Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data

Journal of Proteome Research
Andy LinWilliam S Noble

Abstract

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 m...Continue Reading

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Citations

Apr 25, 2020·International Journal of Molecular Sciences·Chen ChenJianlin Cheng
Feb 18, 2021·Journal of Proteome Research·William E Fondrie, William S Noble
Jul 9, 2021·Journal of Proteome Research·Andy LinWilliam S Noble
Feb 6, 2020·Journal of Proteome Research·William E Fondrie, William S Noble
Aug 28, 2021·Journal of Proteome Research·Polina KudriavtsevaAttila Kertész-Farkas

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