ArticleNature biotechnology2025
Global profiling of protein complex dynamics with an experimental library of protein interaction markers.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Who cites it
10 citing papers in PubMed.
- Proteomic investigation of signaling dynamics: from static maps to network rewiring.Bioscience reports · 2026Review
- Integrated LiP-MS and quantitative proteomics reveal coordinated alterations in protein conformation and expression across tumor and peritumoral regions in hepatocellular carcinoma.Scientific reports · 2026Article
- Subtype-dependent arrestin engagement of the metabotropic glutamate receptors.Nature communications · 2026Article
- 3D Proteomics: Structural, Functional, Chemical and Biomarker Discovery Proteomics With LiP-MS.Molecular & cellular proteomics : MCP · 2026Review
- Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells.Molecular systems biology · 2026Article
- Integrated Structural and Glycoproteomic Profiling Reveals Protein Conformational Remodeling and Biomarkers Across Alzheimer's Disease Progression.ACS central science · 2026Article
- Exploring the interplay between protein conformational changes and phosphorylation in a pancreatic cancer cell and stellate cell coculture system.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- State-of-the-Art and Future Directions in Structural Proteomics.Molecular & cellular proteomics : MCP · 2025Review
- Analysis of Limited Proteolysis-Coupled Mass Spectrometry Data.Molecular & cellular proteomics : MCP · 2025Article
- ProCaliper: functional and structural analysis, visualization, and annotation of proteins.Bioinformatics advances · 2025Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Methods to systematically monitor protein complex dynamics are needed. We introduce serial ultrafiltration combined with limited proteolysis-coupled mass spectrometry (FLiP-MS), a structural proteomics workflow that generates a library of peptide markers specific to changes in PPIs by probing differences in protease susceptibility between complex-bound and monomeric forms of proteins. The library includes markers mapping to protein-binding interfaces and markers reporting on structural changes that accompany PPI changes. Integrating the marker library with LiP-MS data allows for global profiling of protein-protein interactions (PPIs) from unfractionated lysates. We apply FLiP-MS to Saccharomyces cerevisiae and probe changes in protein complex dynamics after DNA replication stress, identifying links between Spt-Ada-Gcn5 acetyltransferase activity and the assembly state of several complexes. FLiP-MS enables protein complex dynamics to be probed on any perturbation, proteome-wide, at high throughput, with peptide-level structural resolution and informing on occupancy of binding interfaces, thus providing both global and molecular views of a system under study.
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Registered trials
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.