Hi Ali, Yes, it will affect the output. It means that the converter does not understand how the modification 57.021 ended up on C, based on the parameters X! Tandem reports at the end of your file. Because, Tandem2XML has not reported a corresponding <aminoacid_modification> tag in the <msms_run_summary>, it will drop this modification, and not report it.
X! Tandem really has a lot of ways to specify modifications in its parameters. When I wrote Tandem2XML, I covered as many as I could, but also put this warning in place to help catch those that I hadn't anticipated. It has generated several reports that improved Tandem2XML's handling of these modifications, but it sounds like you have discovered a new one. Though, I would expect something like carbamidomethylated cysteine to be just a normal static modification. If you attach the end of your .tandem file, where all the paramters are listed, I'll have a look, but I am no longer putting much work into Tandem2XML. I may, however, be able to explain to you a work- around, or point someone else in the right direction for a fix. --Brendan On Aug 25, 3:26 am, Ali <[email protected]> wrote: > Hi > > I've converted my .tandem files to .pep.xml successfully. However, > for some of the files I get this warning message: > > WARNING: Unknown modification 'C' (57.021) for scan 56 > > Can anyone explain this warning for me please. Does it effect the > output. > > Regards > > Ali --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
