Standard Operating Procedure of Bruker Autoflex Maldi-Tof Mass Spectrometer 1. Press Ctrl-Alt-Del and enter your name and password to log into the computer. Allow
time (30-60 s) for background processes to start.
2. Exit the WinTV application by clicking a cross in the right top corner of the window.
3. Double click on the FLEX Control icon on the desktop to launch the instrument control
software. A dialog will appear. Click OK. An information window will open as the
computer establishes communication with the mass spectrometer. The FLEX Control
main window will then open.
4. Select the method to use by clicking on the appropriate method file and OK. The files are
named according to detection mode, polarity and mass range. For example, the method
“LP_0-2kDa” is linear mode method in which negative ions are detected in the mass
range of 0-2000 Dalton. You can change the parameters to suit you particular needs.
These files cannot be changed; you will need to save a modified method file under a
different name in your directory.
L=linear mode, R=reflector mode, P=Positive ions, N=negative ions
5. Place your target plate with prepared samples on the frame. Make sure the plate fits
snugly, hits the three contact points of the frame and there are no gaps between the frame
and the plate. The frame is located in the top right desk drawer and must be returned
when finished for the next user.
6. Push the green Eject/Load button on the side of mass spectrometer. The door will open
and the tray for the target will come out.
CAUTION: The tray and loading mechanism are very fragile. Do not bump or apply any
force on the tray. Always keep the area around the sample tray clear.
7. Place the frame with attached target on the tray so the beveled edges are pointing toward
the mass spectrometer. Press the green Eject/Load button again to load the tray into the
mass spectrometer. It will take several minutes for the target to load and the system to
reach proper vacuum.
8. Click on the Sample Carrier tab and select a spot with your calibration sample. Click on
a crystal in the camera screen to point the laser beam on it.
9. Adjust the number of shots (default=30) by changing the value in a small window below
the camera screen. Use a slide bar to the right of the camera screen to adjust the laser
power. A good starting point is 30%.
10. Click the Start button to fire the laser. There may be a slight delay as the laser warms up.
The spectrum will be displayed in the main screen. The laser power can be adjusted while
a spectrum is being acquired if needed.
11. Examine the spectrum for quality. Is the calibrant peak(s) present? Is signal intensity too
high or too weak? If so, adjustments to the laser power may be needed, or a different
crystal/sample spot selected, and a new spectrum acquired.
12. Click on Calibration tab. Select the calibrant from the pull-down menus. Users can
manually enter calibrant(s) by entering appropriate values into the boxes bellow the
calibrant list. A red line will appear on the spectrum at the expected m/z for the calibrant.
13. Select the calibrant on the spectrum by left-clicking to the left of the calibrant peak. The
system will select the peak. The red line will turn green and a small white arrow will
indicate the selected peak. Click the Accept button to calibrate the spectrum.
14. Select another calibrant and repeat the calibration procedure for other calibrant peaks as
necessary. Click the Accept button to calibrate the spectrum. The instrument is now
calibrated. This calibration will apply to all spectra until another method file is opened or
the target is removed or the FLEXControl program is closed.
15. Click on the Sample Carrier tab and select a spot containing sample to be analyzed.
16. Click the Start button to start acquiring data. Adjust the laser power and spot location to
achieve the best possible quality.
17. Choose Save Buffers As item in the File menu. Change the directory to
D:\your_directory, enter the dataset name and click OK.
18. A region of interest in the spectrum can be enlarged using the mouse. Peaks are labeled
by clicking the PeakLabel button on the main toolbar. The sensitivity of the peak picking
machinery can be adjusted by choosing Tools and then On-line processing.
19. The spectrum can be printed out of FLEXControl program by clicking the printer button
on the toolbar.
20. When finished, press the green Eject/Load button on side of the mass spectrometer. The
door will open and the tray with the target will be ejected. Remove the target. Press the
Eject/Load button again to retract the tray and close the door.
21. Exit the FLEXControl program. Log out from the computer by going Start/Shutdown and
choosing “Log Off” from the shutdown menu.