ArticleNature protocols2020
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it, 67 citations in OpenAlex.
- Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments.Nature methods · 2021Pooled it
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- A pooled image-based CRISPR screen identifies EAF1 as abioRxiv : the preprint server for 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
- A tissue-specific atlas of protein-protein associations enables prioritization of candidate disease genes.Nature biotechnology · 2026Article
- LysG-driven transcriptional network rewiring underlies lineage-specific phenotypes in Mycobacterium tuberculosis.Nature communications · 2026Article
- ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning.Nature communications · 2026Article
- Methods for the Investigation of Protein-Ligands Interactions.Advances in experimental medicine and biology · 2026Review
- A guide to building the matrisome interactome: from computational predictions to experimental validation.The FEBS journal · 2026Review
- There and back again: a cell biologist's journey from organelles to molecules.Biological chemistry · 2025Review
- Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization.Bioinformatics (Oxford, England) · 2025Article
- Article
- SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation.Nature communications · 2025Article
- Unifying proteomic technologies with ProteinProjector.Bioinformatics advances · 2025Article
- Analysis of Complexome Profiles with the Gaussian Interaction Profiler (GIP) Reveals Novel Protein Complexes inJournal of proteome research · 2024Article
- Large-scale map of RNA-binding protein interactomes across the mRNA life cycle.Molecular cell · 2024Article
- Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system.Journal of proteins and proteomics · 2024Article
- Systematic identification of structure-specific protein-protein interactions.Molecular systems biology · 2024Article
- Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 5 countries.
Funding
Abstract
Most catalytic, structural and regulatory functions of the cell are carried out by functional modules, typically complexes containing or consisting of proteins. The composition and abundance of these complexes and the quantitative distribution of specific proteins across different modules are therefore of major significance in basic and translational biology. However, detection and quantification of protein complexes on a proteome-wide scale is technically challenging. We have recently extended the targeted proteomics rationale to the level of native protein complex analysis (complex-centric proteome profiling). The complex-centric workflow described herein consists of size exclusion chromatography (SEC) to fractionate native protein complexes, data-independent acquisition mass spectrometry to precisely quantify the proteins in each SEC fraction based on a set of proteotypic peptides and targeted, complex-centric analysis where prior information from generic protein interaction maps is used to detect and quantify protein complexes with high selectivity and statistical error control via the computational framework CCprofiler (https://github.com/CCprofiler/CCprofiler). Complex-centric proteome profiling captures most proteins in complex-assembled state and reveals their organization into hundreds of complexes and complex variants observable in a given cellular state. The protocol is applicable to cultured cells and can potentially also be adapted to primary tissue and does not require any genetic engineering of the respective sample sources. At present, it requires ~8 d of wet-laboratory work, 15 d of mass spectrometry measurement time and 7 d of computational analysis.
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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.