This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. In shotgun proteomics, the analysis of tandem mass spectrometry data from peptides can benefit greatly from high mass accuracy measurements. In this study we present a software tool, Bullseye, which determines the monoisotopic mass and charge state of the precursor ion of a tandem mass spectrum. By using information throughout the chromatographic elution profile of the peptide, Bullseye discards MS/MS spectra that are a result of the fragmentation of noise and can offer improvements in the accuracy of monoisotopic mass measurements. We have evaluated two database search strategies which use high mass accuracy measurements of the peptide precursor ion. Our results indicate that peptide identifications are improved when spectra are searched with a wide mass tolerance window and precursor mass is used as a filter to discard incorrect matches. Database searches with a peptide dataset constrained to peptides within a narrow mass window resulted in fewer peptide identifications but a significantly faster database search time.
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