Hello, I have search result(.pep.xml) from comet database search. But the result file contains negative PSMs that some spectra match the decoy peptides.
Does anyone knows the options or commands that can filter out the negative PSMs during the process of library generating? Below is my work flow: generated decoy fasta using TPP, so the decoy protein accessions are like DECOY1, DECOY2,... , DECOY1200, ... comet database search -> cometresult.pep.xml (using TPP web interface) peptide prophet + iprophet -> cometresult.ipro.pep.xml (using spectrast command line tool) spectrast -cNlibrary -c_RDYDECOY cometresult.ipro.pep.xml -> libray.splib, library.sptxt, library.spidx, library.pepidx What's the proper way to exclude the decoy? do I need to write another script to delete them by myself? Thanks. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
