ArticleFrontiers in genetics2021
Small Protein Enrichment Improves Proteomics Detection of sORF Encoded Polypeptides.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.Nature communications · 2026Article
- CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.microLife · 2026Article
- Identification of Peptides Encoded by Small Open Reading Frames in Microalgae by Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The hidden bacterial microproteome.Molecular cell · 2025Article
- Cross-Species Proximity-Dependent Protein Biotinylation: A Standardized Approach for Mapping Proxeomes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression.mBio · 2024Article
- Mitochondrial proteome research: the road ahead.Nature reviews. Molecular cell biology · 2024Review
- Microproteins-Discovery, structure, and function.Proteomics · 2023Review
- Exposing the small protein load of bacterial life.FEMS microbiology reviews · 2023Review
- Shift in vacuolar to cytosolic regime of infecting Salmonella from a dual proteome perspective.PLoS pathogens · 2023Article
- Review
- Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides.microLife · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the rapid growth in the number of sequenced genomes, genome annotation efforts became almost exclusively reliant on automated pipelines. Despite their unquestionable utility, these methods have been shown to underestimate the true complexity of the studied genomes, with small open reading frames (sORFs; ORFs typically considered shorter than 300 nucleotides) and, in consequence, their protein products (sORF encoded polypeptides or SEPs) being the primary example of a poorly annotated and highly underexplored class of genomic elements. With the advent of advanced translatomics such as ribosome profiling, reannotation efforts have progressed a great deal in providing translation evidence for numerous, previously unannotated sORFs. However, proteomics validation of these riboproteogenomics discoveries remains challenging due to their short length and often highly variable physiochemical properties. In this work we evaluate and compare tailored, yet easily adaptable, protein extraction methodologies for their efficacy in the extraction and concomitantly proteomics detection of SEPs expressed in the prokaryotic model pathogen
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.