Mass spectrometry-based protein identification with accurate statistical significance assignment

Protein Analysis by Shotgun/Bottom-up Proteomics

(2013) Yaoyang Zhang et al.   CHEMICAL REVIEWS

A Non-parametric Cutout Index for Robust Evaluation of Identified Proteins

(2013) Oliver Serang et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Protein inference: a review

(2012) T. Huang et al.   BRIEFINGS IN BIOINFORMATICS

Computational and Statistical Analysis of Protein Mass Spectrometry Data

(2012) William Stafford Noble et al.   PLoS Computational Biology

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

(2011) Victor Spirin et al.   BIOINFORMATICS

Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

(2011) Benjamin J. Diament et al.   JOURNAL OF PROTEOME RESEARCH

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong

(2011) Nitin Gupta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Combining Independent, Weighted P-Values: Achieving Computational Stability by a Systematic Expansion with Controllable Accuracy

(2011) Gelio Alves et al.   PLoS One

RAId_aPS: MS/MS Analysis with Multiple Scoring Functions and Spectrum-Specific Statistics

(2010) Gelio Alves et al.   PLoS One

Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies

(2010) Brian C. Searle   PROTEOMICS

Decoy Methods for Assessing False Positives and False Discovery Rates in Shotgun Proteomics

(2008) Guanghui Wang et al.   ANALYTICAL CHEMISTRY

On E-values for tandem MS scoring schemes

(2008) M. R. Segal   BIOINFORMATICS

Detection of co-eluted peptides using database search methods

(2008) Gelio Alves et al.   Biology Direct

Enhancing Peptide Identification Confidence by Combining Search Methods

(2008) Gelio Alves et al.   JOURNAL OF PROTEOME RESEARCH

Rapid and Accurate Peptide Identification from Tandem Mass Spectra

(2008) Christopher Y. Park et al.   JOURNAL OF PROTEOME RESEARCH

Statistical characterization of a 1D random potential problem—With applications in score statistics of MS-based peptide sequencing

(2008) Gelio Alves et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Computational Methods for Protein Identification from Mass Spectrometry Data

(2008) Leo McHugh et al.   PLoS Computational Biology