Hello, I've had this problem with chemically labeled tags e.g. di-methyl labeling of amines probably since TPP 4.7 came out, didn't have it in 4.6.x. ASAPRatio does work well for SILAC, but when both light and heavy pairs are chemically labeled it can't find the correct pair for doing the quantification. This occurs regardless of using Tandem or Comet as the search engine. Xpress works well.
The following is from the top of the interact.pep.xml file showing the asapratio command: <asapratio_summary version="3.0 (TPP v4.8.0 PHILAE, Build 201501121721-exported (Ubuntu-x86_64))" author="Xiaojun Li" elution="1" labeled_residues="Kn" area_flag="0" static_quant="N" specified_residue_masses="n28.0313n34.0631K156.12627K162.15809"/> Note that since both light and heavy are labeled I included the monoisotopic masses for both light and heavy residues. The following is the output in the interact.pep.xml file showing what I believe to be the error: <analysis_timestamp analysis="asapratio" time="2015-04-14T10:38:41" id="1"> <asapratio_timestamp quant_label_masses="K[128.095,162.158]n[1.008,34.063]"/> </analysis_timestamp> Notice that the mass for the light n-terminus is the mass of a proton not the mass of the light label which should be 28.0313. Please help. Thanks in advance, Brian -- 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.
