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 <[email protected]> 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 <[email protected]> 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 [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.- 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 [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.
