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 -~----------~----~----~----~------~----~------~--~---
