Hello all, I have some experiments in which the samples were triple dimethyl labeled. Does any of you have any tips on how to analyze these data with later version of TPP?
I looked through the list but only could find a couple of posts. So far my ideas would be to do: 1. Static searches of Heavy, Medium and Light and then analyze H/M, and H/L, and deduce the M/L by dividing the ratios of (H/L)/(H/L) ? So far I'm doing that, however after Peptide/ProteinProphet the results of each vary quite abit and might end up with peptides/proteins with a ratio in just two conditions and not in the three. Usually this also happens in MaxQuant in triple labeled but only in very few hits. 2. Would it be possible to run a variable search for all three modifications in XTandem in one run, Heavy, Medium, Light and then just process H/M and H/L with Peptide/ProteinProphet? Maybe some of you had any experience with this, any tips or help would be appreciated! Thanks, Alejandro -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
