Deep Coverage of theEscherichia coliProteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments

The Problem with Peptide Presumption and the Downfall of Target–Decoy False Discovery Rates

(2012) Bret Cooper   ANALYTICAL CHEMISTRY

False discovery rates in spectral identification

(2012) Kyowon Jeong et al.   BMC BIOINFORMATICS

Microbiology and proteomics, getting the best of both worlds!

(2012) Jean Armengaud   ENVIRONMENTAL MICROBIOLOGY

Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies

(2012) Paul Blakeley et al.   JOURNAL OF PROTEOME RESEARCH

Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability

(2011) D. A. Bitton et al.   GENETICS

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox 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

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic Analysis ofMycobacterium tuberculosisBy High Resolution Mass Spectrometry

(2011) Dhanashree S. Kelkar et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study

(2011) Eli Venter et al.   PLoS One

One-Dimensional Capillary Liquid Chromatographic Separation Coupled with Tandem Mass Spectrometry Unveils theEscherichia coliProteome on a Microarray Scale

(2010) Mio Iwasaki et al.   ANALYTICAL CHEMISTRY

Proteogenomics and systems biology: quest for the ultimate missing parts

(2010) Jean Armengaud   Expert Review of Proteomics

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models

(2010) N. Borchert et al.   GENOME 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

Mass spectrometry at the interface of proteomics and genomics

(2010) Karsten Krug et al.   Molecular BioSystems

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

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

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum

(2009) Scott Bringans et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

(2009) Paola Picotti et al.   CELL

A perfect genome annotation is within reach with the proteomics and genomics alliance

(2009) Jean Armengaud   CURRENT OPINION IN MICROBIOLOGY

Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome

(2009) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

A Dual Pressure Linear Ion Trap Orbitrap Instrument with Very High Sequencing Speed

(2009) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Validating divergent ORF annotation of the Mycobacterium leprae genome through a full translation data set and peptide identification by tandem mass spectrometry

(2009) Gustavo A. de Souza et al.   PROTEOMICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example

(2008) Gustavo A de Souza et al.   BMC GENOMICS

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

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

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

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

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

The GOA database in 2009--an integrated Gene Ontology Annotation resource

(2008) D. Barrell et al.   NUCLEIC ACIDS RESEARCH

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Precision, Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies

(2008) Anjana Srivatsan et al.   PLoS Genetics

The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation

(2008) Dong Xia et al.   GENOME BIOLOGY

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

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