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I'm starting to look at ways to analyze the output of a mass spectrometer. My first searches led to some white papers far from what I'm looking for (complex molecules vs simple atoms for me). With mass spectrometers being over a century old I'd thought it'd be easy to find algorithm to extract data from the spectra, but no luck so far.

So, I have a array of B/I points, I being the intensity which has some peaks I want to match to some atoms with various states of ionization. I also have a list of likely atoms and their possible charges (i.e. species), for instance:

A;Name;Mass;Abundancy;Z
1;H;1.007825037;99.985;1
2;H;2.014101787;0.015;1
3;He;3.016029297;0.00014;2
4;He;4.00260325;99.99986;2
6;Li;6.0151232;7.5;3
...about 300 species listed

The data looks like this:

7.685483E+1     7.456893E-13
7.685368E+1     9.060985E-13
7.685262E+1     1.510505E-13
7.685148E+1     1.550802E-12
7.685043E+1     2.034891E-12
7.684936E+1     -2.060149E-14
7.684825E+1     1.334606E-12
7.684711E+1     1.191975E-12
...60000 lines like that

Now I'm looking for a way to automatically find the species in the scan, and their relative quantities bearing in mind that:

  • some peaks are very large and reach saturation (can't match with a gaussian)
  • some peaks are very narrow (one single sample)
  • some are negative (apparently where the electron beam went through, I'm not clear on that; or when the calibration is off)
  • there's a wild variation in peak intensity, by several orders of magnitude (even looking at the graph in log scale it's hard to see some minor but present ones)
  • some species are far more likely than others (N vs U)
  • it all depends on the charge/mass ratio of the ions via the formula B=a+b*(A/q)^½ where a and B depends on the calibration and should be found by the algo based on some large and always present reference peaks.

Are there standard algorithms for that ? And if not where should I start (I'm not a physicist) ?

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  • $\begingroup$ You might (I am not at all sure) be better asking this in the Matter Modelling or Chemistry groups - more likely the former $\endgroup$
    – Ian Bush
    Oct 14, 2022 at 14:26
  • $\begingroup$ I'd already looked into those low-traffic groups, but there's no mention of mass spectrometry, so not sure if asking will prove useful... $\endgroup$
    – dargaud
    Oct 17, 2022 at 9:32

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