Transferred Subgroup False Discovery Rate for Rare Post-translational Modifications Detected by Mass Spectrometry

A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics

(2013) Harald Marx et al.   NATURE BIOTECHNOLOGY

Bayesian false discovery rates for post-translational modification proteomics

(2013) Yan Fu   Statistics and Its Interface

Modification Site Localization Scoring: Strategies and Performance

(2012) Robert J. Chalkley et al.   MOLECULAR & CELLULAR PROTEOMICS

DeltAMT: A Statistical Algorithm for Fast Detection of Protein Modifications From LC-MS/MS Data

(2011) Yan Fu et al.   MOLECULAR & CELLULAR PROTEOMICS

Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate

(2010) Ding Ye et al.   BIOINFORMATICS

False Discovery Rate Control With Groups

(2010) James X. Hu et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Improving Software Performance for Peptide Electron Transfer Dissociation Data Analysis by Implementation of Charge State- and Sequence-Dependent Scoring

(2010) Peter R. Baker et al.   MOLECULAR & CELLULAR PROTEOMICS

How does multiple testing correction work?

(2009) William S Noble   NATURE BIOTECHNOLOGY

Simultaneous inference: When should hypothesis testing problems be combined?

(2008) Bradley Efron   Annals of Applied Statistics

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry

(2008) L. Kall et al.   BIOINFORMATICS

The Standard Protein Mix Database: A Diverse Data Set To Assist in the Production of Improved Peptide and Protein Identification Software Tools

(2007) John Klimek et al.   JOURNAL OF PROTEOME RESEARCH

False Discovery Rates and Related Statistical Concepts in Mass Spectrometry-Based Proteomics

(2007) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH

Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture Modeling

(2007) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH