Hi, I'm using TPP (4.7.0 Polar Vortex) since some days. I'm interested on performing SILAC quantitation (K+4, R+6) using ASAP ratio (the data are coming from a uhr-TOF). I load my mzXML files, perform Xtandem search, run Peptide Prophet and then ASAP ratio. However, I'm not that much satisfied with the quantitation in several aspects:
1) why it takes as SILAC pair two signals that clearly have different elution times (they are suposed to elute together and it is so by manual inspection of the spectra)? 2) why the background is set different for both peptides in a single pair when they coelute (and ASAP ratio recognises it); it should be about the same (delta m/z is not that big for z<=2)? 3) why the smoothed chromatogram is not fitting close to the raw one (even for good signals)? Therefore, I would like to optimize the quantitation parameters, however, apparently, the results I get are the same (manual inspection of the pepxml tables and ratio windows) if I tick or I don't tick several options (eg: "Quantitate only the charge state where the CID was made" or "Zero out all background" or "Quantitate despite high background", or "Use fixed scan range for Light and Heavy" or use different values "m/z range to include in summation of peak" ). I would appreciate any hint to get better quantitation results. -- 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.
