Thanks for the response, Amit. Sorry, I'm not sure what you mean by "correlation for only those ratios where all three labels (L M H) are present". By definition, I'm only comparing ratios that were present as H/L in one XPress run and M/L in the other (and so L M H are present in one run or the other). Do you mean ratios where all 3 labels have PSMs? That seems a bit stringent.
It's not that I expect the quantitation to suffer when I ignore the light label. It's that, demonstrably, when I compare the heavy from a H/L XPress run and the light from an M/L run, I get very different results from the H/L run's ratio. Meaning that, presumably, the L quantity that's measured is varying significantly across the two runs. For that reason, I expect the H from the H/L run also to be difficult to compare with the M from the M/L run. MaxQuant might be the better option for me. Thanks for the suggestion! Damon On Fri, Jul 3, 2015 at 8:52 AM, Amit Yadav <[email protected]> wrote: > 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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/zr3k_VNUPgQ/unsubscribe > . > To unsubscribe from this group and all its topics, 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. > -- 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.
