intensities_raw in .hdf5 file is different from msms.txt in .zip file

[yxwang97]

intensities_raw in .hdf5 file is different from msms.txt in .zip file

[WassimG]

The hdf5 files contain the data we used for training/validation/testing. In general, we used the top 3 highest scoring spectra per peptide, modification, charge, mass analyzer and collision energy setting for this. The identification data was extracted from MaxQuant (msms.txt), but the intensities were extracted from the raw data itself, since the msms.txt files contain de-charged and de-isotoped intensities. So there is somewhat of a relationship between the intensities on most, but not all fragment peaks. The hdf5 files contain only straight y- and b-fragment ions (no neutral losses or other things) up to charge 3 - again some difference to the msms.txt as this contains fragment peaks with neutral losses. In addition, we used a score cutoff of 70 - if I recall correctly, so some peptide identifications you will find the msms.txt will not be present in the hdf5 files. The intensities in the hdf5 files are scaled to the most intense fragment, thus 0-1.