Hi Damon, Have you tried checking the correlation for only those ratios where all three labels (L M H) are present?. The reason could be that finding any two pairs may have higher chances of false positives which may be distorting your real ratios and therefore resulting in low correlation.
Since you wanted H/M, why do you expect quantitation to suffer when you ignore light label? I don't have idea about this mutilation trick. If possible, a triple SILAC search can be done with ProteinPilot and any ratios can be calculated even post search (M/L, H/L, H/M or any other combination) In freely available software solutions, MaxQuant can be used. On Friday, July 3, 2015 at 6:07:12 AM UTC+5:30, Damon May wrote: > > 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.
