I've got triple-labeled data, heavy-medium-light K. We've discussed before the possibility of supporting this type of data fully, and I know that's not possible yet.
However, I would like to compare medium with heavy (specifically, I'd like to assess M/(M+H)). This is only a comparison of two quantities, but I'm having a hard time figuring out how I might do it with XPress. I tried running XPress twice (H/L and M/L) and using the values for H from one run and M from the other. That did not behave well at all, and when I sanity checked by comparing H/L ratios derived from one XPress run with H/L ratios derived from the H from an H/L run and the L from a M/L run, the low correlation (~0.3) made me realize that I should not expect this to work well. I considered re-running Comet, pretending that there's no light label, and running XPress on the results. This would certainly "work", but I would lose quantitation from all PSMs in which only the light was identified; that's likely quite a lot of peptides. My only other idea is to mutilate the PepXML from my current (L-M-H) Comet searches, dummying them up so that it looks like I ran an M-H only search, and creating dummy M or H IDs for everything that's currently an L ID. That's a really ugly solution, though, and I'm worried it'll fail for some reason I haven't thought of. Can anybody think of another way to do this? Thanks, Damon -- 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.
