I am trying to evaluate data by qualscore and run into some problems. When I run qualscore on a peptide prophet pep.xml file derived from a mascot search it fails to identify any valid high quality spectra and classifies all spectra as bad. Peptide prophet does however report the expected number of good assignments at 1% peptide level FDR.
- Data generated on a Q Exactive - Normal mascot search - RAW > mzXML conversion by msconvert with peackpicking and filtering for top 100 (if I don't filter the file is too big and qualscore fails running it) - dat > pep.xml conversion - peptide prophet - qualscore on mascot.pep.xml with all other files in the same directory, specific settings for qualscore don't change the outcome Any ideas? Do I need to filter differently to get a small enough mzXML yet retain all data that is needed by qualscore? Which msconvert settings should I use? Thanks a lot Philipp -- 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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
