Natalie, Yes, we are already using the most current version (4.3.1) of the TPP from September 2009.
Ronald W. Finnegan Bioinformaticist, NIMH Laboratory of Neurotoxicology 10 Center Drive Room 3D42 Bethesda, MD 20892-1262 301 594 3607 -----Original Message----- From: Natalie Tasman [mailto:[email protected]] Sent: Wednesday, June 30, 2010 4:39 PM To: [email protected] Cc: Markey, Sanford P. (NIH/NIMH) [E]; [email protected] Subject: Re: [spctools-discuss] TPP parsing error during Mascot Search result conversion to pepXML It is possible to try the same analysis on the latest version of the TPP and see if the problem has been already addressed? Please let us know. If you still find the issue after testing the latest software, please upload test files to the newsgroup's file section which generate the same issue, and a description of how you process them, and someone will take a look. -Natalie 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. -- 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.
