Yet another example of why I should search the discussion board *before* posting a question! :)
Thanks Jimmy. :) On Thursday, May 2, 2013 11:20:43 AM UTC-4, Jimmy Eng wrote: > > Damian, > > See this post: > https://groups.google.com/forum/?fromgroups=#!topic/comet-ms/KrbM57S050M > > > On Thu, May 2, 2013 at 3:57 AM, GATTACA <[email protected] <javascript:>>wrote: > >> Hi guys, >> >> I was looking at the pep.xml file generated by the latest release of >> Comet and noticed an inconsistency from other pep.xml files generated for >> Mascot results (for example). >> Normally the top of the file lists the modifications used in the search >> results. >> Traditionally these elements report the mass of the modified residue. But >> in comet the elements just report the mass of the residues unmodified. >> >> Example from Comet-derived pep.xml: >> <aminoacid_modification aminoacid="M" massdiff="15.9949" mass="131.0405" >> variable="Y" symbol="*"/> >> <aminoacid_modification aminoacid="S" massdiff="79.9663" mass="87.0320" >> variable="Y" symbol="#"/> >> <aminoacid_modification aminoacid="T" massdiff="79.9663" mass="101.0477" >> variable="Y" symbol="#"/> >> <aminoacid_modification aminoacid="Y" massdiff="79.9663" mass="163.0633" >> variable="Y" symbol="#"/> >> <aminoacid_modification aminoacid="C" massdiff="57.0215" mass="160.0306" >> variable="N"/> >> >> >> In Mascot-derived pep.xml: >> <aminoacid_modification aminoacid="M" mass="147.035400" >> massdiff="15.994915" variable="Y"/> >> <aminoacid_modification aminoacid="S" mass="166.998359" >> massdiff="79.966331" variable="Y"/> >> <aminoacid_modification aminoacid="T" mass="181.014010" >> massdiff="79.966331" variable="Y"/> >> <aminoacid_modification aminoacid="Y" mass="243.029660" >> massdiff="79.966331" variable="Y"/> >> <aminoacid_modification aminoacid="C" mass="160.030649" >> massdiff="57.021464" variable="N"/> >> >> I'm not sure if this is a bug or simply a difference in how the search >> engine results are reported. >> >> Any thoughts? >> Damian >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> Visit this group at http://groups.google.com/group/spctools-discuss?hl=en >> . >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
