x-Axis label

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We’re starting to get the hang of things. I tried to make some images with MMSIT and decided that BioMap is a lot easier. Now, to see if I’m doing things right:

I’ve divided the range of the scan in Da (48000 Da) by the range of the BioMap image (16000 BioMap volumes) to come up with of 3 Da/BioMap volumes. I then factored in that BioMap volumes start at 0 and the spectrum starts at 1999 Da. Does this sound like the right approach?

[Markus Stoeckli]

No, things are not that simple 😕 . This is all about physics and the properties of a time-of-flight analyzer. The flight time is in a first order approximation proportional to the square root of the mass-to-charge ratio of the flying particle. Since we use a digitizer with a fixed time raster for data acquisition, we end up with data points in the time axis and not in the m/z axis. Most instrument manufacturers use a high order (typ. n > 4) polynomes for time into mass calculation. Since we have not access to most of these calibration equations, we work with a calibration table to our image files (named *.t2m). All the image points are calibrated using this same table. If you load an image in BioMap and a calibration file is present in the same directory, the calibration file is used to label the x-axis. Otherwise, the x-axis is labeled with the volume number.

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