I'm running X! TANDEM CYCLONE TPP (2011.12.01.1) in TPP 4.6.2 on Ubuntu 12.04.2 LTS.
Similarly to the May 17 issue posted by GATTACA, I'm seeing X!Tandem search results with a variable Cys modification not specified in my parameter files. Specifically, from the xtan.xml: <aa type="C" at="117" modified="-17.02655" /> This only appears to happen on peptide n-terminal C residues, and it doesn't appear on all n-terminal Cysteines. This is identical behavior to the "quick pyrolidone" modification for Q: http://www.thegpm.org/tandem/api/pqp.html But it's happening on C as well as Q. If I run a search with this parameter specified: <note type="input" label="protein, quick pyrolidone">no</note> ...then, as expected, I don't get the -17.02655 modification on n-terminal Q, and I also don't get it on n-terminal C. It looks to me like, most likely, the "quick pyrolidone" modification is erroneously (?) declaring a variable modification on n-terminal C and Q, rather than just Q. Can anyone verify that this is what's going on and indicate whether it's intended or not? If it's unintended, might there be a workaround other than disabling "quick pyrolidone"? Thanks, Damon -- 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.
