Hello, It looks like you are compiling a very old version of PeptideProphet, as we no longer use or maintain those executables. For the latest version with full support of Comet results (among others), please use PeptideProphetParser from the latest TPP -- you can just type that into the command-line to get a usage statement. Or you may find it simpler to run it via the xinteract command.
Cheers, --Luis On Fri, Dec 15, 2017 at 4:31 AM, Mohammad Taheri <[email protected] > wrote: > I need to use the tool PeptideProphet > <http://peptideprophet.sourceforge.net/> independently (without TPP) . I > was successful in compiling it in Linux. > > After compilation 4 executable binaries were generated: > > ScoreCalculator, > PeptideProphet, > PeptideProphetOutput and > runPeptideProphet. > > I can execute runPeptideProphet without any problem by passing a html file > as its input argument. But I need to use a pep.xml file (generated by the > tool Comet <http://comet-ms.sourceforge.net/>) as the input argument for > runPeptideProphet. I have already done it via the PeptideProphet in the TPP > tool, but I wonder how to do it for PeptideProphet that I compiled > independently? > May someone please guide me in this problem? > > Respects. > > -- > 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. > -- 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.
