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Rationale: In a shotgun proteomics experiment with data-dependentacquisition, real-time analysis of a precursor scan results in selection of ahandful of peaks for subsequent isolation, fragmentation and secondaryscanning. This peak selection protocol typically focuses on the most abundantpeaks in the precursor scan, while attempting to avoid re-sampling the same m/zvalues in rapid succession. The protocol does not, however, incorporateanalysis of previous fragmentation scans into the peak selection procedure.  Methods: In this work, we investigate the feasibility and utility ofincorporating analysis of previous fragmentation scans into the peak selectionprotocol. We demonstrate that real-time identification of fragmentation spectrais feasible in principle, and we investigate, via simulations, severalstrategies to make use of the resulting peptide identifications during peakselection.  Results: Our simulations fail to provide evidence that peptideidentifications can provide a large improvement in the total number of peptidesidentified by a shotgun proteomics experiment.  Conclusions: These results are significant because they point out thefeasibility of using peptide identifications during peak selection, and becauseour experiments may provide a starting point for others working in thisdirection.

On the feasibility and utility of exploiting real time database search to improve adaptive peak selection