PepXML and ProtXML file parser with estimated FDR filtering
Umpire search result parser(version: v1.0, 2014.11) command : java –jar –Xmx1G Umpire-SearchResultParser.jar [Options] [Combined ProtXML file] [PepXML files...]
ProtXML extension: *.prot.xml or *.ProtXML PepXML extension: *.pep.xml or *.PepXML
Options -fP Protein FDR ex: -fP0.01 (default: 0.01, no filtering: -1) -fp Peptide FDR ex: -fp0.05 (default: 0.01, no filtering: -1) -d Decoy tag prefix ex: -dDECOY (default: rev_) -fa Fasta file -N Output filename -pt Initial protein probability filtering threshold ex: -pt0.5 (default: 0.5, no filtering : -1) -rf R factor threshold, proteins with protein probablity less than the threshold will be used to estimate the R factor ex: -rf0.2 (default: 0.2, do not use R factor: -1)
If the PepXML is iProphet result, the reporeted PSM probability is iProphet probability, same with peptide ion table, the maximum probability will be based on iProphet probability.