Recent advances in mass spectrometry–based peptidomics workflows to identify short-open-reading-frame-encoded peptides and explore their functions

The hidden world of membrane microproteins

(2020) Catherine A. Makarewich   EXPERIMENTAL CELL RESEARCH

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

Miniproteins as a Powerful Modality in Drug Development

(2020) Zachary R. Crook et al.   TRENDS IN BIOCHEMICAL SCIENCES

Comparative proteomic profiling of unannotated microproteins and alternative proteins in human cell lines

(2020) Xiongwen Cao et al.   JOURNAL OF PROTEOME RESEARCH

Large-scale Discovery of Non-conventional Peptides in Maize and Arabidopsis Through an Integrated Peptidogenomic Pipeline

(2020) Shunxi Wang et al.   Molecular Plant

Alternative proteins are functional regulators in cell reprogramming by PKA activation

(2020) Tristan Cardon et al.   NUCLEIC ACIDS RESEARCH

PsORF: a database of small ORFs in plants

(2020) Yanjun Chen et al.   PLANT BIOTECHNOLOGY JOURNAL

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

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

Sequential Precipitation and Delipidation Enables Efficient Enrichment of Low-Molecular Weight Proteins and Peptides from Human Plasma

(2020) Na Li et al.   JOURNAL OF PROTEOME RESEARCH

Complementarity of Different SDS‐PAGE Gel Staining Methods for the Identification of Short Open Reading Frame‐encoded Peptides

(2020) Philipp T. Kaulich et al.   PROTEOMICS

Reference and Ghost Proteins Identification in Rat C6 Glioma Extracellular Vesicles

(2020) Adriana-Natalia Murgoci et al.   iScience

The NBDY Microprotein Regulates Cellular RNA Decapping

(2020) Zhenkun Na et al.   BIOCHEMISTRY

Optimized Proteomics Workflow for the Detection of Small Proteins

(2020) Jürgen Bartel et al.   JOURNAL OF PROTEOME RESEARCH

Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell

(2020) Bing Wang et al.   Journal of Proteomics

A methodology for discovering novel brain-relevant peptides: Combination of ribosome profiling and peptidomics

(2019) Ravi Tharakan et al.   NEUROSCIENCE RESEARCH

Depletion of High-Molecular-Mass Proteins for the Identification of Small Proteins and Short Open Reading Frame Encoded Peptides in Cellular Proteomes

(2019) Liam Cassidy et al.   JOURNAL OF PROTEOME RESEARCH

Integrated transcriptomic and proteomic analysis of human eccrine sweat glands identifies missing and novel proteins

(2019) Chan Hyun Na et al.   MOLECULAR & CELLULAR PROTEOMICS

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Distinct types of short open reading frames are translated in plant cells

(2019) Igor Fesenko et al.   GENOME RESEARCH

Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins

(2019) Tristan Cardon et al.   ANALYTICAL CHEMISTRY

Accurate annotation of human protein-coding small open reading frames

(2019) Thomas F. Martinez et al.   Nature Chemical Biology

Enrichment-Based Proteogenomics Identifies Microproteins, Missing Proteins, and Novel smORFs in Saccharomyces cerevisiae

(2018) Cuitong He et al.   JOURNAL OF PROTEOME RESEARCH

Comprehensive Peptide Analysis of Mouse Brain Striatum Identifies Novel sORF-Encoded Polypeptides

(2018) Harshavardhan Budamgunta et al.   PROTEOMICS

Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics

(2018) Fouzia Yeasmin et al.   Frontiers in Genetics

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

(2018) Florian Meier et al.   MOLECULAR & CELLULAR PROTEOMICS

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

The developmental proteome of Drosophila melanogaster

(2017) Nuria Casas-Vila et al.   GENOME RESEARCH

Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results

(2017) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

Spectral Libraries for SWATH-MS Assays for Drosophila melanogaster and Solanum lycopersicum

(2017) Bertrand Fabre et al.   PROTEOMICS

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

(2017) Sondos Samandi et al.   eLife

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

(2016) Jiao Ma et al.   ANALYTICAL CHEMISTRY

Advancements in Next-Generation Sequencing

(2016) Shawn E. Levy et al.   Annual Review of Genomics and Human Genetics

Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei

(2016) Liam Cassidy et al.   JOURNAL OF PROTEOME RESEARCH

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide

(2016) Akinobu Matsumoto et al.   NATURE

New Peptides Under the s(ORF)ace of the Genome

(2016) Jose I. Pueyo et al.   TRENDS IN BIOCHEMICAL SCIENCES

Primary transcripts of microRNAs encode regulatory peptides

(2015) Dominique Lauressergues et al.   NATURE

Discovery and characterization of smORF-encoded bioactive polypeptides

(2015) Alan Saghatelian et al.   Nature Chemical Biology

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

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

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

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

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

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

Algorithms for thede novosequencing of peptides from tandem mass spectra

(2011) Jens Allmer   Expert Review of Proteomics

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology