Journal
JOURNAL OF PROTEOME RESEARCH
Volume 17, Issue 11, Pages 3644-3656Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.8b00206
Keywords
database search; statistical calibration; high-resolution MS2
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Funding
- NIH [R01 GM121818, P41 GM103533]
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [P41GM103533, R01GM121818] Funding Source: NIH RePORTER
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To achieve accurate assignment of peptide sequences to observed fragmentation spectra, a shotgun proteomics database search tool must make good use of the very high-resolution information produced by state-of-the-art mass spectrometers. However, making use of this information while also ensuring that the search engine's scores are well calibrated, that is, that the score assigned to one spectrum can be meaningfully compared to the score assigned to a different spectrum, has proven to be challenging. Here we describe a database search score function, the residue evidence (res-ev) score, that achieves both of these goals simultaneously. We also demonstrate how to combine calibrated res-ev scores with calibrated XCorr scores to produce a combined p value score function. We provide a benchmark consisting of four mass spectrometry data sets, which we use to compare the combined p value to the score functions used by several existing search engines. Our results suggest that the combined p value achieves state-of-the-art performance, generally outperforming MS Amanda and Morpheus and performing comparably to MS-GF+. The res-ev and combined p-value score functions are freely available as part of the Tide search engine in the Crux mass spectrometry toolkit (http://crux.ms).
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