Although a bit awkward, Tandem does support multiple static modifications, which can be used in a creative manner in cases such as this:
http://thegpm.org/TANDEM/api/rmm.html Eric *From:* [email protected] [mailto: [email protected]] *On Behalf Of *Brian Hampton *Sent:* Tuesday, April 21, 2015 9:23 AM *To:* [email protected] *Subject:* Re: [spctools-discuss] Any tips on how to analyzed triple labeled data? The Tandem API states that it can’t handle more than one variable modification on a given residue. See: http://thegpm.org/TANDEM/api/rpmm.html. There is a work-around in that document where you specify e.g. the light as a static mod and the difference between the heavy and light as a variable mod for a given residue. So I don’ think your triple label search will work with Tandem unless you do three different searches, one for each label and use PeptideProphet to combine them into a single pepXML file for input to ProteinProphet. Then there is Comet. I’ve been using the version of Comet in TPP 4.8 and it seems to work nicely with multiple variable modifications on the same residue. I’m only using a dual di-methyl labeling strategy. Not sure if it would work with triple labeled, but the parameter inputs allow for up to 9 variable mods to be specified: http://comet-ms.sourceforge.net/parameters/parameters_201501/variable_mod01.php How are you planning on doing the quantification once you get the searches to go successfully? Cheers, Brian On Apr 21, 2015, at 5:55 AM, Alejandro <[email protected]> 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. -- 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.
