  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.
