ArticleNature communications2023
SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed, 11 citations in OpenAlex.
- ProteoForge: An Imputation-Aware Framework for Differential Proteoform Discovery in Bottom-Up Proteomics.Journal of proteome research · 2026Article
- IsoPepTracker: An interactive web application for peptide-driven isoform analysis.PLoS computational biology · 2026Article
- Proteogenomic characterization unveils biomarkers associated with chemoresistance in muscle-invasive bladder cancer.Cell reports. Medicine · 2025Article
- Understanding genetic architecture of breast cancer: how can proteome-wide association studies contribute?British journal of cancer · 2024Article
- A proteome-wide association study identifies putative causal proteins for breast cancer risk.British journal of cancer · 2024Article
- Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst.Journal of proteome research · 2024Article
- Giant polyketide synthase enzymes in the biosynthesis of giant marine polyether toxins.Science (New York, N.Y.) · 2024Article
- Multi-Omics Characterization of Colon Mucosa and Submucosa/Wall from Crohn's Disease Patients.International journal of molecular sciences · 2024Article
- Analysis and visualization of quantitative proteomics data using FragPipe-Analyst.bioRxiv : the preprint server for biology · 2024Article
- Giant polyketide synthase enzymes biosynthesize a giant marine polyether biotoxin.bioRxiv : the preprint server for biology · 2024Article
- SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics.Nature communications · 2023Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoform characterization using in silico and experimental data, and then present SEPepQuant, a graph theory-based approach to maximize isoform characterization. Using published data from one induced pluripotent stem cell study and two human hepatocellular carcinoma studies, we demonstrate the ability of SEPepQuant in addressing the key limitations of existing methods, providing more comprehensive isoform-level characterization, identifying hundreds of isoform-level regulation events, and facilitating streamlined cross-study comparisons. Our analysis provides solid evidence to support a widespread role of protein isoform regulation in normal and disease processes, and SEPepQuant has broad applications to biological and translational research.
Indexed as
Identifiers
What OpenQuestion holds
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.