ArticleMolecular & cellular proteomics : MCP2013
Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics.
Article in Molecular & cellular proteomics : MCP, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed.
- TheScience advances · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation.Nature communications · 2025Article
- 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
- Impact of mineral and non-mineral sources of iron and sulfur on the metalloproteome ofApplied and environmental microbiology · 2024Article
- [Applications of high performance liquid chromatography-mass spectrometry in proteomics].Se pu = Chinese journal of chromatography · 2024Review
- Systematic identification of structure-specific protein-protein interactions.Molecular systems biology · 2024Article
- Article
- Molecular complex detection in protein interaction networks through reinforcement learning.BMC bioinformatics · 2023Article
- Large-scale map of RNA binding protein interactomes across the mRNA life-cycle.bioRxiv : the preprint server for biology · 2023Article
- Proteomic discovery of chemical probes that perturb protein complexes in human cells.Molecular cell · 2023Article
- Rapid Profiling of Protein Complex Reorganization in Perturbed Systems.Journal of proteome research · 2023Article
- Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration.Molecular systems biology · 2023Article
- Native Size-Exclusion Chromatography-Based Mass Spectrometry Reveals New Components of the Early Heat Shock Protein 90 Inhibition Response Among Limited Global Changes.Molecular & cellular proteomics : MCP · 2023Article
- Characterization of Native COMPASS Complex in Urothelial Carcinoma Cells by Size Exclusion Chromatography.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803.Genomics, proteomics & bioinformatics · 2022Article
- Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry.Chemical reviews · 2022Review
- Comparative Network Biology Discovers Protein Complexes That Underline Cellular Differentiation in Anabaena sp.Molecular & cellular proteomics : MCP · 2022Article
- Multilocation proteins in organelle communication: Based on protein-protein interactions.Plant direct · 2022Article
26 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Proteins form a diverse array of complexes that mediate cellular function and regulation. A largely unexplored feature of such protein complexes is the selective participation of specific protein isoforms and/or post-translationally modified forms. In this study, we combined native size-exclusion chromatography (SEC) with high-throughput proteomic analysis to characterize soluble protein complexes isolated from human osteosarcoma (U2OS) cells. Using this approach, we have identified over 71,500 peptides and 1,600 phosphosites, corresponding to over 8,000 proteins, distributed across 40 SEC fractions. This represents >50% of the predicted U2OS cell proteome, identified with a mean peptide sequence coverage of 27% per protein. Three biological replicates were performed, allowing statistical evaluation of the data and demonstrating a high degree of reproducibility in the SEC fractionation procedure. Specific proteins were detected interacting with multiple independent complexes, as typified by the separation of distinct complexes for the MRFAP1-MORF4L1-MRGBP interaction network. The data also revealed protein isoforms and post-translational modifications that selectively associated with distinct subsets of protein complexes. Surprisingly, there was clear enrichment for specific Gene Ontology terms associated with differential size classes of protein complexes. This study demonstrates that combined SEC/MS analysis can be used for the system-wide annotation of protein complexes and to predict potential isoform-specific interactions. All of these SEC data on the native separation of protein complexes have been integrated within the Encyclopedia of Proteome Dynamics, an online, multidimensional data-sharing resource available to the community.
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