PXD065707-1

PXD065707 is an original dataset announced via ProteomeXchange.

Title	Accurate and Fast Protein Acylation Identification by Eliminating Position Effects of Cyclic Immonium Ions with Stepped HCD
Description	Cyclic immonium (CycIm) 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-type 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 HCD strategy enables enhanced sequence coverage and robust CycIm ion detection (~99%) of glutarylated and lactylated peptides, thereby improving the depth, reliability and speed of PTM 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 PTM analysis.
HostingRepository	iProX
AnnounceDate	2025-07-02
AnnouncementXML	Submission_2025-07-02_20:29:40.358.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhaoyu Zhu
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-02 20:29:23	ID requested
⏵ 1	2025-07-02 20:29:40	announced

Dataset with its publication pending

submitter keyword: Acylation, BS2G(glutarylation), Trypsin, LysargiNase, Lactylation

Yong Cao
contact affiliation	Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences
contact email	ycao@siii.cas.cn
lab head
Zhaoyu Zhu
contact affiliation	Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences
contact email	zyzhu@siii.cas.cn
dataset submitter

iProX dataset URI