Bernard, We've successfully used ASAPRatio for heavy dimethyl labeled quantitation using the following workflow, which might help you get to where you want:
* Run *two* searches, with the light and heavy methyl n-term and lysine mods specified as *static* modifications, i.e. Search 1: Dimethyl (K) + Dimethyl (n-term) as static mods. Search 2: Dimethyl:2H4 (K) + Dimethyl:2H4 (n-term) as static mods. * Run xinteract on the resulting pair of search results using the static mods option for ASAPRatio, i.e. -A-lnK-S-r0.05 There's no need to run XPRESS if you are only interested in ASAPRatio results. DT On 11 Mar, 07:05, Bernt <[email protected]> wrote: > Dear all, > > I have a question pertaining to ASAPRatio. > > Can I actually get ASAPRatio to give me a ratio of Kmethylated / Kheavy > +methylated (i.e. K142/K148)? If it can be done, how do I specify on > the commandline different modified forms of Lys as the numerator and > denominator of the ratio? Both modifications have been specified under > variable mods in Xtandem. Does Xpress need to be specified everytime > ASAPRatio is run, or can it be omitted? Can the following work? > > xinteract -NinteractHeavyMethyl2.pep.xml -p0 -l6 -OA -A- > lR170.11676K142.11061-F-r0.1-mK148.13061R180.12476 > "*HeavyMethyl.tandem.pep.xml" > > I also tried specifying static mod on Lys (i.e. 1...@k), and variable > mod of 2...@k to represent the Heavy+Methyl form in Xtandem first, > then : > > xinteract -Ninteractstatic.pep.xml -p0 -l6 -OA -X-nR,10K,6 -A-lRK-F- > r0.1-mK148.13061R180.12476 "*static.tandem.pep.xml" > > But in this case, PeptideProphet's probabilities were all 0, > presumably because there were very few significant peptide assignments > due to the static mod specified on all Lys. Does anybody have any idea > how I can get around this problem with ASAPRatio? > > I look forward to any suggestions. Thanks in advance. > > Cheers, > Bernard -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
