N-Terminal-oriented Proteogenomics of the Marine BacteriumRoseobacter DenitrificansOch114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) Labeling and Diagonal Chromatography

Resin-Assisted Enrichment of N-Terminal Peptides for Characterizing Proteolytic Processing

(2013) Jong-Seo Kim et al.   ANALYTICAL CHEMISTRY

An Improved Stable Isotope N-Terminal Labeling Approach with Light/Heavy TMPP To Automate Proteogenomics Data Validation: dN-TOP

(2013) Diego Bertaccini et al.   JOURNAL OF PROTEOME RESEARCH

Time-resolved Analysis of the Matrix Metalloproteinase 10 Substrate Degradome

(2013) Pascal Schlage et al.   MOLECULAR & CELLULAR PROTEOMICS

An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes inZea mays

(2013) Natalie E. Castellana et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

(2013) Gerben Menschaert et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomic Amino-Termini Profiling Reveals Targeting Information for Protein Import into Complex Plastids

(2013) Pitter F. Huesgen et al.   PLoS One

High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade

(2012) Joseph A Christie-Oleza et al.   BMC GENOMICS

The substrate degradome of meprin metalloproteases reveals an unexpected proteolytic link between meprin β and ADAM10

(2012) Tamara Jefferson et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Two Isoforms of Geobacter sulfurreducens PilA Have Distinct Roles in Pilus Biogenesis, Cytochrome Localization, Extracellular Electron Transfer, and Biofilm Formation

(2012) L. V. Richter et al.   JOURNAL OF BACTERIOLOGY

ClpP: A structurally dynamic protease regulated by AAA+ proteins

(2012) John A. Alexopoulos et al.   JOURNAL OF STRUCTURAL BIOLOGY

Comparative Large Scale Characterization of PlantversusMammal Proteins Reveals Similar and IdiosyncraticN-α-Acetylation Features

(2012) Willy V. Bienvenut et al.   MOLECULAR & CELLULAR PROTEOMICS

N-terminal Protein Processing: A Comparative Proteogenomic Analysis

(2012) Stefano Bonissone et al.   MOLECULAR & CELLULAR PROTEOMICS

C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation

(2012) Bas F. J. Wanschers et al.   NUCLEIC ACIDS RESEARCH

RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors

(2012) Roman Häuser et al.   PLoS Genetics

Two promoters and two translation start sites control the expression of the Shigella flexneri outer membrane protease IcsP

(2011) Christopher T. Hensley et al.   ARCHIVES OF MICROBIOLOGY

A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF

(2011) Lina Zhao et al.   BMC GENOMICS

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

(2011) Charles Ansong et al.   BMC GENOMICS

Protein alpha-N-acetylation studied by N-terminomics

(2011) Petra Van Damme et al.   FEBS Journal

A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry

(2011) R. Chaerkady et al.   GENOME RESEARCH

Statistics of N-terminal alignment as a guide for refining prokaryotic gene annotation

(2011) Naoki Sato et al.   GENOMICS

Proteogenomic Analysis of Candida glabrata using High Resolution Mass Spectrometry

(2011) T. S. Keshava Prasad et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Proteogenomics of TwelveRoseobacterExoproteomes Reveals Different Adaptive Strategies Among These Marine Bacteria

(2011) Joseph Alexander Christie-Oleza et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic Analysis ofMycobacterium tuberculosisBy High Resolution Mass Spectrometry

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

A larger transcript is required for the synthesis of the smaller isoform of ferredoxin:NADP oxidoreductase

(2011) Amin Omairi-Nasser et al.   MOLECULAR MICROBIOLOGY

Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates

(2011) Oded Kleifeld et al.   Nature Protocols

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

(2011) An Staes et al.   Nature Protocols

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

(2011) Eli Venter et al.   PLoS One

A proteomic view of mycobacteria

(2011) Gustavo A. de Souza et al.   PROTEOMICS

Proteogenomics and systems biology: quest for the ultimate missing parts

(2010) Jean Armengaud   Expert Review of Proteomics

Using comparative genome analysis to identify problems in annotated microbial genomes

(2010) M. S. Poptsova et al.   MICROBIOLOGY-SGM

Multiplex N-terminome Analysis of MMP-2 and MMP-9 Substrate Degradomes by iTRAQ-TAILS Quantitative Proteomics

(2010) Anna Prudova et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass spectrometry at the interface of proteomics and genomics

(2010) Karsten Krug et al.   Molecular BioSystems

Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

(2010) Oded Kleifeld et al.   NATURE BIOTECHNOLOGY

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

Efficient and clean charge derivatization of peptides for analysis by mass spectrometry

(2010) Mingrui An et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa

(2009) Véronique Dupierris et al.   BIOINFORMATICS

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

(2009) Jean Armengaud   CURRENT OPINION IN MICROBIOLOGY

Proteomics-based Refinement ofDeinococcus desertiGenome Annotation Reveals an Unwonted Use of Non-canonical Translation Initiation Codons

(2009) Mathieu Baudet et al.   MOLECULAR & CELLULAR PROTEOMICS

Begin at the beginning: evolution of translational initiation

(2009) Dario Benelli et al.   RESEARCH IN MICROBIOLOGY

Alliance of Proteomics and Genomics to Unravel the Specificities of Sahara Bacterium Deinococcus deserti

(2009) Arjan de Groot et al.   PLoS Genetics

Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea

(2009) Yvan Zivanovic et al.   GENOME BIOLOGY

The ClpP N-Terminus Coordinates Substrate Access with Protease Active Site Reactivity†

(2008) Laura D. Jennings et al.   BIOCHEMISTRY

Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol

(2008) S. Gallien et al.   GENOME RESEARCH

Turned on for degradation: ATPase-independent degradation by ClpP

(2008) Maria C. Bewley et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)

(2008) An Staes et al.   PROTEOMICS

Extent of N-terminal modifications in cytosolic proteins from eukaryotes

(2008) Aude Martinez et al.   PROTEOMICS

Selective isolation of N-terminal peptides from proteins and theirde novosequencing by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry without regard to unblocking or blocking of N-terminal amino acids

(2008) Minoru Yamaguchi et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

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

(2008) K. Baerenfaller et al.   SCIENCE