ArticleNature protocols2017
Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry.
Article in Nature protocols, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers.
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Who cites it
152 citing papers in PubMed, 287 citations in OpenAlex.
- Peptide-centric local stability assay (PELSA) for sensitive identification of ligand-targeting proteins and binding sites at proteome scale.Nature protocols · 2026Review
- Catechol-Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- ProteoMeter: a pipeline for integrating multi-PTM and limited proteolysis data to reveal modification-structure coupling at the residue level.NAR genomics and bioinformatics · 2026Article
- High-Ratio Partial Proteolysis with Carrier Proteome (HOLSER) Enables Global Structure Profiling and Site-Resolved Elucidation of Ligand-Protein Interactions.Analytical chemistry · 2026Article
- Structural proteomics reveals that misfolded nascent proteins expose buried lysines for ubiquitination and rapid proteasomal degradation.Cell reports · 2026Article
- Rapid Adaptation of Cyanobacteria to Environmental Perturbations Is Achieved Through Structural Remodeling of the Proteome.Molecular & cellular proteomics : MCP · 2026Article
- Recent advances in proteomic strategies for target identification of traditional Chinese medicine.Journal of pharmaceutical analysis · 2026Review
- Tumor cell intrinsic dsRNA innate immune response triggered by PARP inhibitor is compromised in BRCA1-deficient breast cancer by repressing IRF3.Protein & cell · 2026Article
- Mechanism of palytoxin-induced ferroptosis in HaCaT cells via targeting TrxR1.Cell biology and toxicology · 2026Article
- Aggregation Methods for Quantifying PTM and Structural Changes in Bottom-Up Proteomics.Journal of proteome research · 2026Article
- Structure-function relationship of alpha-synuclein fibrillar polymorphs derived from distinct synucleinopathies.Molecular systems biology · 2026Article
- Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data.bioRxiv : the preprint server for biology · 2026Article
- Structural alterations in PPP1R13L, SAE1, ATP5A1 and PCK2 disrupt NF-κB signalling and mitochondrial metabolism in primary dermal fibroblasts in systemic sclerosis.Rheumatology (Oxford, England) · 2026Article
- Data-Independent Acquisition (DIA) Strategy for Measuring Protein Stability Using Stability of Proteins from Rates of Oxidation (SPROX).Journal of the American Society for Mass Spectrometry · 2026Article
- 3D Proteomics: Structural, Functional, Chemical and Biomarker Discovery Proteomics With LiP-MS.Molecular & cellular proteomics : MCP · 2026Review
- Chemoproteomics identifies STAT3 as a key target of baicalin in ameliorating liver fibrosis.National science review · 2026Article
- Label-Free Target Discovery Strategy for Natural Active Products.Biomolecules · 2026Review
- Above-Filter Digestion Proteomics Reveals Drug Targets and Localizes Ligand Binding Site.Journal of proteome research · 2026Article
- Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells.Molecular systems biology · 2026Article
- Advancing DIA-Based Limited Proteolysis Workflows: Introducing DIA-LiPA.Analytical chemistry · 2026Article
92 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein structural changes induced by external perturbations or internal cues can profoundly influence protein activity and thus modulate cellular physiology. A number of biophysical approaches are available to probe protein structural changes, but these are not applicable to a whole proteome in a biological extract. Limited proteolysis-coupled mass spectrometry (LiP-MS) is a recently developed proteomics approach that enables the identification of protein structural changes directly in their complex biological context on a proteome-wide scale. After perturbations of interest, proteome extracts are subjected to a double-protease digestion step with a nonspecific protease applied under native conditions, followed by complete digestion with the sequence-specific protease trypsin under denaturing conditions. This sequential treatment generates structure-specific peptides amenable to bottom-up MS analysis. Next, a proteomics workflow involving shotgun or targeted MS and label-free quantification is applied to measure structure-dependent proteolytic patterns directly in the proteome extract. Possible applications of LiP-MS include discovery of perturbation-induced protein structural alterations, identification of drug targets, detection of disease-associated protein structural states, and analysis of protein aggregates directly in biological samples. The approach also enables identification of the specific protein regions involved in the structural transition or affected by the binding event. Sample preparation takes approximately 2 d, followed by one to several days of MS and data analysis time, depending on the number of samples analyzed. Scientists with basic biochemistry training can implement the sample preparation steps. MS measurement and data analysis require a background in proteomics.
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