On the feasibility and utility of exploiting real time database search   to improve adaptive peak selection
  Rationale: In a shotgun proteomics experiment with data-dependent acquisition, real-time analysis of a precursor scan results in selection of a handful of peaks for subsequent isolation, fragmentation and secondary scanning. This peak selection protocol typically focuses on the most abundant peaks in the precursor scan, while attempting to avoid re-sampling the same m/z values in rapid succession. The protocol does not, however, incorporate analysis of previous fragmentation scans into the peak selection procedure.   Methods: In this work, we investigate the feasibility and utility of incorporating analysis of previous fragmentation scans into the peak selection protocol. We demonstrate that real-time identification of fragmentation spectra is feasible in principle, and we investigate, via simulations, several strategies to make use of the resulting peptide identifications during peak selection.   Results: Our simulations fail to provide evidence that peptide identifications can provide a large improvement in the total number of peptides identified by a shotgun proteomics experiment.   Conclusions: These results are significant because they point out the feasibility of using peptide identifications during peak selection, and because our experiments may provide a starting point for others working in this direction. 
Benjamin J. Diament, Michael J. MacCoss, William Stafford Noble
q-bio.QM q-bio.BM