MS2-prepro

Python scripts and Jupyter notebooks for MS/MS spectra pre-processing

Remove precursor peak

Remove fragment peak(s) close to the precursor m/z.

    Parameters
    ----------
    input_file : path to the mgf file to remove precursor peak
    output_file : name of the mgf file with the precursor peak removed
    fragment_tol_mass : float
        Fragment mass tolerance around the precursor mass to remove the
        precursor peak.
    fragment_tol_mode : {'Da', 'ppm'}
        Fragment mass tolerance unit. Either 'Da' or 'ppm'.
    isotope : int
        The number of precursor isotopic peaks to be checked (the default
        is 0 to check only the mono-isotopic peaks).
        
    Returns
    -------
    Nothing, it writes an mgf file with the name set in 'output_file'

Usage example: python remove_precursor_peak.py input.mgf output.mgf Da 10

Rank TIC normalization

Normalizes spectra intensities by computing the sum of all raw intensities I(pk) in P that are smaller than I(pi) and dividing this sum by the total ion current (TIC) of P. So,the highest peak I(pj) equals 1. All other peaks pi are scaled relative to the total ion current of all peaks.

Parameters
----------
    input_file : path to the mgf file to normalize
    output_file : name of the mgf file normalized
    
Returns
-------
    Nothing, it creates an mgf file with the intensities normalized in 'output_file'

Usage example: python rank_TIC_normalization.py input.mgf output.mgf