pFindStudio
TMT and iTRAQ ratio
Hi pFind team, I got some questions about how pFind process the TMT or iTRAQ data, specifically: 1, in the pQuant-ms2_result.spectra file, what does Mass1 and Mass2 represented for? 2, I think I figured out Ratio=log2(ReportIntX/ReportInt0), but what's does the RatioVSN represented for? 3, in the pQuant-ms2_result.protein file, I simply can not figure out how the protein ratio was calculated by pFind. I assumed this is based on some combination of peptide ratios, but how exactly? 4, opening pQuant-ms2_result.protein in Excel will generate a table looks weird, I found out there is a unneccessary "CR" mark after every protein description, remove this you can get nicely organized table in the Excel. I will suggest the pFind team to fix it.
thank you!
Sun
