ArticleInternational journal of molecular sciences2021
Improved Identification of Small Open Reading Frames Encoded Peptides by Top-Down Proteomic Approaches and De Novo Sequencing.
Article in International journal of molecular sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 28 citations in OpenAlex.
- Single-Position Peptide Clustering for Peptidomics Reveals Novel Disease Biomarkers and Dysregulated Proteolytic Characteristics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Proteogenomic analysis of Cyprinid herpesvirus 2 using high-resolution mass spectrometry.Journal of virology · 2025Article
- Small open reading frame-encoded microproteins in cancer: identification, biological functions and clinical significance.Molecular cancer · 2025Review
- Enhanced Discovery of Alternative Proteins (AltProts) in Mouse Cardiac Development Using Data-Independent Acquisition (DIA) Proteomics.Analytical chemistry · 2025Article
- Micropeptides Encoded by Noncoding RNAs: Biological Functions and Roles in Diseases.Research (Washington, D.C.) · 2025Review
- Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World.International journal of molecular sciences · 2023Review
- Review
- Identification and analysis of short open reading frame-encoded peptides in different regions of mouse brain.iScience · 2023Article
- Proteoforms expand the world of microproteins and short open reading frame-encoded peptides.iScience · 2023Review
- Employing non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome.iScience · 2023Article
- Review
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Mapping Microproteins and ncRNA-Encoded Polypeptides in Different Mouse Tissues.Frontiers in cell and developmental biology · 2021Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Small open reading frames (sORFs) have translational potential to produce peptides that play essential roles in various biological processes. Nevertheless, many sORF-encoded peptides (SEPs) are still on the prediction level. Here, we construct a strategy to analyze SEPs by combining top-down and de novo sequencing to improve SEP identification and sequence coverage. With de novo sequencing, we identified 1682 peptides mapping to 2544 human sORFs, which were all first characterized in this work. Two-thirds of these new sORFs have reading frame shifts and use a non-ATG start codon. The top-down approach identified 241 human SEPs, with high sequence coverage. The average length of the peptides from the bottom-up database search was 19 amino acids (AA); from de novo sequencing, it was 9 AA; and from the top-down approach, it was 25 AA. The longer peptide positively boosts the sequence coverage, more efficiently distinguishing SEPs from the known gene coding sequence. Top-down has the advantage of identifying peptides with sequential K/R or high K/R content, which is unfavorable in the bottom-up approach. Our method can explore new coding sORFs and obtain highly accurate sequences of their SEPs, which can also benefit future function research.
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