Implementation method of molecular omics data structure based on data independent acquisition mass spectra

An implementation method of a molecular omics data structure based on data independent acquisition mass spectra, comprising the following steps:

• step A:
• converting an original mass spectrometry data file into a mzXML format file, and performing centroiding for the original mass spectrometry data, the obtained mzXML format file comprising all necessary information of MS1 and MS2 data;
• step B:
• extracting required mass spectrometry data from the mzXML format file obtained in step A, the mass spectrometry data comprising at least the following attributes:
• scan level, scan index, retention time, precursor ion mass-to-charge ratio, fragment ion mass-to-charge ratio and fragment ion intensity;
• step C:
• counting the total number of cycles and cycle indexes for the mass spectrometry data extracted in step B according to the scan level and scan index, performing loss scan detection, filling in 0 placeholders in all lost positions, and obtaining windows and cycle indexes of precursor ions corresponding to fragment ions in the data;
• step D:
• binning the mass spectrometry data obtained in step C according to the attribute of the fragment ion mass-to-charge ratio, and summing intensity values of fragment ions falling in the same fragment ion mass-to-charge ratio bin;
• step E:
• reordering the mass spectrometry data processed in step D, wherein the reordering refers to obtaining corresponding window indexes according to the precursor ion mass-to-charge ratio data corresponding to the MS2, and rearranging the MS2 having the same window index in order of cycle indexes;
• and
• step F:
• constituting tensor data of MS2 fragment ion intensity from the data processed in step E based on three dimensions:
• a cycle index, a fragment ion mass-to-charge ratio, and a precursor ion window index corresponding to a fragment ion.