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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Profiling the proteome-wide selectivity of diverse electrophiles.

Patrick R A Zanon^1,2, Fengchao Yu³, Patricia Z Musacchio⁴

¹Department of Chemistry, Technical University of Munich, Garching, Germany.

Nature Chemistry

|October 31, 2025

Summary

Researchers developed a new method to compare electrophile probes for monitoring amino acids in proteins. This unbiased workflow identified probes targeting nine amino acids and the protein amino terminus.

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Area of Science:

Chemical Biology
Proteomics
Drug Discovery

Background:

Covalent inhibitors not reliant on enzymatic activity primarily target cysteine residues.
Proteomics methods, particularly competitive residue-specific proteomics, have advanced cysteine-directed covalent inhibitor development by assessing proteome-wide selectivity.
Existing probes can monitor other amino acids, and numerous electrophiles can modify proteins, but direct comparisons of electrophile selectivity are lacking.

Purpose of the Study:

To develop an unbiased workflow for analyzing electrophile selectivity on a proteome-wide scale.
To directly compare the selectivity of 56 alkyne probes with diverse reactive groups.
To identify and verify probes capable of monitoring various amino acids and the protein amino terminus.

Main Methods:

Development of an unbiased proteome-wide workflow for electrophile selectivity analysis.
Direct comparison of 56 alkyne probes featuring diverse reactive groups.
Utilizing competitive residue-specific proteomics principles.

Main Results:

Successfully established and applied an unbiased workflow for proteome-wide electrophile selectivity analysis.
Directly compared 56 alkyne probes, revealing their varying reactivity and selectivity.
Verified and identified probes capable of monitoring nine distinct amino acids and the protein amino terminus across the proteome.

Conclusions:

The developed workflow provides a robust platform for unbiased, proteome-wide assessment of electrophile selectivity.
This study identified novel probes for monitoring a broader range of amino acids and the protein N-terminus.
The findings facilitate the development of targeted covalent inhibitors and chemical probes for diverse biological applications.