Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data

Journal of Proteome Research
Rachel M MillerLloyd M Smith

Abstract

Peptides detected by tandem mass spectrometry (MS/MS) in bottom-up proteomics serve as proxies for the proteins expressed in the sample. Protein inference is a process routinely applied to these peptides to generate a plausible list of candidate protein identifications. The use of multiple proteases for parallel protein digestions expands sequence coverage, provides additional peptide identifications, and increases the probability of identifying peptides that are unique to a single protein, which are all valuable for protein inference. We have developed and implemented a multi-protease protein inference algorithm in MetaMorpheus, a bottom-up search software program, which incorporates the calculation of protease-specific q-values and preserves the association of peptide sequences and their protease of origin. This integrated multi-protease protein inference algorithm provides more accurate results than either the aggregation of results from the separate analysis of the peptide identifications produced by each protease (separate approach) in MetaMorpheus, or results that are obtained using Fido, ProteinProphet, or DTASelect2. MetaMorpheus' integrated multi-protease data analysis decreases the ambiguity of the protein group list,...Continue Reading

References

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Citations

Mar 5, 2021·Journal of Proteome Research·Rachel M MillerLloyd M Smith
Mar 9, 2021·Journal of Proteome Research·Michael R ShortreedLloyd M Smith
Sep 25, 2020·Journal of Proteome Research·Anthony J CesnikLloyd M Smith
Apr 8, 2021·Analytical Chemistry·Jinghan YangYan Fu
Jun 26, 2020·Journal of Proteome Research·Leah V SchafferLloyd M Smith
Feb 19, 2020·Journal of Proteome Research·Juraj LenčoFrantišek Švec
Aug 20, 2020·Journal of the American Society for Mass Spectrometry·Kristina SrzentićMowei Zhou
Nov 6, 2021·Journal of Proteome Research·Zach Rolfs, Lloyd M Smith

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