Improving the TFold test for differential shotgun proteomics | Zendy

Paulo C. Carvalho | Zendy; John R. Yates | Zendy; Valmir C. Barbosa | Zendy

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Improving the TFold test for differential shotgun proteomics

Author(s) -

Paulo C. Carvalho,

John R. Yates,

Valmir C. Barbosa

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts247

Subject(s) - shotgun proteomics , estimator , cutoff , shotgun , computer science , software , proteomics , sensitivity (control systems) , value (mathematics) , computational biology , biology , mathematics , statistics , programming language , machine learning , genetics , physics , engineering , gene , quantum mechanics , electronic engineering

We present an updated version of the TFold software for pinpointing differentially expressed proteins in shotgun proteomics experiments. Given an FDR bound, the updated approach uses a theoretical FDR estimator to maximize the number of identifications that satisfy both a fold-change cutoff that varies with the t-test P-value as a power law and a stringency criterion that aims to detect lowly abundant proteins. The new version has yielded significant improvements in sensitivity over the previous one.

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