ArticleNature chemical biology2022
A modification-centric assessment tool for the performance of chemoproteomic probes.
Article in Nature chemical biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Protein thiol alterations drive pathologic liquid-liquid phase separation in the aging brain.Nature structural & molecular biology · 2026Article
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- 4-Oxo-2-Nonenal Crosslinks Vicinal Cysteine-Lysine Pairs in Cellular Proteins.Molecular & cellular proteomics : MCP · 2026Article
- α-Halothioamide warheads with enhanced cysteine reactivity and specificity for covalent protein labelling.Nature communications · 2026Article
- Defining and refining the cysteine redoxome through sulfur chemical biology.Nature chemical biology · 2026Review
- Friends, foes and signals.Nature chemical biology · 2026Article
- One-step labeling with a fluorinated porphyrin-based probe enablesInnovation (Cambridge (Mass.)) · 2025Article
- Profiling the proteome-wide selectivity of diverse electrophiles.Nature chemistry · 2025Article
- Catalyst-free late-stage functionalization to assemble α-acyloxyenamide electrophiles for selectively profiling conserved lysine residues.Communications chemistry · 2024Article
- Improved deconvolution of natural products' protein targets using diagnostic ions from chemical proteomics linkers.Beilstein journal of organic chemistry · 2024Review
- Article
- Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome.Cell chemical biology · 2023Article
- Review
- Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides.Nature communications · 2023Article
- Protein-RNA interactions: from mass spectrometry to drug discovery.Essays in biochemistry · 2023Article
- Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome.bioRxiv : the preprint server for biology · 2023Article
- Probing the secrets of probes.Nature chemical biology · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chemoproteomics has emerged as a key technology to expand the functional space in complex proteomes for probing fundamental biology and for discovering new small-molecule-based therapies. Here we report a modification-centric computational tool termed pChem to provide a streamlined pipeline for unbiased performance assessment of chemoproteomic probes. The pipeline starts with an experimental setting for isotopically coding probe-derived modifications that can be automatically recognized by pChem, with masses accurately calculated and sites precisely localized. pChem exports on-demand reports by scoring the profiling efficiency, modification homogeneity and proteome-wide residue selectivity of a tested probe. The performance and robustness of pChem were benchmarked by applying it to eighteen bioorthogonal probes. These analyses reveal that the formation of unexpected probe-derived modifications can be driven by endogenous reactive metabolites (for example, bioactive aldehydes and glutathione). pChem is a powerful and user-friendly tool that aims to facilitate the development of probes for the ever-growing field of chemoproteomics.
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