Stepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions

doi:10.1038/s42004-025-01826-2

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	Stepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions
	Zhu, Zhao-Yu 1,2; Mao, Peng-Zhi 2,3; Tarn, Ching 2,3; Cao, Yong 4
	2025-12-09
发表期刊	COMMUNICATIONS CHEMISTRY
ISSN	2399-3669
卷号	9 期号:1 页码:14
摘要	Mass spectrometry-based proteomics is indispensable for studying post-translational modifications. Cyclic immonium ions serve as invaluable diagnostic markers for lysine acylations, yet the principles governing their generation efficiency are poorly understood. Here, we systematically investigate this question and uncover a robust "position effect": the generation of immonium ions is strongly favored when the modified residue is located near the N-terminus of a tryptic peptide. Utilizing LysargiNase digestion and isotope-labeled synthetic peptides, we demonstrate that this effect is likely driven by the inherent instability of b-type fragment ions during collision-induced dissociation. Furthermore, we show that a stepped higher-energy collision dissociation strategy enables enhanced sequence coverage and robust cyclic immonium ion detection (similar to 99%), thereby improving the depth, reliability and speed of acylation identification. Collectively, this work provides fundamental understanding of immonium ion formation and establishes an optimized acquisition and analysis strategy that enhances the efficiency and confidence of protein acylation analysis.
DOI	10.1038/s42004-025-01826-2
收录类别	SCI
语种	英语
WOS研究方向	Chemistry
WOS类目	Chemistry, Multidisciplinary
WOS记录号	WOS:001662788900002
出版者	NATURE PORTFOLIO
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/42900
专题	中国科学院计算技术研究所
通讯作者	Cao, Yong
作者单位	1.Chinese Acad Sci, Shanghai Inst Mat Med, Shanghai, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing, Peoples R China 4.Chinese Acad Sci, Shanghai Inst Immun & Infect, Shanghai, Peoples R China
推荐引用方式 GB/T 7714	Zhu, Zhao-Yu,Mao, Peng-Zhi,Tarn, Ching,et al. Stepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions[J]. COMMUNICATIONS CHEMISTRY,2025,9(1):14.
APA	Zhu, Zhao-Yu,Mao, Peng-Zhi,Tarn, Ching,&Cao, Yong.(2025).Stepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions.COMMUNICATIONS CHEMISTRY,9(1),14.
MLA	Zhu, Zhao-Yu,et al."Stepped collisional energy improves protein acylation identification by eliminating positional bias of cyclic immonium ions".COMMUNICATIONS CHEMISTRY 9.1(2025):14.