http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Mascot2XML/
This just points you to the Mascot2XML source files (which are dependent on other source files in the TPP project). On Thu, Jul 1, 2010 at 6:22 AM, Ronald W. Finnegan <r...@mail.nih.gov> wrote: > Jimmy, > > I am using the Mascot2XML from the last TPP version released > 9-9-2009. Can you please point me to the trunk where I can download > rev 4945 from your April 15, 2010 check-in? > > thanks > > Ron > > On Jun 30, 7:02 pm, Jimmy Eng <jke...@gmail.com> wrote: >> I have faint memories of dealing with this but I'm away from work so >> can't confirm. This might've been fixed in rev 4945 check-in on April >> 15th; my check-in log message for Mascot2XML was "parsing update for >> entry with protein n-term modification which doesn't seem to be >> handled by current code". >> >> Are you able to compile Mascot2XML from trunk and see if the problem >> goes away? Otherwise, I'll follow-up with this next week when I'm >> back at work. >> >> On Tue, Jun 29, 2010 at 5:59 AM, Ronald W. Finnegan <r...@mail.nih.gov> >> wrote: >> >> >> >> > Can anyone tell me if this bug reported back in April 2009 has been >> > fixed: >> >> > Thermo Orbitrap RAW file is inputted into tpp -> convert to mzxml -> >> > convert to mgf -> run mascot -> convert to pepXML >> >> > The problem is as follows: >> >> > When I use the mascot default modification Acetyl (protein N-term), >> > the TPP converter that converts the mascot output .DAT file to pepXML >> > format creates the following header in the pepXML file: >> >> > <aminoacid_modification aminoacid=" " mass="42.010559" >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > <aminoacid_modification aminoacid="N" mass="156.053486" >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > <aminoacid_modification aminoacid="-" mass="42.010559" >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > <aminoacid_modification aminoacid="t" mass="42.010559" >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > <aminoacid_modification aminoacid="e" mass="42.010559" >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > <aminoacid_modification aminoacid="r" mass="42.010559" >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> > <aminoacid_modification aminoacid="m" mass="42.010559" >> > massdiff="42.010559" peptide_terminus="n" variable="Y"/> >> >> > If you look at this header closely, the entries are not only >> > meaningless, but there is something funny to be seen if you look at >> > the aminoacid="" entries: >> >> > aminoacid=" " >> > aminoacid="N" >> > aminoacid="-" >> > aminoacid="t" = N - term >> > aminoacid="e" >> > aminoacid="r" >> > aminoacid="m" >> >> > as far as I know the aminoacid property should indicate aminoacid >> > letters and not be spelling out N-term. This is obviously a parsing >> > error occurring somewhere during the conversion. >> >> > Here is the link the original thread: >> >> >http://groups.google.com/group/spctools-discuss/browse_thread/thread/... >> >> > thanks >> >> > Ron >> >> > -- >> > 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.- Hide quoted text >> > - >> >> - Show quoted text - > > -- > 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 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 spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
