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.
