Hi all, I am also trying to use TPP for quantification of SILAC labeled ubiquitin-remnant peptides (variable +114 on K). When I get the Xpress results I noticed none of the ratios make sense. A closer look shows that Xpress is correctly extracting the light mass in place of the heavy mass, and the light mass one SILAC label less than the light mass.
What is the correct way to run xpress on peptide identifications that contain variable lysine modifications (+114) as well as SILAC-labeled lysine (K+8.014). Thank you, Jesse On Monday, September 8, 2008 12:58:23 PM UTC-7, Oded wrote: > > Hi all, > I'm doing SILAC experiments of ubiquitinated proteins and I'm mostly > interested at the actual lysine linkage sites which should contain > (after tryptic digest) a gly-gly modification in addition to the light > or heavy SILAC lysine. > What would be the best way to quantify these peptides using Xpress or > ASAPratio? > In addition I wonder if there a way to optimize the search parameters > (preferably X!Tandem) to identify such "gly-gly" peptides while > limiting these gly-gly modifications only internal lysine sits. > Thanks, > Oded > > > > > > > > -- 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. For more options, visit https://groups.google.com/d/optout.
