Dear all, Anyone used Thermo Fisher's PD to identify phosphopeptides? I recently ran a phosphopeptide sample enriched by TiO2. The Mass spect is Orbitrap Velos, MS1 the FT at 30K resolution, MS2 the ion trap CID fragmentation. Although nearly every spectrum had a clear-cut feature of neutral loss of phosphoric acid, the identification was far from satisfactory. As many as 6,000 phosphopeptides were identified in a single run, 4500 of them did not pass the peptide confidence threshold (low or medium confidence). When I look at QC identification results (e.g., E.coli digests, etc.), 80% of peptides were of high confidence.
I am not sure why the peptide confidence was so low when it comes to phosphopeptide identification in PD? Has any one of you encountered a similar problem? How did you configure the software, or just use HCD to run the sample again? Best, Siyuan -- 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.
