Recently I made a large spectral library made 30 raw files from the Q-Exactive. After the mzXML conversion with msconvert I did a database search with X!Tandem (using TPP) and retrieved 30 pep.xml files. Subsequently I merged the 30 files with Peptideprophet into one interact.pep.xml file.This file I used to build a spectral library with SpectraST (also using the TPP). This resulted in a huge spectral library with a filesize of 5GB. I was wondering why this was such a huge file so I inspected the file with spectral library viewer in Skyline. I noticed that there many duplicate entries in the spectral library. I know that one peptide can be assigned to different spectra so peptides in the library does not have to be unique. But I found out that the spectral library contained the same peptide assigned to the same spectra multiple (between 10 and 25) times. Is there a particular reason why the spectral library have so many exactly the same entries and is there a possibility to remove them, so that at least every spectra in the library is unique?
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