Hi Rebekah, Using -Og as an xinteract option will enable the use of the Glyco model to modify the probabilities. If you are using xinteract you should not have to run PeptideProphetParser separately, xinteract will do it for you and enable all the correct options.
-David On Thu, Jun 11, 2009 at 9:09 AM, Ruby<[email protected]> wrote: > > I am a bit confused on the best manner in which to process data from > an N-linked glyco capture experiment, analyzed via the orbitrap. I > know how to 'highlight' those peptides with the NxS/T motif, but am > hoping that there is also a way that the algorithms can somehow reward > or otherwise consider the motif in the probability calculations as > well. > > What is the difference between the following options: > 1) PeptideProphetParser interact.xml GLYC - which "uses peptide NxS/T > motif in probability calculation" > 2) -Og - which "uses N-glyc motif information in PeptideProphet" > > It seems like either option would affect the data at the > peptideprophet level, and 'reward' those peptides that contain the > motif. Correct? > > When I try option #1 by typing in "PeptideProphetParser interact.xml > GLYC", I get an error: "cannot parse input file PeptideProphetParser" > Help!!??? > > Thanks! > Rebekah > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
