I can get xpress working with L/M/H SILAC. But I loath the thought of the work it would take to interface it within the TPP (updating pepXML schema, xinteract wrapper tool, XPressPeptideRatioParser, XPressProteinRatioParser, PepXMLViewer, the protein viewer, etc.).
I will play with my standalone, rewritten xpress (runs much more efficiently) to get it a bit more functional, including L/M/H SILAC support, and then maybe we can find another developer to integrate it back into the TPP. On Thu, Apr 30, 2015 at 10:48 AM, Damon May <[email protected]> wrote: > I have the same issue; I'm running a single search with Comet and then > PeptideProphet, then copying the output pepXml and running XPress > separately for H/L and M/L. This gives me answers, but I'd have a lot more > confidence in an enhanced XPress that was aware of all three labels (in my > case, light-medium-heavy SILAC) and was choosing scan extents appropriately > across all the labels. > > If anyone's mulling over this kind of enhancement, it would be really > valuable! > > Thanks, > Damon > > > On Friday, April 24, 2015 at 3:41:02 AM UTC-7, Alejandro wrote: >> >> Hi all, >> >> Well, so far I've done static searches for each label or doing the >> variable search as Brian commented, followed by Peptide/ProteinProphet to >> combine the files, and it somehow works, of course it get's a little bit >> tricky to handle all of the files. I haven't tried so far used Comet in >> this setup, I will try and see, looks promising. Regarding the XTandem, I >> have indeed used it like with several modifications, but I had forgotten >> that setup, I will try it and see if the ID numbers goes down, compared to >> doing the three searches. >> >> As for the quantification this is where it gets more troublesome. The >> data that I'm using is Qexactive data, and so far I haven't had so good >> experience using ASAP ratio, I think we discussed it in a post, was really >> slow in 4.7, but since TPP 4.8 it is faster, but I see better results using >> Xpress. So, my strategy so far has been to run it in pairs, do Xpress with >> Peptide/Protein Prophet to Heavy/Medium and then Heavy/Light and deduce the >> M/L by dividing the two. The problem so far is in this last step. How to >> normalize the data (substracting median, etc) when the heavy part is gone. >> Plus how to handle when one ID is not found in one channel or when the >> quantification also didn't work in one/two channels. >> >> Any ideas? >> >> Alejandro >> >> >> >> On Tuesday, April 21, 2015 at 11:55:58 AM UTC+2, Alejandro wrote: >>> >>> 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. > -- 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.
