N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

(2016) Jiao Ma et al.   ANALYTICAL CHEMISTRY

Proteogenomics: Opportunities and Caveats

(2016) L. Dimitrakopoulos et al.   CLINICAL CHEMISTRY

N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries

(2016) Brynne E. Lycette et al.   JOURNAL OF PROTEOME RESEARCH

Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy

(2016) Anthony J. Cesnik et al.   JOURNAL OF PROTEOME RESEARCH

Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves

(2016) Lam Dai Vu et al.   JOURNAL OF PROTEOME RESEARCH

Positional proteomics reveals differences in N-terminal proteoform stability

(2016) D. Gawron et al.   Molecular Systems Biology

Six alternative proteases for mass spectrometry–based proteomics beyond trypsin

(2016) Piero Giansanti et al.   Nature Protocols

Super-resolution ribosome profiling reveals unannotated translation events inArabidopsis

(2016) Polly Yingshan Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

(2016) Anil Raj et al.   eLife

A note on the false discovery rate of novel peptides in proteogenomics

(2015) Kun Zhang et al.   BIOINFORMATICS

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer

(2015) Kelly V. Ruggles et al.   MOLECULAR & CELLULAR PROTEOMICS

MS2PIP prediction server: compute and visualize MS2peak intensity predictions for CID and HCD fragmentation

(2015) Sven Degroeve et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events inArabidopsis thaliana

(2015) A. Saskia Venne et al.   PROTEOMICS

Annotating N Termini for the Human Proteome Project: N Termini and Nα-Acetylation Status Differentiate Stable Cleaved Protein Species from Degradation Remnants in the Human Erythrocyte Proteome

(2014) Philipp F. Lange et al.   JOURNAL OF PROTEOME RESEARCH

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

(2014) Céline Bland et al.   MOLECULAR & CELLULAR PROTEOMICS

N-terminal Proteomics and Ribosome Profiling Provide a Comprehensive View of the Alternative Translation Initiation Landscape in Mice and Men

(2014) Petra Van Damme et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

Araport: the Arabidopsis Information Portal

(2014) Vivek Krishnakumar et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Natural Variability of Kozak Sequences Correlates with Function in a Zebrafish Model

(2014) Steven J. Grzegorski et al.   PLoS One

Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence

(2014) Hong-Dong Li et al.   PROTEOMICS

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

(2014) Alexander Koch et al.   PROTEOMICS

The proteome under translational control

(2014) Daria Gawron et al.   PROTEOMICS

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

Combining Results of Multiple Search Engines in Proteomics

(2013) David Shteynberg 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

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

The immediate upstream region of the 5′-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana

(2013) Younghyun Kim et al.   NUCLEIC ACIDS RESEARCH

Small open reading frames associated with morphogenesis are hidden in plant genomes

(2013) K. Hanada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amino Termini of Many Yeast Proteins Map to Downstream Start Codons

(2012) Claire T. Fournier et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Pseudogene Recoding Revealed from Proteomic Analysis of Salmonella Serovars

(2012) Ye Feng et al.   JOURNAL OF PROTEOME RESEARCH

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Bioinformatics Analysis of aSaccharomyces cerevisiaeN-Terminal Proteome Provides Evidence of Alternative Translation Initiation and Post-Translational N-Terminal Acetylation

(2011) Kenny Helsens et al.   JOURNAL OF PROTEOME RESEARCH

A Face in the Crowd: Recognizing Peptides Through Database Search

(2011) Jimmy K. Eng et al.   MOLECULAR & CELLULAR PROTEOMICS

SPT6L Encoding a Putative WG/GW-Repeat Protein Regulates Apical–Basal Polarity of Embryo in Arabidopsis

(2011) Xiao-Lu Gu et al.   Molecular Plant

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

(2011) An Staes et al.   Nature Protocols

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

NatF Contributes to an Evolutionary Shift in Protein N-Terminal Acetylation and Is Important for Normal Chromosome Segregation

(2011) Petra Van Damme et al.   PLoS Genetics

ArabidopsisStromal-derived Factor2 (SDF2) Is a Crucial Target of the Unfolded Protein Response in the Endoplasmic Reticulum

(2010) Andrea Schott et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics

(2010) Danielle L. Swaney et al.   JOURNAL OF PROTEOME RESEARCH

Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin

(2010) Tilman Schneider-Poetsch et al.   Nature Chemical Biology

Alternative translation start sites are conserved in eukaryotic genomes

(2010) G. A. Bazykin et al.   NUCLEIC ACIDS RESEARCH

Global Analysis of the Mitochondrial N-Proteome Identifies a Processing Peptidase Critical for Protein Stability

(2009) F.-Nora Vögtle et al.   CELL

Control of the pattern-recognition receptor EFR by an ER protein complex in plant immunity

(2009) Vladimir Nekrasov et al.   EMBO JOURNAL

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

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

Participation of Leaky Ribosome Scanning in Protein Dual Targeting by Alternative Translation Initiation in Higher Plants

(2009) Y. Wamboldt et al.   PLANT CELL

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans

(2009) T. Arnesen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

(2009) Andrew R. Jones et al.   PROTEOMICS

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

(2008) S. Gallien et al.   GENOME RESEARCH

Rapid and Accurate Peptide Identification from Tandem Mass Spectra

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

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

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

(2008) K. Baerenfaller et al.   SCIENCE