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/2537c64c225b9e65/dbd1d6677f44ea50?lnk=gst&q=aminoacid_modification#dbd1d6677f44ea50 > > 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 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.
