Hello. I came across this post while doing a google search for "conversion of msf files to pepXML". I am trying to use Proteome Discoverer output with a protein assembly tool called "IDpicker", but of course it is impossible to export pepXML format from Proteome Discoverer. Has there been a consensus reached on how to make the conversion to pepXML? Thanks Patrick
On Tuesday, April 5, 2011 10:33:43 PM UTC-4, Christine Vogel wrote: > > Hi All, > > Reposting Thomas' question from earlier -- what is a good converter > from Thermo's .msf to TPP suitable files (i.e. pepXML)? > > I tried to find it on the list, and the discussion let me to here: > > https://github.com/itmat/thermo_msf/blob/master/README.rdoc#readme > > But I am unable to successfully install/use this. Any help on this > converter/installation? > > Thanks a lot, > > Christine > > > ----- > > From: Thomas DV <thomas.devijl...@ua.ac.be> > Date: Sun, 5 Dec 2010 08:43:28 -0800 (PST) > Local: Sun, Dec 5 2010 12:43 pm > Subject: proteome discoverer 1.1 to pepXML > Reply to author | Forward | Print | Individual message | Show original > | Report this message | Find messages by this author > Hello everybody, > > I'm new to this group and in fact rather new to proteome data analysis > as a whole. > > We are using Thermo's proteome discoverer at the lab, which gives .msf > output files. > I wanted to try the Ascore program to see whether this could help in > localizing the phosphorylation site in peptides we measured. > but this requires pepXML input. I've tried to find a converter > for .msf into pepXML but it doesn't seem to exist, is that right? > > is there any possibility to extract a SEQUEST .out file from within > proteome discoverer or any work-around to create pepXML from proteome > discoverer results through other data output formats? > > thanks kindly for any help! > Thomas > > student, University of Antwerp, Belgium > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/bwRjQKorGkwJ. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
