Software Manual Section 06

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Mass Calibration
	Introduction The relationship between the mass and the magnetic field "B-field" is in theory pretty simple: Mass = Factor * (B-field)2 In practice, however, we need to make a few correction to this equations, which are empirically determined for a number of selected calibration masses. These masses are stored in a mass array file together with some correction factors. In the figure above, the red dots represent the masses that are part of the current mass array. The vertical axis shows the correction factors for each of these masses. If you want to go to a mass that is not in the mass array, the correction factors of the neighboring masses are used for interpolation. This is indicated by the red connection line. While the exact numerical meaning of the vertical axis is not important for a general understanding of the mass calibration, it is important to note that the red line does describe a relatively smooth curve. Were we to change the correction factor for mass 165 in the way indicated by the white line (still in the figure above), we would not get the same smooth curve. That would be a good indication that something is really wrong with the mass calibration. The adjustments that you make here will be stored in the active mass array file and the correction factors will be used each time a conversion from mass to B-field or vice-versa is necessary.
	Select Existing Mass If you want to select a mass that is in the current calibration table, simply select it from this pull-down menu. This will move the mass spectrometer of the 3f to the selected mass.
	Cross Bar The selected mass will indicated in the diagram by yellow cross bars.
	Up/Down Buttons Use these buttons to move up or down through the masses that are in the current mass array.
	Enter a New Mass If you want to enter a mass to the mass array that wasn't in there before, enter its value here. Only integer mass numbers are allowed. The new mass will be added to the mass array and its initial correction factor will be determined by interpolation between the nearest masses. In other words, the red dot for the new mass will be placed right on the straight connection line between the neighboring red dots. If you add a new mass that is higher than any previous masses, the trend of the correction curve is extrapolated from the last two known points. It is not usually the case that mass 1 is not part of the current mass array. But if it isn't and you add it new, something intelligent is done to give it an initial correction value. At the moment it escapes me what exactly I had the program do in this situation.
	Change Mass Range Shown Here you can change the range of masses that are displayed in the diagram. "Full" shows the entire range, while "Local" only displays the area of plus/minus two masses around the current selection. Sometimes it is better to see details in the "Local" view, while we definitely need "Full" for the big picture.
	B-Field Display This small display of the current B-Field value may be helpful at times. It is being updated every second or so, just like the big diagram.
	Calibration Modes There are two different modes for mass calibration: "Update Array" and "Local Calibration". Both work pretty much the same way they always did on the old HP computer. It is important to know the differences between these modes, whose cryptic names are not really helpful. In this program, you can always see what changes exactly you are about to make before you commit yourself (i.e. before you click "Calibrate Here"). I think this graphical interface really helps to see the differences between both modes of calibration.
	Calibration Mode "Update Array" Whenever this mode is selected, the calibration curve plot will look somewhat like the example on the left. The red curve indicates the old calibration data and the white curve shows the changes that would be introduced if we would calibrate now. In other words, if we click "Calibrate Here", a new red line would follow the white line at this mass and the old red line would disappear. Obviously, this mode of calibration affects only one given mass and does not affect other calibration masses. As mentioned earlier, it would be unusual to have a "bump" in the calibration curve like it is shown here. Please note that this calibration curve plot is dynamic! That means you can manually change the B-Field on the 3f control panel while this window is open and the white curve will follow all changes (the white dot in the picture on the left will move up and down on the vertical yellow line). This should be the normal way of operation: You manually try to center the peak (e.g. by centering the crossover image on the channel plate in slit mode), then verify that the calibration curve looks 'reasonable' and then click "Calibrate Here", if necessary.
	Calibration Mode "Local Calibration" When the calibration mode is changed to "Local Calibration", the calibration curve plot will change to this - even without any changes to the magnetic field. Again the white curve indicates what the calibration curve will be changed to if "Calibrate Here" is clicked. In this mode, any calibration affects all masses and therefore there it does not make much sense to do a "Local Calibration" for more than one mass - all changes of the first "Local Calibration" would be completely undone by a following one. Again, this plot is dynamic and you can see all possible changes in the calibration while manually changing the B-Field. Note: If you ever don't see any white line, that's probably because it is hidden 'behind' the red line. Just move the B-Field knob a little bit and the white line will show up.
	Calibrate Here Clicking here will make changes to the calibration table as described above. The white line will be replaced by a new red line.
	Changes Made... Here you will find a brief list of all the changes to the mass calibration table that you have made since this calibration window was opened.
	Undo If you are really unhappy with calibrations that you have made, here is the button to save your day. All changes will be cancelled.
	Exit Once you click here, all changes of the mass calibration will become permanent. To exit without any changes, click "Undo" first and then "Exit".

FJ Stadermann	Back to Top	Next Section