Damon: "If a peptide has an N-terminal Q or E, it will spontaneously eliminate -17 Da (-NH3) or -18 (-H2O) respectively, to form an N-terminal pyrolidone carboxylic acid. If the N-terminal residue is C and it has been modified by iodoacetimide, it also has an analogous reaction (-17, -NH3). Because they are rather special (they always occur to some degree), they are the only potential modifications that are built into X! Tandem."
On Fri, May 24, 2013 at 12:07 PM, Damon May <[email protected]> wrote: > 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. > > > -- 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.
