Hello, There is an option to output pepXML directly from OMSSA. Also OMSSA provides a pepXML converter. When you run the TPP on OMSSA results you have to specify the special option -P to InteractParser to fix the protein names in the OMSSA output, also the enzyme option should be given at the InteractParser step. To analyze OMSSA results with the TPP the current model requires the use of the non-parametric model, which requires Decoy in the database. Since OMSSA maybe biased in the order in which it reports equivalent hits, it is also recommended that you randomly order the sequences in your fasta database.
Hope this helps, -David On Wed, Nov 18, 2009 at 12:41 AM, Loïc JOFFRE <[email protected]> wrote: > Thank you Brian, but I have already seen those post and they only > explain taht issues exist but no how to do. > If anyone knows? > > Thanks a lot, > Loïc > > On 17 nov, 17:04, Brian Pratt <[email protected]> wrote: >> I don't personally know anything about it, but a quick googling brings up >> this thread that may help you find someone who >> does:http://groups.google.com/group/spctools-discuss/tree/browse_frm/month... >> >> - Brian Pratt >> >> >> >> On Tue, Nov 17, 2009 at 6:08 AM, Loïc JOFFRE <[email protected]> wrote: >> >> > Hello everyone, >> >> > I have .omx result files (from OMSSA browser 2.1.1) and I would like >> > to use the PeptideProphet (TPP v4.3.1). >> > However, the PeptideProphet only accepts .pepxml files, how could I do >> > to run this process from my OMSSA result files? >> >> > I have seen that a converter tool exist (omssa2pepxml) but I do not >> > understand how to use it, I have just found the source code of this >> > program on the web. >> >> > I am working on Windows XP. >> >> > Thanks a lot, >> >> > Loïc Joffre > > -- > > 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=. > > > -- 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=.
