IO N not match your MassHunter Workstation software, refer to the manuals and online help supplied with the software for more information. 5975 Series MSD Operation Manual for MassHunter...
Page 53: Operating The Msd From The Data System
Menu mode allows you to query various aspects of the GC/MSD and to initiate some actions like running a method or sequence or preparing to vent the system. To access a particular menu option: Press [Menu] until the desired menu appears. 5975 Series MSD Operation Manual for MassHunter...
Page 54 After you make your selection, or if you cycle through all available menus, the display automatically returns to Status mode. Pressing [Menu], then [No/Cancel], will always display the Status mode. Pressing [No/Cancel] twice will always return to the Status mode. 5975 Series MSD Operation Manual for MassHunter...
Page 55: Lcp Status Messages
These messages indicate that the MSD has not received its unique IP address from the Windows Service. If the messages persist after you have logged onto your account in the MassHunter Data Acquisition program, consult the Troubleshooting section of the Software Installation manual. 5975 Series MSD Operation Manual for MassHunter...
Page 56: Loading Os
Loading OS • Press sideplate • Loading MSD Firmware 2 Continue to press the sideplate of the MSD until the MSD Ready message appears. This helps the instrument to pump down more quickly. 5975 Series MSD Operation Manual for MassHunter...
Page 57: Lcp Menus
Displays the name of the instrument if connected to MassHunter Data Acquisition online session. The name of the instrument is the name assigned to the MSD by the MassHunter Data Acquisition Configuration dialogue. 5975 Series MSD Operation Manual for MassHunter...
Page 58 Displays the subnet mask for the MSD. ChemStation IP Displays the IP address for the MassHunter Data Acquisition. GC IP Address Displays the IP address for the GC. Ping gateway Checks communication with the gateway. 5975 Series MSD Operation Manual for MassHunter...
Page 59 Controller menu Action Description Reboot controller Starts the LAN/MS control card. Test LCP? Initiates a diagnostic test of the two-line display. Test HTTP link to GC/MSD Checks the status of the HTTP server. ChemStation? 5975 Series MSD Operation Manual for MassHunter...
Page 60: The Ei Gc/Msd Interface
CI GC/MSD interface can be used with either source. See Also “To Install a Capillary Column in the GC/MSD Interface” The GC/MSD interface operates at high temperatures. If you touch it when it is hot, WARNING it will burn you. 5975 Series MSD Operation Manual for MassHunter...
Page 61 Operating in Electron Impact (EI) Mode Heater sleeve Insulation Column Ionization chamber GC oven Analyzer chamber Heater/Sensor assembly Column end protrudes 1 to 2 mm into the ionization chamber. Figure 12 The EI GC/MSD interface 5975 Series MSD Operation Manual for MassHunter...
Page 62: Before You Turn On The Msd
MSD has been pumped down. If the vacuum pumps are off, hydrogen will accumulate in the MSD and an explosion may occur. Read “Hydrogen Safety” before operating the MSD with hydrogen carrier gas. 5975 Series MSD Operation Manual for MassHunter...
Page 63: Pumping Down
The GC/MSD interface temperature can be set and monitored from the data system or from the GC. 5975 Series MSD Operation Manual for MassHunter...
Page 64: Controlling Column Flow
The MSD can be used to measure actual column flow. You inject a small amount of air or other unretained chemical and time how long it takes to reach the MSD. With this time measurement, you can calculate the column flow. See page 5975 Series MSD Operation Manual for MassHunter...
Page 65: Venting The Msd
Do not vent while the turbo pump is still spinning at more than 50%. Do not exceed the maximum recommended total gas flow. See “5975 series MSD models and features” 5975 Series MSD Operation Manual for MassHunter...
Page 66: To View Msd Temperature And Vacuum In Manual Tune
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 venting or pumpdown, even though both the MSD zones are turned off. 5975 Series MSD Operation Manual for MassHunter...
Page 67: To Set Monitors For Msd Temperature And Vacuum Status
Click OK. The new monitors will be stacked on top of each other in the lower right corner of the Instrument Control window. Select Window > Arrange Monitors, or click and drag each monitor to the desired position. 5975 Series MSD Operation Manual for MassHunter...
Page 68 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. 5975 Series MSD Operation Manual for MassHunter...
Page 69: To Set Analyzer Temperatures From The Instrument Control View
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. Do not exceed 200 °C for the quadrupole or 350 °C for the source. CA UT IO N 5975 Series MSD Operation Manual for MassHunter...
Page 70 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. 5975 Series MSD Operation Manual for MassHunter...
Page 71: To Set The Gc/Msd Interface Temperature From Masshunter
When setting the GC/MS interface temperature, never exceed the maximum for your column. Click Apply to download setpoints or click OK to download setpoints and close the window. To make the new settings part of the method, select Save from the Method menu. 5975 Series MSD Operation Manual for MassHunter...
Page 72: To Monitor High Vacuum Pressure
In the Tune and Vacuum Control view select Turn Vacuum Gauge on/off from the Vacuum menu. Select Manual Tune from the Parameters menu to display the Manual Tune dialog. Select the Values tab to view the HiVac reading. 5975 Series MSD Operation Manual for MassHunter...
Page 73 In the Instrument Control view you can set up an MS Monitor for displaying this vacuum reading. The vacuum can also be read on the LCP or from the Manual Tune screen. 5975 Series MSD Operation Manual for MassHunter...
Page 74: To Calibrate Column Flow Linear Velocity
In the Instrument Control view, select GC Parameters from the Instrument menu. Select the Configuration tab and then select the Columns tab. Select your installed column from the table. Click the Calibrate button to display the Calibrate Column dialog. 5975 Series MSD Operation Manual for MassHunter...
Page 75 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 often measured rather than volumetric flow rate. 5975 Series MSD Operation Manual for MassHunter...
Page 76 Calculation for volumetric flow rate 0.785 D --------------------------- - Volumetric flow rate (mL/min) = where: D = Internal column diameter in millimeters L = Column length in meters t = Retention time in minutes 5975 Series MSD Operation Manual for MassHunter...
Page 77: To Tune The Msd In Ei Mode
Click OK to close this dialog and start the tune. If the MSD temperatures are not stable, you are prompted to wait or override the wait by clicking Override. Wait for the tune to complete and generate the report. 5975 Series MSD Operation Manual for MassHunter...
Page 78 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 MassHunter Data Acquisition software for additional information about tuning. 5975 Series MSD Operation Manual for MassHunter...
Page 79: To Verify System Performance
Click OK to run the method. When the method is completed, an evaluation report will be printed. Verify that rms signal-to-noise ratio meets the published specification. Please see the Agilent Web site at www.agilent.com/chem for specifications. 5975 Series MSD Operation Manual for MassHunter...
Page 80: To Perform High-Mass Testing (5975 Series Msds)
“To Tune the MSD in EI Mode” on page 77. Resolve the PFHT.M method under x\5975\PFHT.M where x is the instrument number being used. Update and save the method. Load the PFHT calibration sample into a vial and place in position 2.
Page 81 Operating in Electron Impact (EI) Mode Results Figure 13 PFHT high mass report 5975 Series MSD Operation Manual for MassHunter...
Page 82 Click Done to close the Manual Tune dialog. Load the PFHT.M, then load the saved tune file, and then save the method. Rerun test mixture (repeat high-mass checkout). If the correction is within 5 units, no further adjustments are required. 5975 Series MSD Operation Manual for MassHunter...
Page 83: To Remove The Msd Covers
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. Dangerous voltages are present under other covers. WARNING 5975 Series MSD Operation Manual for MassHunter...
Page 84 Latch Analyzer cover Left side cover Figure 14 Removing covers Do not use excessive force or the plastic tabs that hold the cover to the mainframe will CA UT IO N break off. 5975 Series MSD Operation Manual for MassHunter...
Page 85: To Vent The Msd
MSD with hydrogen carrier gas. Be sure the GC oven and the GC/MSD interface are cool before turning off carrier gas CA UT IO N flow to prevent damage to the column. 5975 Series MSD Operation Manual for MassHunter...
Page 86 Vacuum Control dialog. Remove the analyzer window cover (see “To Remove the MSD Covers” page 83).  Click Vent to begin the automated shutdown of the MSD. Follow the instructions presented. 5975 Series MSD Operation Manual for MassHunter...
Page 87 Vent valve knob Figure 15 Venting the MSD 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. 5975 Series MSD Operation Manual for MassHunter...
Page 88: To Open The Analyzer Chamber
In the next step, if you feel resistance, stop. Do not try to force the side plate open. CA UT IO N Verify that MSD is vented. Verify that both the front and rear side plate screws are completely loose. 4 Gently swing the side plate out. 5975 Series MSD Operation Manual for MassHunter...
Page 89 Do not touch any part until you are sure it is cool. Always wear clean gloves to prevent contamination when working in the analyzer CA UT IO N chamber. 5975 Series MSD Operation Manual for MassHunter...
Page 90 Operating in Electron Impact (EI) Mode Thumbscrews Side plate Analyzer cover CHAMBER CLOSED Detector Side plate Feedthrough board Ion source CHAMBER OPEN Analyzer Figure 16 The analyzer chamber 5975 Series MSD Operation Manual for MassHunter...
Page 91: To Close The Analyzer Chamber
Board, top right (ION FOC) Ion focus lens Blue (1) Board, top right (ENT LENS) Entrance lens Green beaded (2) Ion source heater Board, bottom left (HTR) White (2) Ion source sensor Board, bottom (RTS) 5975 Series MSD Operation Manual for MassHunter...
Page 92 1 FILAMENT - 1 Red wire to repeller FILAMENT - 2 Black wires to filament 2 Ion source heater wires (green) Ion source sensor wires (white) SOURCE Figure 17 Feedthrough board wiring 5975 Series MSD Operation Manual for MassHunter...
Page 93 Make sure the O-ring has a very light coat of Apiezon L high vacuum grease. If the O-ring is very dry, it may not seal well. If the O-ring looks shiny, it has too much grease on it. (Refer to the 5975 Series MSD Troubleshooting and Maintenance Manual for lubricating instructions.)
Page 94 Do not overtighten the thumbscrew; it can cause air leaks or prevent successful CA UT IO N pumpdown. Do not use a screwdriver to tighten the thumbscrew. 8 Once the MSD has pumped down, close the analyzer cover. 5975 Series MSD Operation Manual for MassHunter...
Page 95: To Pump Down The Msd In Ei Mode
Start the MassHunter Data Analysis program. In the Instrument Control view, from the Instrument menu, select MS Vacuum Control to display the Vacuum Control dialog. 5975 Series MSD Operation Manual for MassHunter...
Page 96 The temperature setpoints are stored in the current autotune (*.u) file. 11 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. 5975 Series MSD Operation Manual for MassHunter...
Page 97: To Move Or Store The Msd
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.
Page 98 The MSD must remain upright at all times. If you need to ship your MSD to another CA UT IO N location, contact your Agilent Technologies service representative for advice about packing and shipping. 5975 Series MSD Operation Manual for MassHunter...
Page 99: To Set The Interface Temperature From The Gc
If you want the new setpoint to become part of the current method, click Save under the Method menu. Otherwise, the first time a method is loaded, all the setpoints in the method will overwrite those set from the GC keyboard. 5975 Series MSD Operation Manual for MassHunter...
Page 100 Operating in Electron Impact (EI) Mode 5975 Series MSD Operation Manual for MassHunter...
Page 101 To Monitor CI Mode High Vacuum Pressure This chapter provides information and instructions for operating the 5975 Series CI MSDs in Chemical Ionization (CI) mode. Most of the information in the preceding chapter is also relevant. Most of the material is related to methane chemical ionization but one section discusses the use of other reagent gases.
Page 102: Operating In Chemical Ionization (Ci) Mode
• 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. 5975 Series MSD Operation Manual for MassHunter...
Page 103: The Ci Gc/Msd Interface
See Also “To Install a Capillary Column in the GC/MSD Interface” Never exceed the maximum column temperature, either in the GC/MSD interface, the CA UT IO N GC oven, or the inlet. 5975 Series MSD Operation Manual for MassHunter...
Page 104 The GC/MSD interface operates at high temperatures. If you touch it when it is hot, WARNING it will burn you. Spring-loaded seal GC oven Reagent gas in Column end protrudes 1 to 2 mm into the ionization chamber. Figure 20 The CI GC/MSD interface 5975 Series MSD Operation Manual for MassHunter...
Page 105: To Operate The Ci Msd
NCI, there are no reagent gas ions to monitor. It is difficult to diagnose an air leak and difficult to tell whether a good seal is being created between the interface and the ion volume. 5975 Series MSD Operation Manual for MassHunter...
Page 106: To Switch From The Ei Source To The Ci Source
. Take antistatic precautions before you open the analyzer chamber. 4 Install the CI ion source. See page 162. 5 Install the interface tip seal. See page 164. 6 Close the analyzer. 7 Pump down the MSD. See page 107. 5975 Series MSD Operation Manual for MassHunter...
Page 107: To Pump Down The Msd In Ci Mode
Set the GC/MSD interface to 280 °C. Set Gas A (methane) to 20%. Let the system bake out and purge for at least 2 hours. If you will be running NCI, for best sensitivity, bake out the MSD overnight. 5975 Series MSD Operation Manual for MassHunter...
Page 108: To Set Up The Software For Ci Operation
Max electron energy, eV Notes for Table • 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. 5975 Series MSD Operation Manual for MassHunter...
Page 109 • Maximum emission current Optimum emission current maximum for NCI is very compound-specific and must be selected empirically. Optimum emission current for pesticides, for example, may be about 200 µA. 5975 Series MSD Operation Manual for MassHunter...
Page 110: To Operate The Reagent Gas Flow Control Module
In the Operations area, select Admit a reagent gas for the current tune file. Selecting Gas A Valve or Gas B Valve displays the gas valve A or B in the Gas field and the gas name in the Gas Name field. 5975 Series MSD Operation Manual for MassHunter...
Page 111 If you are not using a second reagent gas, cap the OTHER fitting to prevent accidental admission of air to the analyzer. Supply reagent gases at 25 to 30 psi (170 to 205 kPa). 5975 Series MSD Operation Manual for MassHunter...
Page 112 EI mode Gas A Open Closed Open Closed Closed Closed Gas B Closed Open Closed Open Closed Closed       setpoint setpoint 100% 100% 100% 5975 Series MSD Operation Manual for MassHunter...
Page 113 Gas A with Gas B flow module vented, or EI mode Shutoff valve Open Open Open Open Open Closed The Open and Closed states are shown in the monitors as 1 and 0 respectively. 5975 Series MSD Operation Manual for MassHunter...
Page 114: To Set Up Methane Reagent Gas Flow
Select Methane Pretune from the Setup menu and follow the system prompts. See the MassHunter online help for additional information. The methane pretune tunes the instrument for optimum monitoring of the ratio of methane reagent ions m/z 28/27. 5975 Series MSD Operation Manual for MassHunter...
Page 115 • The peak at m/z 19 (protonated water) is less than 50% of the peak at m/z 17. When prompted, click OK to perform the methane Flow Adjust. Figure 22 Reagent ion scans 5975 Series MSD Operation Manual for MassHunter...
Page 116 Note the low abundance of m/z 19 and absence of any visible peak at m/z 32. Your MSD will probably show more water at first, but the abundance of m/z 19 should still be less than 50% of m/z 17. 5975 Series MSD Operation Manual for MassHunter...
Page 117: To Use Other Reagent Gases
To Use Other Reagent Gases This section describes the use of isobutane or ammonia as the reagent gas. You should be familiar with operating the CI-equipped 5975 Series MSD with methane reagent gas before attempting to use other reagent gases.
Page 118 Addition and proton transfer are the ionization mechanisms most often associated with isobutane. The sample itself influences which mechanism dominates. 5975 Series MSD Operation Manual for MassHunter...
Page 119 NCI tune file for the specific gas. Be sure to read the following application note: Implementation of Ammonia Reagent NO T E Gas for Chemical Ionization on the Agilent 5975 Series MSDs (5989-5170EN). 5975 Series MSD Operation Manual for MassHunter...
Page 120 Ammonia tends to break down vacuum pump fluids and seals. Ammonia CI makes more frequent vacuum system maintenance necessary. (See the 5975 Series MSD Troubleshooting and Maintenance Manual.) When running ammonia for 5 or more hours a day, the foreline pump must be ballasted CA UT IO N (flushed with air) for at least 1 hour a day to minimize damage to pump seals.
Page 121: To Switch From The Ci Source To The Ei Source
Electrostatic discharges to analyzer components are conducted to the side board CA UT IO N where they can damage sensitive components. Wear a grounded antistatic wrist strap and take other antistatic precautions before you open the analyzer chamber. page 137. 5975 Series MSD Operation Manual for MassHunter...
Page 122: Ci Autotune
Always verify MSD performance in EI before switching to CI operation. See page CA UT IO N Always set up the CI MSD in PCI first, even if you are going to run NCI. 5975 Series MSD Operation Manual for MassHunter...
Page 123 150 °C 150 °C 150 °C 150 °C 150 °C 150 °C 150 °C Interface 280 °C 280 °C 280 °C 280 °C 280 °C 280 °C 280 °C temp Autotune N/A Not available 5975 Series MSD Operation Manual for MassHunter...
Page 124: To Perform A Pci Autotune (Methane Only)
The autotune report contains information about air and water in the system. “PCI autotune” on page 125. The 19/29 ratio shows the abundance of water. The 32/29 ratio shows the abundance of oxygen. 5975 Series MSD Operation Manual for MassHunter...
Page 125 Operating in Chemical Ionization (CI) Mode Figure 23 PCI autotune 5975 Series MSD Operation Manual for MassHunter...
Page 126: To Perform An Nci Autotune (Methane Reagent Gas)
127). If the tune sets the electron multiplier voltage (EMVolts) at or above 2600 V, however, you may not be able to acquire data successfully if your method sets EMVolts to “+400” or higher. 5975 Series MSD Operation Manual for MassHunter...
Page 127 Operating in Chemical Ionization (CI) Mode Figure 24 NCI autotune 5975 Series MSD Operation Manual for MassHunter...
Page 128: To Verify Pci Performance
122. Run the PCI sensitivity method BENZ_PCI.M using 1 µL of 100 pg/µL benzophenone. Verify that the system conforms to the published sensitivity specification. Please see the Agilent Web site at www.agilent.com/chem specifications. 5975 Series MSD Operation Manual for MassHunter...
Page 129: To Verify Nci Performance
Autotune completes, it passes. Run the NCI sensitivity method: OFN_NCI.M using 2 µL of 100 fg/µL OFN. Verify that the system conforms to the published sensitivity specification. Please see the Agilent Web site at www.agilent.com/chem specifications. 5975 Series MSD Operation Manual for MassHunter...
Page 130: To Monitor Ci Mode High Vacuum Pressure
131). They were taken with the following set of conditions. Note that these are typical PCI temperatures: Source temperature 250 °C Quad temperature 150 °C Interface temperature 280 °C Helium carrier gas flow 1 mL/min 5975 Series MSD Operation Manual for MassHunter...
Page 131 Measurements will vary by as much as 30% from one MSD and gauge controller to the next. 5975 Series MSD Operation Manual for MassHunter...
Page 132 Operating in Chemical Ionization (CI) Mode 5975 Series MSD Operation Manual for MassHunter...
Page 133: General Maintenance
Agilent 5975 Series MSD Operation Manual for MassHunter General Maintenance Before Starting Maintaining the Vacuum System To Replace the Primary Fuses To Remove the EI Ion Source To Disassemble the EI Source To Clean the EI Source To Assemble an EI Source...
Page 134: Before Starting
Every 3 months for CI MSDs using ammonia reagent gas. † Vacuum seals other than the side plate O-ring and vent valve O-ring do not need to be lubricated. Lubricating other seals can interfere with their correct function. 5975 Series MSD Operation Manual for MassHunter...
Page 135 Some procedures in this chapter require access to the inside of the MSD while the power switch is on. Do not remove any of the electronics safety covers in any of these procedures. To reduce the risk of electric shock, follow the procedures carefully. 5975 Series MSD Operation Manual for MassHunter...
Page 136 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 all foreline 5975 Series MSD Operation Manual for MassHunter...
Page 137 If that is not possible, it should be connected to a conductive (metal) part of the assembly being worked on, but to electronic components, exposed wires or traces, or pins on connectors. 5975 Series MSD Operation Manual for MassHunter...
Page 138 Antistatic precautions are not 100% effective. Handle electronic circuit boards as little as possible and then only by the edges. Never touch components, exposed traces, or pins on connectors and cables. 5975 Series MSD Operation Manual for MassHunter...
Page 139: Maintaining The Vacuum System
Other procedures Tasks such as replacing a foreline vacuum gauge or Micro-Ion vacuum gauge should be performed only when needed. See the 5975 Series MSD Troubleshooting and Maintenance manual and see the online help in the MSD MassHunter software for symptoms that indicate this type of maintenance is required.
Page 140: To Replace The Primary Fuses
(Figure 25) counterclockwise until it pops out. The fuse holders are spring loaded. Remove the old fuse from the fuse holder. Install a new fuse in the fuse holder. Reinstall the fuse holder. 5975 Series MSD Operation Manual for MassHunter...
Page 141 Figure 25 Primary fuses (turbo model shown) Repeat steps 3 through 5 for the other fuse. Always replace both fuses. Reconnect the MSD power cord to the electrical outlet. Pump down the MSD. 5975 Series MSD Operation Manual for MassHunter...
Page 142: To Remove The Ei Ion Source
Connects to Number of leads Blue Entrance lens Orange Ion focus White Filament 1 (top filament) Repeller Black Filament 2 (bottom filament) Pull on the connectors, not on the wires. CA UT IO N 5975 Series MSD Operation Manual for MassHunter...
Page 143 The analyzer operates at high temperatures. Do not touch any part until you are sure WARNING it is cool. Source feedthrough board Ion source Thumbscrews Source heater and temperature sensor wires Source radiator Figure 26 Removing the ion source 5975 Series MSD Operation Manual for MassHunter...
Page 144: To Disassemble The Ei Source
Unscrew the interface socket. A 10-mm open-end wrench fits the flats on the interface socket. Remove the entrance lens and ion focus lens from the lens insulator. 5975 Series MSD Operation Manual for MassHunter...
Page 145 Interface socket Repeller insulator Source heater assembly Repeller insulator Washer Repeller nut Lens insulator Filament (1 of 2) Entrance lens Ion focus lens Drawout cylinder Drawout plate Figure 27 Disassembling the EI ion source 5975 Series MSD Operation Manual for MassHunter...
Page 146: To Clean The Ei Source
 Collect the following parts to be cleaned for an EI source: • Repeller Interface socket • Source body • Drawout plate • Drawout cylinder • Ion focus lens • • Entrance lens 5975 Series MSD Operation Manual for MassHunter...
Page 147 Methylene chloride (reagent-grade) • Acetone (reagent-grade) • Methanol (reagent-grade) • For routine cleaning, cleaning with methanol is sufficient. All of these solvents are hazardous. Work in a fume hood and take all appropriate WARNING precautions. 5975 Series MSD Operation Manual for MassHunter...
Page 148 Take care to avoid recontaminating cleaned and dried parts. Put on new, clean gloves NO T E before handling the parts. Do not set the cleaned parts on a dirty surface. Set them only on clean, lint-free cloths. 5975 Series MSD Operation Manual for MassHunter...
Page 149: To Assemble An Ei Source
Install the interface socket. Attach the repeller assembly to the source body using the two gold plated screws and spring washers. Install the filaments using the two gold plated screws and spring washers. 5975 Series MSD Operation Manual for MassHunter...
Page 150 General Maintenance Do not overtighten the interface socket. Overtightening could strip the threads. CA UT IO N 5975 Series MSD Operation Manual for MassHunter...
Page 151 Source heater assembly Repeller insulator Washer Repeller nut (do not over-tighten) Interface socket Ion focus lens Drawout cylinder Drawout plate Lens insulator (1 of 2) Entrance lens Figure 28 Assembling the ion source 5975 Series MSD Operation Manual for MassHunter...
Page 152: To Replace A Filament In An Ei Source
Open the analyzer chamber. See “To Open the Analyzer Chamber” page 88. Remove the ion source. See “To Remove the EI Ion Source” on page 142. Remove the gold plated screw and washer for the filament(s). 5975 Series MSD Operation Manual for MassHunter...
Page 153 13 Enter the filament number that gave the best results. If you decide to use the first filament number, run Autotune again to make sure the tune parameters are compatible with the filament. 14 Select Save Tune Parameters from the File menu. 5975 Series MSD Operation Manual for MassHunter...
Page 154: To Reinstall The Ei Ion Source
30). 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. 5975 Series MSD Operation Manual for MassHunter...
Page 155 General Maintenance 4 Pump down the MSD. See page Ion source Thumbscrews Source radiator Figure 30 Installing the EI ion source 5975 Series MSD Operation Manual for MassHunter...
Page 156: To Replace The Electron Multiplier Horn
Open the retaining clip. Lift the arm of the clip up and then swing the clip away from the electron multiplier horn. Electron multiplier horn Retaining clip Figure 31 Electron multiplier horn Remove the electron multiplier horn. 5975 Series MSD Operation Manual for MassHunter...
Page 157 Incorrect installation will result in poor sensitivity or no signal. Close the analyzer chamber. See “To Close the Analyzer Chamber” page 91. Pump down the MSD. See “To Pump Down the MSD in EI Mode” page 95. 5975 Series MSD Operation Manual for MassHunter...
Page 158 General Maintenance 5975 Series MSD Operation Manual for MassHunter...
Page 159: Ci Maintenance
To Clean the CI Source To Assemble the CI Source To Replace a Filament in a CI Source This chapter describes maintenance procedures and requirements that are unique to 5975 Series MSDs equipped with the Chemical Ionization hardware. Agilent Technologies...
Page 160: General Information
Always purge the MSD with methane after using ammonia. Be sure to install the ammonia so the tank is in an upright position. This will help prevent liquid ammonia from getting into the flow module. 5975 Series MSD Operation Manual for MassHunter...
Page 161: To Set Up Your Msd For Ci Operation
• Make sure the reagent gas inlet line(s) are equipped with gas purifiers (not applicable for ammonia). • Use extra-high purity reagent gases; 99.99% or better for methane and as pure as is available for other reagent gases. 5975 Series MSD Operation Manual for MassHunter...
Page 162: To Install The Ci Ion Source
3 Remove the CI ion source from its storage box and insert the ion source into the radiator. 4 Reinstall the thumbscrews (Figure 32). 5 Connect the wiring as described in “To Close the Analyzer Chamber” page 91. 5975 Series MSD Operation Manual for MassHunter...
Page 163 CI Maintenance Ion source Thumbscrews Source radiator Figure 32 Installing the CI ion source 5975 Series MSD Operation Manual for MassHunter...
Page 164: To Install The Ci 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.
Page 165: To Remove The Ci Source
Trace the wires for the ion source heater and temperature sensor to the feedthrough board. Use the pliers to pull on the metal connectors to remove these four wires from the feedthrough board connections. 5975 Series MSD Operation Manual for MassHunter...
Page 166 Pull the ion source out of the source radiator. The analyzer operates at high temperatures. Do not touch any part until you are sure WARNING it is cool. Ion source Thumbscrews Source radiator Figure 33 Removing the CI ion source 5975 Series MSD Operation Manual for MassHunter...
Page 167: To Disassemble The Ci Source
Remove the setscrew for the lenses. Pull the lens assembly out of the source body. Remove the drawout cylinder and drawout plate from the source body. Separate the ion focus lens, entrance lens and insulator. 5975 Series MSD Operation Manual for MassHunter...
Page 168 CI dummy filament CI interface tip seal CI ion focus lens CI drawout cylinder CI drawout plate CI lens insulator (1 of 2) Entrance lens Figure 34 Exploded view of the CI ion source 5975 Series MSD Operation Manual for MassHunter...
Page 169: To Clean The Ci Source
These are the parts that contact the sample or ion beam. The other parts normally should not require cleaning. Clean the parts as described in “To Clean the EI Source” on page 146. 5975 Series MSD Operation Manual for MassHunter...
Page 170 If the insulators are dirty, clean them with a cotton swab dampened with reagent-grade CA UT IO N methanol. If that does not clean the insulators, replace them. Do not abrasively or ultrasonically clean the insulators. 5975 Series MSD Operation Manual for MassHunter...
Page 171: To Assemble The Ci Source
Do not overtighten the repeller nut or the ceramic repeller insulators will break when CA UT IO N the source heats up. The nut should only be finger-tight. Reinstall the filaments using the gold plated screws and spring washers. 5975 Series MSD Operation Manual for MassHunter...
Page 172 CI dummy filament CI interface tip seal CI ion focus lens CI drawout cylinder CI drawout plate CI lens insulator (1 of 2) Entrance lens Figure 35 Exploded view of the CI ion source 5975 Series MSD Operation Manual for MassHunter...
Page 173: To Replace A Filament In A Ci Source
“To Pump Down the MSD in EI Mode” page 95. 10 Perform a PCI autotune with methane. See “To Perform a PCI Autotune (Methane Only)” on page 124. 11 Select Save Tune Parameters from the File menu. 5975 Series MSD Operation Manual for MassHunter...
Page 174 CI Maintenance 5975 Series MSD Operation Manual for MassHunter...
Page 175: A Chemical Ionization Theory
Agilent 5975 Series MSD Operation Manual for MassHunter Chemical Ionization Theory Chemical Ionization Overview Positive CI Theory Negative CI Theory Agilent Technologies...
Page 176: Chemical Ionization Overview
A large peak at m/z 19 (H 3 0 + ) in positive CI is a diagnostic symptom of water contamination. In high enough concentrations, especially when combined with calibrant, water contamination will result in a heavily 5975 Series MSD Operation Manual for MassHunter...
Page 177 Mass Spectrometry”, Mass Spectrometry Reviews (1996), 14, 327-343. E. A. Stemmler, R. A. Hites, Electron Capture Negative Ion Mass Spectra of Environmental Contaminants and Related Compounds, VCH Publishers, New York, NY (1988) ISBN 0-89573-708-6. 5975 Series MSD Operation Manual for MassHunter...
Page 178: Positive Ci Theory
The presence of air or water in the system, especially in the presence of PFDTD calibrant, quickly contaminates the ion source. 5975 Series MSD Operation Manual for MassHunter...
Page 179 Chemical Ionization Theory Figure 36 Methyl stearate (MW = 298): EI, methane PCI, and ammonia PCI 5975 Series MSD Operation Manual for MassHunter...
Page 180 “soft” ionization, but the degree of the softness depends on the proton affinities of both the analyte and the reagent gas, as well as on other factors including ion source temperature. 5975 Series MSD Operation Manual for MassHunter...
Page 181 Acetic acid Methyl chloride Acetone Methyl cyanide Benzene Methyl sulfide 2-Butanol Methyl cyclopropane Cyclopropane Nitroethane Dimethyl ether Nitromethane Ethane n-Propyl acetate Ethyl formate Propylene Formic acid Toluene trans-2-Butene Hydrobromic acid Hydrochloric acid Trifluoroacetic acid 5975 Series MSD Operation Manual for MassHunter...
Page 182 Chemical Ionization Theory Table 25 Proton affinities of selected organic compounds for PCI (continued) Molecule Proton affinity Molecule Proton affinity (kcal/mole) (kcal/mole) Isopropyl alcohol Xylene Methanol 5975 Series MSD Operation Manual for MassHunter...
Page 183 In ammonia CI, a series of ion-molecule + , [NH ] + , and reactions takes place, resulting in the formation of NH ] + . In particular, the ammonium ion, NH + , will give rise to an 5975 Series MSD Operation Manual for MassHunter...
Page 184 Charge-exchange chemical ionization is not widely used for general analytical applications. It can, however, be used in some cases when other chemical ionization processes are not thermodynamically favored. 5975 Series MSD Operation Manual for MassHunter...
Page 185: Negative Ci Theory
MSD is operating in negative ion mode. This operating mode reverses the polarity of all the analyzer voltages. Carbon dioxide is often used as a buffer gas in NCI. It has obvious cost, availability, and safety advantages over other gases. 5975 Series MSD Operation Manual for MassHunter...
Page 186 Chemical Ionization Theory Figure 37 Endosulfan I (MW = 404): EI and methane NCI 5975 Series MSD Operation Manual for MassHunter...
Page 187 Contaminants cause the negative ion to be formed by the slower ion-molecule reaction. This generally results in less sensitivity. All potential contamination sources, especially oxygen (air) and water sources, must be minimized. 5975 Series MSD Operation Manual for MassHunter...
Page 188 Instead, the sample molecule fragments in such a way that the electrons are distributed unevenly and positive and negative ions are generated. 5975 Series MSD Operation Manual for MassHunter...
Page 189 Ion-molecule reactions compete with electron capture reactions. The more ion-molecule reactions that occur, the fewer electron capture reactions occur. 5975 Series MSD Operation Manual for MassHunter...
Page 190 Chemical Ionization Theory 5975 Series MSD Operation Manual for MassHunter...

Agilent Technologies 5975 Operation Manual

Table of Contents

1 Introduction

2 Installing Gc Columns

3 Operating in Electron Impact (Ei) Mode

4 Operating in Chemical Ionization (CI) Mode

5 General Maintenance

6 CI Maintenance

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