Umpire-SearchResultParser v1.1

Umpire search result parser(version: v1.1, 2015.07)

Umpire search result parser(version: v1.0, 2014.11)

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.