Detailed Procedure for Extrel Benchmark Mass Spectrometer

The first step in using a departmental instrument is to login with the users notebook.
Samples can be submitted for analysis.

---

1. Turn on the monitor, the Sun computer and related computers system are not turned off. The computer and laser printer are turned on from a single switch on the circuit breaker box. The monitor is turned off when not in use with the on/off switch on the lower right front side of the monitor.

2. Turn on the main switch for the Benchmark it turns on the vacuum system and the instrument. Note that both vacuum controllers will begin in the acceleration mode and will switch to the normal mode after a few minutes. Normally about 2 minutes for the upper turbo molecular pump controller and about 3 minutes for the lower controller. If the controllers remain in the acceleration mode for more than 5 minutes turn off the system. The left-front panel can be removed to observe the status of the turbomolecular pumps.

3. At the login type xbench in lower case. The Sun computer has a Unix operating system. Unix is case sensitive. Type in the password: benchmark.

A message will appear indicating there is mail. The Open Windows screen appears and several icons will open (clock, wastebasket, and console)

4. The operator must wait three (3) minutes before beginning to open the software for the instrument. Really 3 minutes, if you do not wait three minutes the system will open in the Demo (Demonstration) Mode, a message indicating Demo Mode appears in the lower right hand corner of the window you must begin again. You can not run the instrument in Demo Mode.

5. Use the right mouse button anywhere on the BLANK part of the screen to bring up the menu. The menu includes IonStation, Programs, and Exit. The other programs are not present and do not function.

6. Push the Reset Button on the 1st or left most board of the Mass Spec Instrument. Select IonStation from the Toolbox when the window opens select
                       Properties,
                                       Instrument,
                                                    Benchmark ThermoBeam,
and then select Apply. The software will begin to load.

7. Repeat step 6 and select Start instead of apply. The software will indicate " extrel_bmk completed " and the red light goes on for the CPU or MIZER Panel (2nd panel from the rear).

8. Double click on the Tune icon and with the left mouse button to open the Tune program. Select File and Load tune file named ei.tune or create a new program. Open Tune Status Window Increase Source Temperature to 200° C, it will take 15 minutes Increase the Expansion Region Temperature to 90°C. Set the Gas Control to CALibration

9. Double click on the Scope icon and open File and Load a Monitor File i.e. select pta_ei.mon and select Load. Under Property select Control.

10. Begin calibration by opening the black- manual valve to the PTA calibration standard. Under the Tune window select Gas Control then CAL and Apply. The standard contains perfluorotributylamine. The following table show the distribution of masses for PTA. Wait a full minute after opening the PTA valve before changing the status of the filament from off or standby to on. The wait will protect the hot filament from being suddenly exposed to the standard. Make certain there is a visible filament glow.

Always return the filament to the standby position when it is not in use, to conserve its lifetime. It is easy to visually check the front-top view port for a filament glow if you are doubt about the filaments condition. The filament may automatically revert to the standby condition, during an analysis. Turn the filament on again and analyze the sample again.

Select Calibrate from the Scope window and under Data select unslope mode. Begin calibration with mass 69. If the mass 69 peak is not exactly at 69, then double click the center of the mass peak and select Apply from the Scope Control window to move the peak to the correct position¹. Repeat the process for each peak. When calibration is finished turn off the black valve on the instrument, return the CAL gas to off the CAL gas in the software and return filament to Standby. The following is an abridged version of the Tune Parameters Window.

The tune status window show the temperatures of the Source, Expansion Region, Nebulizer Control, and Nebulizer Tip. The status must not indicate Open as that means a cable is not connected or the thermocouple is broken.
11. Open Method from the IonStation Toolbox. Select File, Load Method, e.g. Select keb.mth and Load. The following selections are shown and can be modified.

The window will display the TIC (Total Ion Chromatography). Select Load Method (.mth) and under Prop (method) select Sample and Apply. Complete step #12 before beginning to Acquire data.

12. Before connecting the Waters high-pressure pump to the mass spectrometer:

A. Turn on both speedy² valves for the two roughing pumps

B. Remove the quick lock from the inlet port.

C. Start the pump with the nebulizer³ outside of the vacuum chamber to inspect the flow of methanol at 0.5 mL per minute. The on/off switch is at the base of the pump. The only other control that may need adjustment is the flow rate, i.e. increase the flow to 1.5 mL per minute. Observe the flow and if it is satisfactory return it to 0.5 ml per minute. Inspect the spray to be certain it is continuous before turning on the helium. The helium pressure is set at 100 psig.
D. Increase the nebulizer tip temperature to 90° C, while the nebulizer is outside of the instrument.
E. Remove the vacuum flange and attach the nebulizer to the vacuum system. Be careful not to bend or break the capillary tubing at the end of the nebulizer.

F. Leave both speedy valves to the two-roughing pumps open while the nebulizer is attached to the instrument, as well as anytime the vacuum system is open. These valves can be closed only when the vacuum chamber is completely closed.

13. Use a 25-microliter syringe to inject a methanol solution containing about 10 mg/mL of the pure compound. Make about 4 injections of about 5 microliters each. Turn on the filament, after the samples have been prepared, the injection syringe has been properly rinsed and is filled with the sample under the Acquire Window select Start. The data file will append information to a new data file, e.g. if the file is named GAscan1. The new name will GAscan1_01. Click on Stop after the sample has been injected a few times. The next sample injected will be called GAscan1_02. Look at the data during and after the injections are complete to insure the sample shows a signal thousands of times above the background. Change the filament Status to Standby once the sample have been nebulized.

14. Do not begin to review the mass spectra until all samples have been analyzed and the nebulizer has been returned to the Standby position. Click twice on the Review icon in the IonStation toolbox. This option allows you to examine collected data. To open a file under Review select: File, Load Data, and then select the proper file name e.g. 1unk_04.scan and then Load the file Once the file is loaded a window will open the labeled Chromatogram showing the base line and a peak for each injection. The peaks must be much higher than the background.

Note: the software does not allow for additional identification of samples being analyzed; therefore, it is important to make a hand copy of the scan number and general name relative to the sample ID. For instance, 1unk-14 must have a handwritten cross reference such as: 14 Jul -- MW 267, cpd #231a. If files are deleted from a sequence the higher numbers will be decreased.

15. To view the mass spectra first point the cursor at the beginning of the area you want to select and depress the left mouse button and drag the cursor to the end of the area you wish to obtain mass spectra and release the mouse button. Normally an area under a maximum is selected. Select a couple of background points with the SHIFT key held down, as you point to valleys on either side of the selected mass spectra area. Select the Mass Spectra button to view the spectra. It will be labeled with the given name plus the selected scan time and the points used to subtract background.

In order to view the lines of the spectra select the area of the mass spectra and under the Chromatography window select Graph and Quantitation. The data can not be printed from quick print but from the Review Chromatography print menu after selection of Item and Quantitation List.

16. The software also allows identification of compounds under Quick Search. First select a portion of the scan under Review: Chromatography and obtain a mass spectra for that area. Then highlight an area of the spectrum that best describes the compound and with the right mouse button select Quick Search from the drop down menu.

The search program will find ten most likely known compounds that may be the unknown compound. Each compound is ranked against a known relative to the known spectra and then to the difference between the known and unknown. In addition to the three displayed spectra the IUPAC compound name, its molecular weight, CAS number, EPA accession number and normally a structural formula is shown.

17. Print under Review Chromatography has four selections under Item. Normally the selection is left at Mass Spectra Window. Other choices are: Chromatographic Window, Search Window, or Quantitation List.

18. Shut Down Procedure (Check to make certain the filament is Standby or Off)

A. Reduce the nebulizer control temperature to about room temperature 25° C.
B. Lower the Expansion Region temperature to about room temperature.
C. Disconnect the solvent interface between the instrument and the methanol nebulizer.
D. Check the nebulizer tip temperature and turn off solvent flow through the capillary and the helium.
E. Turn off the pump.
F. Place the o-ring seal and stainless steel flange cover over the open nebulization port.
G. Manually, turn the speedy valves off for the roughing pumps.
H. Close all windows and exit the software.
I. Turn the instrument off at the main switch and turn off the monitor.

19. Routine Maintenance

The ion volume needs to be cleaned on a regular basis. When the injection quality degrades cleaning is required.