While I also have not come across such as tool, I would like to add my name to the list of those interested in having an open-source option for Proteome Discoverer msf files. I do know that Scaffold by ProteomeSoftware can accept msf files as input, so their team must have developed some flavor of parsing tool. Though I seem to recall when talking to Proteome Software support that achieving this compatibility between msf and Scaffold was not trivial. -Todd
On Apr 6, 12:15 pm, Eric Deutsch <[email protected]> wrote: > Hi Angel, have you been able to transform MSF files to pepXML with your > library, or have ideas about how we might easily accomplish that? > > Thanks, > Eric > > > > > > > > > -----Original Message----- > > From: [email protected] [mailto:spctools- > > [email protected]] On Behalf Of gcrynen > > Sent: Wednesday, April 06, 2011 6:53 AM > > To: spctools-discuss > > Subject: [spctools-discuss] Re: Proteome Discoverer's .msf to TPP input > > files (pepXML) > > > Hi > > I have the same problem, I cant even use TPP since I cant even sequest > > that is now under proteome discoverer. Thermo is not supporting > > Bioworks anymore so we definitely need a converter for msf files > > g > > > On Apr 5, 10:33 pm, Christine Vogel <[email protected]> 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 <[email protected]> > > > 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 post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to spctools- > > [email protected]. > > For more options, visit this group at > >http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
