I have downloaded the MascotConverter.cxx source file. How do I compile the MascotConverter file so that the TPP source file dependencies are met?
On Jul 1, 12:35 pm, Jimmy Eng <[email protected]> wrote: > http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteom... > > 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 <[email protected]> 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 <[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 > > 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.
