ArticleNature communications2021
Systematic detection of functional proteoform groups from bottom-up proteomic datasets.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis that pooled it.
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Who cites it
54 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments.Nature methods · 2021Pooled it
- ProteoForge: An Imputation-Aware Framework for Differential Proteoform Discovery in Bottom-Up Proteomics.Journal of proteome research · 2026Article
- Review
- Membrane Protein Glycosylation Revisited: Functional Dynamics and Emerging Clinical Insights.International journal of molecular sciences · 2026Review
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Advances in Mass Spectrometry Instrumentation and Methodology for Analysis of Alternative Protein Isoforms.Journal of mass spectrometry : JMS · 2026Review
- ProteoformDB: A Built-In Application to Generate Proteoform Database.Journal of proteome research · 2026Article
- Proteomics of aging: biomarkers for physiological systems and diseases.Frontiers in aging · 2026Review
- Top-Down Proteomics: Why and When?Proteomics · 2025Article
- Considering Measurement Time and Depth in diaPASEF Plasma Proteomics.Journal of proteome research · 2025Article
- A Flexible End-to-End Automated Sample Preparation Workflow Enables Standardized and Scalable Bottom-up Proteomics.Analytical chemistry · 2025Article
- Uncovering hidden protein modifications with native top-down mass spectrometry.Nature methods · 2025Article
- Multiplex Targeted Proteomic Analysis of Cytokine Ratios for ICU Mortality in Severe COVID-19.Proteomes · 2025Article
- Normalized and Directional Interplay Scoring for the Interrogation of Proteoform Data.Journal of proteome research · 2025Article
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments.Nature machine intelligence · 2025Article
- Spatial top-down proteomics for the functional characterization of human kidney.Clinical proteomics · 2025Article
- Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach.Bioinformatics (Oxford, England) · 2025Article
- Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets.Nature communications · 2025Article
- Defining proteoform-specific interactions for drug targeting in a native cell signalling environment.Nature chemistry · 2025Article
- SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation.Nature communications · 2025Article
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10 authors.
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Abstract
To a large extent functional diversity in cells is achieved by the expansion of molecular complexity beyond that of the coding genome. Various processes create multiple distinct but related proteins per coding gene - so-called proteoforms - that expand the functional capacity of a cell. Evaluating proteoforms from classical bottom-up proteomics datasets, where peptides instead of intact proteoforms are measured, has remained difficult. Here we present COPF, a tool for COrrelation-based functional ProteoForm assessment in bottom-up proteomics data. It leverages the concept of peptide correlation analysis to systematically assign peptides to co-varying proteoform groups. We show applications of COPF to protein complex co-fractionation data as well as to more typical protein abundance vs. sample data matrices, demonstrating the systematic detection of assembly- and tissue-specific proteoform groups, respectively, in either dataset. We envision that the presented approach lays the foundation for a systematic assessment of proteoforms and their functional implications directly from bottom-up proteomic datasets.
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