Peptide Database Search Strategies to Improve Peptide Identifications Using High Resolution Mass Spectrometry

摘要

Bullseye offers improvements in assigning high resolution precursor masses compared to the onboard data processor of the LTQ-FT Ultra. By filtering spectra without persistent peptide isotope distributions, Bullseye is able to remove poor quality spectra which are placed in the Unmatched dataset. Database searching with a wide mass tolerance window, followed by a post-search mass accuracy filter increases the sensitivity of the positive peptide-spectrum-matches made. Database searching with a narrow mass constrained search window offers the advantage of greatly reducing the computational time needed to perform the search. Mass accuracy represents only one discriminating element that allows for distinguishing correct and incorrect PSMs. Other elements, such as enzyme cleavage specificity and predicted retention times, can be used to discriminate incorrect PSMs and when used in conjunction with mass accuracy should result in the best peptide identification results.