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

TL;DR

This paper explores whether real-time analysis of fragmentation spectra can enhance peak selection in shotgun proteomics, finding that while feasible, it does not significantly increase peptide identifications in simulations.

Contribution

It investigates the feasibility of incorporating real-time peptide identification into peak selection, providing a foundation for future research in adaptive proteomics methods.

Findings

Real-time identification of fragmentation spectra is feasible.

Incorporating peptide identifications does not significantly improve peptide yield.

The study offers a starting point for future adaptive peak selection strategies.

Abstract

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.