Hi all, I'm using Xpress and ASAPratio for analysis of SILAC experiments (using X!tandem branch on TPP 4.2.1 on windows or OS X). It seems to me that currently in proteinXML viewer, changing the peptide probability value alter only the listed peptides but got no effect on the ratio calculation which is actually not altered by such change. This might lead to a situation that the protein ratio was determine by peptides that were not used for it's identification. It might be very useful to find a way to allow that setting different minimal peptide probability will also change the selection of the peptides that are using to calculate the protein ratio. Alternatively maybe it might be easier to find a way to give more weight in the protein ratio calculation to the higher probability peptide over the low probability ones (kind of combined average maybe). Right now I run peptide prophet with relatively high probability threshold which is giving me higher confidence in the protein ratios but on the other hand this way I'm losing some possible identifications and getting more single hits wonders. Thanks, Oded
--~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
