Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

How to talk about protein-level false discovery rates in shotgun proteomics

(2016) Matthew The et al.   PROTEOMICS

Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less

(2015) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

A Decoy-Free Approach to the Identification of Peptides

(2015) Giulia Gonnelli et al.   JOURNAL OF PROTEOME RESEARCH

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass spectrometry-based protein identification with accurate statistical significance assignment

(2014) Gelio Alves et al.   BIOINFORMATICS

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

(2014) Sean McIlwain et al.   JOURNAL OF PROTEOME RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass Fingerprinting of Complex Mixtures: Protein Inference from High-Resolution Peptide Masses and Predicted Retention Times

(2013) Luminita Moruz et al.   JOURNAL OF PROTEOME RESEARCH

Variation and genetic control of protein abundance in humans

(2013) Linfeng Wu et al.   NATURE

A review of statistical methods for protein identification using tandem mass spectrometry

(2013) William Noble et al.   Statistics and Its Interface

Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics

(2012) Viktor Granholm et al.   Journal of Proteomics

Assigning spectrum-specific P-values to protein identifications by mass spectrometry

(2011) Victor Spirin et al.   BIOINFORMATICS

Efficient Marginalization to Compute Protein Posterior Probabilities from Shotgun Mass Spectrometry Data

(2010) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule

(2009) Nitin Gupta et al.   JOURNAL OF PROTEOME RESEARCH

Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data

(2009) Edward J. Hsieh et al.   JOURNAL OF PROTEOME RESEARCH

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY