ArticleMolecular & cellular proteomics : MCP2019
A Label-free Mass Spectrometry Method to Predict Endogenous Protein Complex Composition.
Article in Molecular & cellular proteomics : MCP, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it, 43 citations in OpenAlex.
- Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments.Nature methods · 2021Pooled it
- Systems-level proteomic models of cotton fiber development: a high-resolution data resource to analyze cell dynamics and trait engineering.Plant physiology · 2026Article
- AtGPP2 encodes a 3-deoxy-manno-octulosonate-8-phosphatase required for the synthesis of KDO in rhamnogalacturonan II.The Plant journal : for cell and molecular biology · 2026Article
- Ethylene reshapes protein assemblies in the dark.Plant physiology · 2025Article
- Integrating CORUM and co-fractionation mass spectrometry to create enhanced benchmarks for protein complex predictions.Briefings in bioinformatics · 2025Article
- A cell fractionation and quantitative proteomics pipeline to enable functional analyses of cotton fiber development.The Plant journal : for cell and molecular biology · 2025Article
- Complete end-to-end learning from protein feature representation to protein interactome inference.GigaScience · 2025Article
- Past accomplishments and future challenges of the multi-omics characterization of leaf growth.Plant physiology · 2022Review
- Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry.Chemical reviews · 2022Review
- A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone.The Plant cell · 2021Article
- Mapping the plant proteome: tools for surveying coordinating pathways.Emerging topics in life sciences · 2021Review
- PCprophet: a framework for protein complex prediction and differential analysis using proteomic data.Nature methods · 2021Article
- Multimerization variants as potential drivers of neofunctionalization.Science advances · 2021Article
- Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient.Computational and structural biotechnology journal · 2021Article
- Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold StandardMolecular & cellular proteomics : MCP · 2020Article
- Emerging mass spectrometry-based proteomics methodologies for novel biomedical applications.Biochemical Society transactions · 2020Review
- Article
- Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks.Molecular & cellular proteomics : MCP · 2020Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Information on the composition of protein complexes can accelerate mechanistic analyses of cellular systems. Protein complex composition identifies genes that function together and provides clues about regulation within and between cellular pathways. Cytosolic protein complexes control metabolic flux, signal transduction, protein abundance, and the activities of cytoskeletal and endomembrane systems. It has been estimated that one third of all cytosolic proteins in leaves exist in an oligomeric state, yet the composition of nearly all remain unknown. Subunits of stable protein complexes copurify, and combinations of mass-spectrometry-based protein correlation profiling and bioinformatic analyses have been used to predict protein complex subunits. Because of uncertainty regarding the power or availability of bioinformatic data to inform protein complex predictions across diverse species, it would be highly advantageous to predict composition based on elution profile data alone. Here we describe a mass spectrometry-based protein correlation profiling approach to predict the composition of hundreds of protein complexes based on biochemical data. Extracts were obtained from an intact organ and separated in parallel by size and charge under nondenaturing conditions. More than 1000 proteins with reproducible elution profiles across all replicates were subjected to clustering analyses. The resulting dendrograms were used to predict the composition of known and novel protein complexes, including many that are likely to assemble through self-interaction. An array of validation experiments demonstrated that this new method can drive protein complex discovery, guide hypothesis testing, and enable systems-level analyses of protein complex dynamics in any organism with a sequenced genome.
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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.