ArticleNature methods2019
EPIC: software toolkit for elution profile-based inference of protein complexes.
Article in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 2 of them syntheses that pooled it.
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Who cites it
46 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry.Nature communications · 2023Pooled it
- Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments.Nature methods · 2021Pooled it
- PCIPG: A comprehensive framework for protein complex identification based on a probabilistic graphical model.PLoS computational biology · 2026Article
- Mass spectrometry proteomics for studying mitostasis.Protein science : a publication of the Protein Society · 2026Review
- The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease.NPJ systems biology and applications · 2026Article
- Emerging approaches for characterizing spatial and temporal dynamics of pathogen-induced organelle remodeling.Cell systems · 2026Review
- Global profiling of protein complex dynamics with an experimental library of protein interaction markers.Nature biotechnology · 2025Article
- SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation.Nature communications · 2025Article
- Complete end-to-end learning from protein feature representation to protein interactome inference.GigaScience · 2025Article
- Analysis of Complexome Profiles with the Gaussian Interaction Profiler (GIP) Reveals Novel Protein Complexes inJournal of proteome research · 2024Article
- Systematic identification of structure-specific protein-protein interactions.Molecular systems biology · 2024Article
- DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes.Nature methods · 2024Article
- Tapioca: a platform for predicting de novo protein-protein interactions in dynamic contexts.Nature methods · 2024Article
- Co-fractionation-mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain.Nature protocols · 2023Article
- Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution.PLoS computational biology · 2023Article
- Rapid Profiling of Protein Complex Reorganization in Perturbed Systems.Journal of proteome research · 2023Article
- Protein complexes in cells by AI-assisted structural proteomics.Molecular systems biology · 2023Article
- CyanoMapDB: a database integrating experimentally validated protein-protein interactions in cyanobacteria.Plant physiology · 2023Article
- Discovering Protein-Protein Interactions using Co-Fractionation-Mass Spectrometry with Label-Free Quantitation.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Rewiring of the protein-protein-metabolite interactome during the diauxic shift in yeast.Cellular and molecular life sciences : CMLS · 2022Article
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12 authors.
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Abstract
Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectrometry analysis (chromatographic fractionation-mass spectrometry, CF-MS), but the resulting data are challenging to process and interpret. Here, we describe EPIC (elution profile-based inference of complexes), a software toolkit for automated scoring of large-scale CF-MS data to define high-confidence multi-component macromolecules from diverse biological specimens. As a case study, we used EPIC to map the global interactome of Caenorhabditis elegans, defining 612 putative worm protein complexes linked to diverse biological processes. These included novel subunits and assemblies unique to nematodes that we validated using orthogonal methods. The open source EPIC software is freely available as a Jupyter notebook packaged in a Docker container (https://hub.docker.com/r/baderlab/bio-epic/).
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