ArticleMolecular & cellular proteomics : MCP2025
Detection and Quantitation of Small Proteins Using Mass Spectrometry.
Article in Molecular & cellular proteomics : MCP, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- SpEchinoidin, a C-type lectin and a member of an expanded CTL family, is up-regulated by phagocytes in sea urchins responding to immune challenge.Developmental and comparative immunology · 2026Article
- Proteomic Evidence Indicates Ultrasound-Assisted Extraction Enhances Recovery of Membrane-Associated Proteins inJournal of agricultural and food chemistry · 2026Article
- Phosphorylation of YBX1 in the Kidneys is Altered in Legumain Knockout-Mice.Journal of proteome research · 2026Article
- Microproteins in Human Physiology and Pathology.Biochemistry · 2026Review
- Proteome characterization of single gene deletion mutants lacking zinc finger µ-proteins inmicroLife · 2026Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small proteins or microproteins, despite long being ignored, have important roles in the regulation of larger protein complexes, metabolic pathways, and gene expression. However, these proteins remain under-represented in proteomics studies because of low detection efficiency in traditional mass spectrometry (MS) workflows. Their inherent characteristics often lead to depletion during sample preparation and a low detection efficiency in LC-MS. To improve detection and quantitation, we took advantage of the large set of documented small proteins in Escherichia coli and systematically compared and optimized different sample preparation and LC-MS approaches. We evaluated different top-down and bottom-up approaches, including data-dependent acquisition, data-independent acquisition, and parallel reaction monitoring. Our data highlight the benefit of top-down proteomics for identifying new small proteins and bottom-up preparation coupled with parallel reaction monitoring acquisition for quantitation of protein levels in different growth conditions. Our systematic comparison can serve as a guideline for MS detection of small proteins in all organisms.
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