Dear TPP team, I just noticed there some questions posted in this forum regarding the incompatibility of ASAPratio with 3-plex SILAC. One compromised strategy is to search each label separately and then do the H/L, M/L ratio separately. Then I realized that the skyline can do quantitation based on MS1 chromatogram, so, is it possible to process 3-plex SILAC or 3plex Dimethylation data with TPP-skyline without ASAPratio? If possible, shall I search each label separately in TPP and import 3 separate pep.xml to skyline? or search each label together in TPP and import just one single pep.xml to skyline?
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