Hi guys. Just started to do SILAC and whated to try Xpress and ASAPRatio for quant analysis.
My sample is the HeLa cells labelled with heavy lysine only just to asses labeling efficiency. I mixed cell lysates 1 to 1 by protein concentration. Run TPP analysis using Sequest with heavy K as variable modification. And afterwords ran the post search with this XInteract options command line. -OAp -X-m0.1-nK,8.0142 -A-lK-mK136.109163-F I am trying to implement this Petunia settings. As recommended in ASAPRatio tutorial. "In the “PeptideProphet Options” pane select to “Use accurate mass binning” and “Run ProteinProphet Afterwards”. In the “XPRESS Options” pane select “RUN XPRESS”. Change “XPRESS Mass Tolerance” to 0.1, set “Change XPRESS residue mass difference:” with K 8.0142. In the “ASAPRatio Options” pane select “RUN ASAPRatio”. Change “Labeled Residues” to K , set “m/z range to include in summation of peak:” to 0.05. Set “Specified masses:” to K 136.10916. Check the “Use fixed scan range” option." Except I couldn't fine the syntax for this part --- "set “m/z range to include in summation of peak:” to 0.05." Everything looked OK. I 've got my ratios and for the most part they looked reasonable at least by Xpress. For ASAPRatio data I have a message that "no normalisation data found" for every protein quant record. And, yes, I don't see normalised ratios and p-values. Does anybody know what might be the problem? We have 4.0.2 version of TPP. Thank you very much. -- 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.
