ArticleJournal of bacteriology2022
A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.
Article in Journal of bacteriology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
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- Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs.Nucleic acids research · 2026Article
- Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics.Nature communications · 2026Article
- The Proteome ofProteomes · 2026Article
- Turning Agricultural Waste Into Enzymatic Treasure: Bromelain Stability in Pineapple Crown and Peel Waste From Subang District, Indonesia.Biochemistry research international · 2026Article
- Proteome characterization of single gene deletion mutants lacking zinc finger µ-proteins inmicroLife · 2026Article
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- Review
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- Functional analysis and transcriptional profiling of non-coding RNAs in yeast.The Biochemical journal · 2025Review
- Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin.BMC genomics · 2025Article
- The producer cell type of HSV-1 alters the proteomic contents and infectious capacity of virions.Journal of virology · 2025Article
- Detection and Quantitation of Small Proteins Using Mass Spectrometry.Molecular & cellular proteomics : MCP · 2025Article
- PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes.Nucleic acids research · 2025Article
- CXXC5 is a ubiquitinated protein and is degraded by the ubiquitin-proteasome pathway.Protein science : a publication of the Protein Society · 2025Article
- Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes.Bioinformatics (Oxford, England) · 2025Article
- Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni.Nature communications · 2025Article
- Innovations in heart failure management: The role of cutting-edge biomarkers and multi-omics integration.Journal of molecular and cellular cardiology plus · 2025Review
- How Small Proteins Adjust the Metabolism of Cyanobacteria Under Stress: The Role of Small Proteins in Cyanobacterial Stress Responses.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.
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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 Socratic graph.