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.
