Hi, I'm performing TPP analysis for my 14N/15N metabolic labeling experiments and have some questions regarding the data processing steps:
The raw data were searched one time with the normal 14N masses, and once with the 15N enriched amino acids set as fixed modification by Sequest in the Bioworks package. After conversion to pepXML, both searches were processed by Peptideprophet and XPress using 'IDs are normal...' and 'IDs are 15N heavy...' respectively, and saved as separate interact files. These two files were then merged in ProteinProphet with XPress ratio imported. My questions: how is the protein xpress ratio calculated? Does it include xpress ratios from both light and heavy peptides? Clicking on the protein xpress ratio only shows light peptides even if the protein is identified from both light and heavy peptides. Many thanks in advance! Samy --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
