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. 2025 Feb;22(2):278-282.
doi: 10.1038/s41592-024-02553-7. Epub 2024 Dec 10.

A peptide-centric local stability assay enables proteome-scale identification of the protein targets and binding regions of diverse ligands

Kejia Li  1   2   3 , Shijie Chen  4 , Keyun Wang  1 , Yan Wang  1 , Lianji Xue  1   2 , Yuying Ye  1   2 , Zheng Fang  1   2 , Jiawen Lyu  1   2   5 , Haiyang Zhu  1   2 , Yanan Li  1 , Ting Yu  1   2 , Feng Yang  4 , Xiaolei Zhang  1 , Siqi Guo  4 , Chengfei Ruan  1   2 , Jiahua Zhou  1   2 , Qi Wang  1   2 , Mingming Dong  6 , Cheng Luo  7   8 , Mingliang Ye  9   10
Affiliations

A peptide-centric local stability assay enables proteome-scale identification of the protein targets and binding regions of diverse ligands

Kejia Li et al. Nat Methods. 2025 Feb.

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.

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Conflict of interest statement

Competing interests: A patent application related to this work has been filed by Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.

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