Hello Peter, Currently there is no way to do this in Petunia. You would have to perform this step using command line. Open the command line by going to start and running the cmd command. Once there use the cd command to change directories to the directory containing your mzid files. You will then need to run the following command on the mzid files to fix the problems with MSGF+ mzid format:
perl -pi -e 's/"\?"/"-"/' MY_FILE.mzid Now you can need to run the idconvert tool and rename the file: idconvert MY_FILE.mzid --pepXML mv MY_FILE.pepXML MY_FILE.pep.xml Eventually this should become possible to do with Petunia in an future release. Cheers, -David On Wed, Jul 8, 2015 at 9:55 PM, [email protected] <[email protected]> wrote: > Hi, > > > I want to use the TPP to combine, Mascot, X!Tandem and MSGF+ searches > (amongst other things). I'm having trouble getting around some of the > basics. I have successfully used the TPP in the past to process samples, > but only with Mascot data. > > Once I get my MSGF+ output files converted to pepXML I should be fine. I > cannot work out how I get the MSGF+ files converted. The output generated > by MSGF+ is an mzid file. I am also unclear as to where the database (with > decoys) and mzXML files, used for searching, need to be located when > generating this pepXML file. I have noticed error messages in the logs > about accessing the database and mzXML file. I am generally using the > Petunia interface as it's much nicer to work with multiple files. > > > Thanks, > > > Peter > > -- > 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. > -- 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.
