No params file it is set in either workflow or standalone sequest que. They are dropdowns to choose pre-populated mods (variable and static). So doing the mods is easy. I can send ex. workflow but if you are using PD you would see these readily.
Converter for msf would be tough but the app does export prot.xml (completely diff. than protxml) or zip of dtas or mgf or excel of reports. If you export excel of peptide tab (view) from PD you will find it contains same info as pep.xml file. I will look into quick export to pep.xml. Out of curiosity if working w/ PD why do you want to get it into peptide prophet? DD On Mar 4, 7:08 pm, Jimmy Eng <jke...@gmail.com> wrote: > You should search your Proteome Discoverer box for a file named > 'sequest.params' as I don't have access to the Thermo version. In > fact, I wouldn't even know if sequest.params still exists under > Discoverer. > > Here's the current params file we use at the UW (which is similar to > but not directly the same as Thermo's version of this file). Example > modifications include a +16 variable mod on methionine and a static > mod of +57 on cysteines: > http://proteomicsresource.washington.edu/sequest_params.php > > What we really need is someone to contribute a .msf to pep.xml converter! > > On Thu, Mar 4, 2010 at 3:49 PM, Ping <yanpp...@gmail.com> wrote: > > Thanks Jimmy! > > > Is there any sequest.params sample with modifications I can get? > > > Thanks again! > > > Ping > > > On Mar 3, 5:16 pm, Jimmy Eng <jke...@gmail.com> wrote: > >> unless there's a way to convert .msf to pep.xml, and I'm not aware of > >> any tool that does this, you'll have to go the .out route. > > >> On Mar 3, 2:18 pm, Ping <yanpp...@gmail.com> wrote: > > >> > Hi All, > > >> > The output of the Proteome Discover is *.msf. Is there an easy way to > >> > compute peptide prophet from it? Or I have to run sequest.exe to get > >> > *.out to do so? > > >> > Thanks! > > >> > Ping > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to spctools-disc...@googlegroups.com. > > To unsubscribe from this group, send email to > > spctools-discuss+unsubscr...@googlegroups.com. > > For more options, visit this group > > athttp://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 spctools-disc...@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.
