When I run from Discoverer, it asked me to select all the options and generated a template which can be used later. As I search the computer, no sequest.params files exists. But if I run sequest.exe from command line, it asks for sequest.params file.
I tried the params file you attached, it seems that the format is not compatible :( Thanks again! On Mar 4, 4:08 pm, Jimmy Eng <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > 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 [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.
