Doubtful but not sure. PD doesnt detail how it calcs. its prob. On Mar 5, 1:14 am, Ping <yanpp...@gmail.com> wrote: > Thanks for the response. > > I find the function to export prot.xml, but the probability there is > not peptide > prophet, right? > > We need peptide prophet from the sequest search, and thus we can > make comparison with other search results which are measured by > peptide > prophet. > > On Mar 4, 5:39 pm, DD <d.d1...@gmail.com> wrote: > > > 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.
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