Transfer posterior error probability estimation for peptide identification

Quality control of single amino acid variations detected by tandem mass spectrometry

(2018) Xinpei Yi et al.   Journal of Proteomics

PTMiner: localization and quality control of protein modifications detected in an open search and its application to comprehensive PTM characterization in human proteome

(2018) Zhi-Wu An et al.   MOLECULAR & CELLULAR PROTEOMICS

Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments

(2017) Honglan Li et al.   JOURNAL OF PROTEOME RESEARCH

Mass spectrometrists should search for all peptides, but assess only the ones they care about

(2017) Adriaan Sticker et al.   NATURE METHODS

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes

(2016) Jia Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass spectrometrists should search only for peptides they care about

(2015) William Stafford Noble   NATURE METHODS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

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

(2013) Yan Fu et al.   MOLECULAR & CELLULAR PROTEOMICS

Bayesian false discovery rates for post-translational modification proteomics

(2013) Yan Fu   Statistics and Its Interface

A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet

(2012) Kelvin Ma et al.   BMC BIOINFORMATICS

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics

(2011) Jing Li et al.   MOLECULAR & CELLULAR PROTEOMICS

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

A Survey on Transfer Learning

(2009) Sinno Jialin Pan et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

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

Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based Proteomics

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

Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin

(2007) Lukas Käll 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