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

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

(2015) Oliver Serang 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

On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra

(2014) Uri Keich et al.   JOURNAL OF PROTEOME RESEARCH

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm 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

MSSimulator: Simulation of Mass Spectrometry Data

(2011) Chris Bielow et al.   JOURNAL OF PROTEOME RESEARCH

On Using Samples of Known Protein Content to Assess the Statistical Calibration of Scores Assigned to Peptide-Spectrum Matches in Shotgun Proteomics

(2011) Viktor Granholm et al.   JOURNAL OF PROTEOME RESEARCH

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

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

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics

(2009) Yong Fuga Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

(2009) Lukas Reiter et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

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

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH