How to find a specific mass in your MS data?

With the help of python we can make a simple script to look for a specific ion. We’ll use the python bindings of the OpenMS library fo MS data processing functions, found here pyopenms. We’ll use raw mzML file and search fopr mz within a 20 ppm range.

test_file = "path/to/whereever/your/file/is/file.mzML"
e = MSExperiment()
MzMLFile().load(test_file, e)

We’ll look for the occurence of a pure glycine peak, which has the monoisotopic mass 57.021463735. The function will look for the occurence of a glycine mass return a list with the number of found peaks per MS/MS.

def find_mz(exp, mass, ppm = 20):

  peak_count_list = []
  
    for s in exp:
        peak_count = 0

        for mz, i in zip(*s.get_peaks()):
            ppm_range = (ppm * mz) / 1_000_000
            
            if mz - ppm_range <= mass <= mz + ppm_range:
                  peak_count += 1

        peak_count_list.append(peak_count)

    return peak_count_list

Call it.

gly = 57.021463735
counts = find_mz(e, gly)

You can modifiy this further to look for specific sets of m/z datapoints in your own data. Happy coding. :)

How to github