ChemIntelligence Enables Antibody-Free, Ultra-Low-Input Profiling of Lysine Lactylation and Diverse Acyl-Proteomes
- 1China Pharmaceutical University
Abstract
Lysine acylations, including lactylation (Klac), are pivotal regulators of cellular physiology. However, their analysis is currently bottlenecked by antibody enrichment strategies that suffer from sequence bias and require milligram-scale protein inputs, severely precluding the profiling of scarce clinical biopsies and rare cell populations. Here we present ChemIntelligence, an acyl-NHS chemistry-empowered derivatization strategy that rapidly generates unprecedented acylation-specific spectral libraries, exemplified by over 2.5x10^9 human Klac peptides, enabling cross-species reference atlases. Integrated with Prosit-based rescoring, these libraries substantially increase Klac identifications across diverse proteomic datasets. Leveraging this spectral resource, we devised ChemIntelligence Scope, a reproducible, multiplexed parallel reaction monitoring (PRM) platform that quantifies hundreds of Klac peptides per injection from as little as ~200 ng of cell lysates, clinical biopsies, and even true single cells - revealing functional Klac signatures inaccessible to conventional methods. The ChemIntelligence pipeline also extends seamlessly to lysine nicotinylation, underscoring its broad adaptability for discovering and profiling new acylations. Together, these chemical and computational advances establish a scalable, antibody-free framework for acyl-proteome mapping that overcomes input constraints and enables deep functional insights from otherwise intractable biological samples.
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BibTeX
@misc{shao2026chemintelligence,
title = {{ChemIntelligence Enables Antibody-Free, Ultra-Low-Input Profiling of Lysine Lactylation and Diverse Acyl-Proteomes}},
author = {C. Shao and Z. He and Q. Yuan and V.-G. Giurcoiu and X. He and X. Cao and H. Huang and Y. Zhang and Y. Zhang and D. Wang and Q. Jiang and Z. Guo and H. Hao and M. Wilhelm and H. Ye},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.28.746934},
url = {https://www.biorxiv.org/content/10.64898/2026.08.28.746934v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - ChemIntelligence Enables Antibody-Free, Ultra-Low-Input Profiling of Lysine Lactylation and Diverse Acyl-Proteomes
AU - C. Shao
AU - Z. He
AU - Q. Yuan
AU - V.-G. Giurcoiu
AU - X. He
AU - X. Cao
AU - H. Huang
AU - Y. Zhang
AU - Y. Zhang
AU - D. Wang
AU - Q. Jiang
AU - Z. Guo
AU - H. Hao
AU - M. Wilhelm
AU - H. Ye
PY - 2026
DA - 2026/08/28
PB - bioRxiv
DO - 10.64898/2026.08.28.746934
UR - https://www.biorxiv.org/content/10.64898/2026.08.28.746934v1
AB - Lysine acylations, including lactylation (Klac), are pivotal regulators of cellular physiology. However, their analysis is currently bottlenecked by antibody enrichment strategies that suffer from sequence bias and require milligram-scale protein inputs, severely precluding the profiling of scarce clinical biopsies and rare cell populations. Here we present ChemIntelligence, an acyl-NHS chemistry-empowered derivatization strategy that rapidly generates unprecedented acylation-specific spectral libraries, exemplified by over 2.5x10^9 human Klac peptides, enabling cross-species reference atlases. Integrated with Prosit-based rescoring, these libraries substantially increase Klac identifications across diverse proteomic datasets. Leveraging this spectral resource, we devised ChemIntelligence Scope, a reproducible, multiplexed parallel reaction monitoring (PRM) platform that quantifies hundreds of Klac peptides per injection from as little as ~200 ng of cell lysates, clinical biopsies, and even true single cells - revealing functional Klac signatures inaccessible to conventional methods. The ChemIntelligence pipeline also extends seamlessly to lysine nicotinylation, underscoring its broad adaptability for discovering and profiling new acylations. Together, these chemical and computational advances establish a scalable, antibody-free framework for acyl-proteome mapping that overcomes input constraints and enables deep functional insights from otherwise intractable biological samples.
ER -