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Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus.

ABSTRACT: MetaMorpheus is a free, open-source software program for the identification of peptides and proteoforms from data-dependent acquisition tandem MS experiments. There is inherent uncertainty in these assignments for several reasons, including the limited overlap between experimental and theoretical peaks, the m/z uncertainty, and noise peaks or peaks from coisolated peptides that produce false matches. False discovery rates provide only a set-wise approximation for incorrect spectrum matches. Here we implemented a binary decision tree calculation within MetaMorpheus to compute a posterior error probability, which provides a measure of uncertainty for each peptide-spectrum match. We demonstrate its utility for increasing identifications and resolving ambiguities in bottom-up, top-down, proteogenomic, and nonspecific digestion searches.

SUBMITTER: Shortreed MR

PROVIDER: S-EPMC8377504 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus.

Shortreed Michael R MR Millikin Robert J RJ Liu Lei L Rolfs Zach Z Miller Rachel M RM Schaffer Leah V LV Frey Brian L BL Smith Lloyd M LM

Journal of proteome research 20210308 4

MetaMorpheus is a free, open-source software program for the identification of peptides and proteoforms from data-dependent acquisition tandem MS experiments. There is inherent uncertainty in these assignments for several reasons, including the limited overlap between experimental and theoretical peaks, the <i>m</i>/<i>z</i> uncertainty, and noise peaks or peaks from coisolated peptides that produce false matches. False discovery rates provide only a set-wise approximation for incorrect spectrum ...[more]

PMID: 33683901

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