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] [mailto: [email protected]] *On Behalf Of *Christine Vogel *Sent:* Thursday, April 07, 2011 10:34 AM *To:* [email protected] *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]> 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]. 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. -- 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]. 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. -- 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.
