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Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data

View ORCID ProfileAndy Lin, J. Jeffry Howbert, View ORCID ProfileWilliam Stafford Noble
doi: https://doi.org/10.1101/290858
Andy Lin
1Department of Genome Sciences University of Washington
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J. Jeffry Howbert
2Department of Genome Sciences University of Washington
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William Stafford Noble
3Department of Genome Sciences Department of Computer Science and Engineering University of Washington
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  • For correspondence: williamnoble@uw.edu
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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—i.e., 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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 30, 2018.
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Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data
Andy Lin, J. Jeffry Howbert, William Stafford Noble
bioRxiv 290858; doi: https://doi.org/10.1101/290858
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Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data
Andy Lin, J. Jeffry Howbert, William Stafford Noble
bioRxiv 290858; doi: https://doi.org/10.1101/290858

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