mProphet: Automated Data Processing and Statistical Validation for Large-Scale SRM Experiments

Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak M, Hengartner MO, Aebersold R. Nature Methods.

Selected Reaction Monitoring (SRM), also referred to as Multiple Reaction Monitoring (MRM), is the gold standard in proteomics quantification. As the throughput of assay development improved, manual evaluation of the quality of the data became tedious. Reiter and coworkers tackled the challenge of confident identification of target peptides by introducing mProphet, a tool that computes identification error rates by combining multiple features into a probabilistic scoring model to maximize specificity and sensitivity in targeted data extraction. Later, that concept was transferred by the authors and other group members to the targeted extraction from DIA/SWATH data.

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