Ahhh, so it's intended, and it's appropriately part of "quick pyrolidone". Sorry about that.
Thanks! Damon On Friday, May 24, 2013 3:09:03 PM UTC-7, Jimmy Eng wrote: > > 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]<javascript:> > > 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] <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.
