I am not sure if Eric or anybody in ISB/SPC has fixed this issue. TPP doesn't seem to read the pep.xml files generated from Proteome Discoverer. I appreciate any advice or suggestion. Thanks Hfaz
On Thursday, April 7, 2011 at 2:38:26 PM UTC-4, Eric Deutsch wrote: > > Thank you all for posting this. Since there seems to be quite a bit of > interest in this, we will try to get this working seamlessly in the TPP. > However, we don’t have MSF results. Can someone provide an example dataset > that we could test with? Some raw data, a FASTA file, and the resulting MSF? > > > > Thanks, > > Eric > > > > > > *From:* [email protected] <javascript:> [mailto: > [email protected] <javascript:>] *On Behalf Of *Christine Vogel > *Sent:* Thursday, April 07, 2011 10:34 AM > *To:* [email protected] <javascript:> > *Subject:* Re: [spctools-discuss] Re: Proteome Discoverer's .msf to TPP > input files (pepXML) > > > > > Thanks, Taejoon. You're awesome! > > Christine > > On Thu, Apr 7, 2011 at 1:27 PM, Taejoon Kwon <[email protected] > <javascript:>> wrote: > > Here's my simple, crude python code to convert MSF to SQT format, and > I confirm that it can be converted to pepxml with TPP Sqt2XML script. > > Few things to mention: > > * Sqt2XML script truncate terminal AA at both ends, but MSF does not > have that info. So I put a dummy AA 'X' at both end. > * I still cannot find the AA modification info in MSF, so calculated > mass in ''Match' record can be incorrect depending on modification. > * deltaCn has various definitions (I didn't know that). > http://mspire.rubyforge.org/spec_id/srf.html > I took the original definition for this script. > > http://www.marcottelab.org/users/taejoon/MS/msf-to-sqt.py.txt > > You can run this with the following simple command (after changing > filename & permission, of course): > > ./msf-to-sqt.py my_file.msf > > I think there is an expert for this kind of task (inside TPP project). > I post this to save his/her time to dig MSF schema (that's what I did > yesterday). Of course I am happy to see him/her to take my code, and > make a single script to convert MSF to pepxml directly. :-) > > Cheers, > > Taejoon > > -- > > 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] > <javascript:>. > To unsubscribe from this group, send email to > [email protected] <javascript:>. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > > > > -- > > > > Christine Vogel, PhD > > NYU-Biology > > Center for Genomics & Systems Biology > > 12 Waverly Place, #403 (office) or 8th floor (mail) > > New York, NY 10003 > > phone: +1-212-998-3976 > > fax: +1-212-995-4015 > > > > http://www.nyu.edu/projects/vogel/ > > > > > > -- > 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] > <javascript:>. > To unsubscribe from this group, send email to > [email protected] <javascript:>. > 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 unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
