Maybe it's related to the fact that X!Tandem applies a variable Q-17 modification to N-terminal Qs whether you want it or not. I bet you'll find that those scan numbers you list yield a PSM with an N-terminal Q. Maybe Tandem2XML doesn't know what to do about two possible variable mods on these Qs??
> -----Original Message----- > From: [email protected] [mailto:spctools- > [email protected]] On Behalf Of Rachel > Sent: Tuesday, September 14, 2010 11:33 PM > To: spctools-discuss > Subject: [spctools-discuss] Warnings in Tandem search. > > Hi, > > I did TPP tandem search with the following parameters, > > modification mass 57.021...@c > potential modification mass 15.994...@m > potential modification mass 15.994...@m,0.9...@n,0.9...@q > > However, many warnings popped up when i convert the .tandem file > to .pep.xml file. > i.e. > Tandem2XML.exe ./$x.tandem ./$x.tandem.pep.xml > WARNING: Multiple variable modifications on Q for scan 11685. > WARNING: Multiple variable modifications on Q for scan 11257. > WARNING: Multiple variable modifications on Q for scan 11086. > WARNING: Multiple variable modifications on Q for scan 11062. > .... > .... > etc. > > There are 100+ such WARNINGS. > > I am very grateful if any expert can point it out to me what is the > problem? > > -Thanks in advance > > -- > 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 spctools- > [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.
