Inference and Validation of Protein Identifications

Proteome Coverage Prediction for Integrated Proteomics Datasets

(2011) Manfred Claassen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski 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

Generic Comparison of Protein Inference Engines

(2011) Manfred Claassen et al.   MOLECULAR & CELLULAR PROTEOMICS

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

A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas

(2011) Terry Farrah et al.   MOLECULAR & CELLULAR PROTEOMICS

The Importance of Peptide Detectability for Protein Identification, Quantification, and Experiment Design in MS/MS Proteomics

(2010) Yong Fuga Li 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

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of 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

An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome

(2010) Danny A. Bitton et al.   PLoS One

Protein and gene model inference based on statistical modeling in k-partite graphs

(2010) S. Gerster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteome coverage prediction with infinite Markov models

(2009) M. Claassen et al.   BIOINFORMATICS

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.

(2009) Sandra N Loevenich et al.   BMC BIOINFORMATICS

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Directed mass spectrometry: towards hypothesis-driven proteomics

(2009) Alexander Schmidt et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function

(2009) M. A. Grobei et al.   GENOME RESEARCH

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics

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

An Iterative Strategy for Precursor Ion Selection for LC-MS/MS Based Shotgun Proteomics

(2009) Alexandra Zerck 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

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

(2008) G. E. Merrihew et al.   GENOME RESEARCH

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

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

An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures

(2008) Alexander Schmidt et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE