Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol

Most non-canonical proteins uniquely populate the proteome or immunopeptidome

(2021) Maria Virginia Ruiz Cuevas et al.   Cell Reports

Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides

(2021) Philipp T. Kaulich et al.   JOURNAL OF PROTEOME RESEARCH

Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

(2021) Puneet Sharma et al.   Nature Communications

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

N-Terminal Proteoforms in Human Disease

(2020) Annelies Bogaert et al.   TRENDS IN BIOCHEMICAL SCIENCES

Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data

(2020) Alina Glaub et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reconsidering proteomic diversity with functional investigation of small ORFs and alternative ORFs

(2020) Marie A. Brunet et al.   EXPERIMENTAL CELL RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Cycloheximide can distort measurements of mRNA levels and translation efficiency

(2019) Daniel A Santos et al.   NUCLEIC ACIDS RESEARCH

PROTEOFORMER 2.0: further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms

(2019) Steven Verbruggen et al.   MOLECULAR & CELLULAR PROTEOMICS

Towards a complete map of the human long non-coding RNA transcriptome

(2018) Barbara Uszczynska-Ratajczak et al.   NATURE REVIEWS GENETICS

Publisher Correction: Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

(2018) Yafeng Zhu et al.   Nature Communications

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

(2018) Yafeng Zhu et al.   Nature Communications

MIEF1 Microprotein Regulates Mitochondrial Translation

(2018) Annie Rathore et al.   BIOCHEMISTRY

The translation of non-canonical open reading frames controls mucosal immunity

(2018) Ruaidhrí Jackson et al.   NATURE

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Non-AUG translation: a new start for protein synthesis in eukaryotes

(2017) Michael G. Kearse et al.   GENES & DEVELOPMENT

Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini

(2017) Chan Hyun Na et al.   GENOME RESEARCH

Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products

(2017) Kenneth Verheggen et al.   JOURNAL OF PROTEOME RESEARCH

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

(2017) Patrick Willems et al.   MOLECULAR & CELLULAR PROTEOMICS

eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs

(2017) Daria Fijałkowska et al.   NUCLEIC ACIDS RESEARCH

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

Small Proteins Encoded by Unannotated ORFs are Rising Stars of the Proteome, Confirming Shortcomings in Genome Annotations and Current Vision of an mRNA

(2017) Vivian Delcourt et al.   PROTEOMICS

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Comprehensive analysis of human protein N-termini enables assessment of various protein forms

(2017) Jeonghun Yeom et al.   Scientific Reports

Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

(2017) Sondos Samandi et al.   eLife

Mapping the non-standardized biases of ribosome profiling

(2016) Alexander Bartholomäus et al.   BIOLOGICAL CHEMISTRY

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

Ribonuclease selection for ribosome profiling

(2016) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

First Things First: Vital Protein Marks by N-Terminal Acetyltransferases

(2016) Henriette Aksnes et al.   TRENDS IN BIOCHEMICAL SCIENCES

Trapping mammalian protein complexes in viral particles

(2016) Sven Eyckerman et al.   Nature Communications

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

(2016) James C. Wright et al.   Nature Communications

Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish

(2016) Guo-Liang Chew et al.   Nature Communications

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

Death of a dogma: eukaryotic mRNAs can code for more than one protein

(2015) Hélène Mouilleron et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

N-terminal modifications of cellular proteins: The enzymes involved, their substrate specificities and biological effects

(2015) Sylvia Varland et al.   PROTEOMICS

Identifying (non-)coding RNAs and small peptides: Challenges and opportunities

(2014) Andrea Pauli et al.   BIOESSAYS

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

A Human Short Open Reading Frame (sORF)-encoded Polypeptide That Stimulates DNA End Joining

(2014) Sarah A. Slavoff et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue

(2014) Jiao Ma et al.   JOURNAL OF PROTEOME RESEARCH

N- and O-acetylation of threonine residues in the context of proteomics

(2014) Jean-Baptiste Boyer et al.   Journal of 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

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Quantitative profiling of initiating ribosomes in vivo

(2014) Xiangwei Gao et al.   NATURE METHODS

Genome-wide identification and quantification of protein synthesis in cultured cells and whole tissues by puromycin-associated nascent chain proteomics (PUNCH-P)

(2014) Ranen Aviner et al.   Nature Protocols

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

Translation inhibitors cause abnormalities in ribosome profiling experiments

(2014) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

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

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

From Cells to Peptides: “One-Stop” Integrated Proteomic Processing Using Amphipols

(2013) Zhibin Ning et al.   JOURNAL OF PROTEOME RESEARCH

Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames

(2013) Adam G. Schwaid et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

QuaNCAT: quantitating proteome dynamics in primary cells

(2013) Andrew J M Howden et al.   NATURE METHODS

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME 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

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

(2011) Nicholas T. Ingolia et al.   CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

The functional role of long non-coding RNA in human carcinomas

(2011) Ewan A Gibb et al.   Molecular Cancer

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics

(2010) Kenny Helsens et al.   PROTEOMICS

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

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

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

(2008) An Staes et al.   PROTEOMICS