ArticleNature methods2025
A peptide-centric local stability assay enables proteome-scale identification of the protein targets and binding regions of diverse ligands.
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Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 30 papers.
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30citing papers in PubMed
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Who cites it
30 citing papers in PubMed.
- Peptide-centric local stability assay (PELSA) for sensitive identification of ligand-targeting proteins and binding sites at proteome scale.Nature protocols · 2026Review
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- High-Ratio Partial Proteolysis with Carrier Proteome (HOLSER) Enables Global Structure Profiling and Site-Resolved Elucidation of Ligand-Protein Interactions.Analytical chemistry · 2026Article
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- DT-TRAP enables accurate target recognition via simplified dosing and low-temperature incubation.Journal of pharmaceutical analysis · 2026Article
- Detecting protein higher-order structural changes using kinase as a phospho-labeler.Cell reports methods · 2026Article
- Recent advances in proteomic strategies for target identification of traditional Chinese medicine.Journal of pharmaceutical analysis · 2026Review
- Discovery of chirally dependent protein modifications by D- and L-2-hydroxyglutarates.Nature chemistry · 2026Article
- Global protein-ligand binding affinity profiling via photocatalytic labeling.Nature communications · 2026Article
- Oxysterol undersulfation promotes osteoarthritis by fueling chondrocyte lipid accumulation.Nature communications · 2026Article
- An approach for the systematic profiling of drug-induced remodeling of RNA-RBP (RNA-binding protein) interactions.RSC advances · 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
- Regulation of RNA-binding proteins by small biomolecules.Nature reviews. Molecular cell biology · 2026Review
- Paeoniflorin alleviates hypobaric hypoxia-triggered lung injury through targeting MEK2 to modulate ERK2-SGK1 signaling.Acta pharmaceutica Sinica. B · 2026Article
- Targeting MEK2 by paeoniflorin: Mechanism underlying its protection against hypobaric hypoxia-induced lung injury.Acta pharmaceutica Sinica. B · 2026Article
Corrections and comments
- Erratum issued
Authors and funding
20 authors.
Kejia LiState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Shijie ChenDrug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
Keyun WangState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Yan WangState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Lianji XueState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Yuying YeState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Zheng FangState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.ORCID http://orcid.org/0000-0003-2139-3256
Jiawen LyuState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Haiyang ZhuState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Yanan LiState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Ting YuState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Feng YangDrug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
Xiaolei ZhangState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Siqi GuoDrug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
Chengfei RuanState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Jiahua ZhouState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Qi WangState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
Mingming DongMOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, China.ORCID http://orcid.org/0000-0002-0770-7880
Cheng LuoDrug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. cluo@simm.ac.cn.ORCID http://orcid.org/0000-0003-3864-8382
Mingliang YeState Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China. mingliang@dicp.ac.cn.ORCID http://orcid.org/0000-0002-5872-9326
Funding
National Natural Science Foundation of China (National Science Foundation of China) 22137002National Natural Science Foundation of China (National Science Foundation of China) 22437007National Natural Science Foundation of China (National Science Foundation of China) 92153302National Natural Science Foundation of China (National Science Foundation of China) 92253303Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS) 2022279
Abstract
By using a limited-proteolysis strategy that employs a large amount of trypsin to generate peptides directly from native proteins, we found that ligand-induced protein local stability shifts can be sensitively detected on a proteome-wide scale. This enabled us to develop the peptide-centric local stability assay, a modification-free approach that achieves unprecedented sensitivity in proteome-wide target identification and binding-region determination. We demonstrate the broad applications of the peptide-centric local stability assay by investigating interactions across various biological contexts.
Indexed as
PeptidesProteomeProteomicsBinding SitesHumansLigandsProtein BindingProtein StabilityProteolysisTrypsinLigandsPeptidesProteomeTrypsin
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PMID
39658593What OpenQuestion holds
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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.