PXD065604-1

PXD065604 is an original dataset announced via ProteomeXchange.

Title	Improved identification of peptides, modification sites, and cross-link sites by Target-enhanced Accurate Inclusion Mass Screening (TAIMS)
Description	Chemical cross-linking of proteins coupled with mass spectrometry provides structural insights by identifying cross-linked peptide pairs, abbreviated as cross-links. Presently, cross-link identification suffers from ambiguity and poor sensitivity, because they are typically of lower abundance and consequently of lower MS2 quality than linear peptides present in the same sample. Here, we present Target-enhanced Accurate Inclusion Mass Screening (TAIMS), a meticulously optimized targeted mass spectrometry method. TAIMS significantly improved the quality of MS2 as indicated by fragment ion coverage (FIC) and other metrics. On cross-linked E. coli lysate or yeast ribosome samples, the percentage of high-FIC cross-links increased from 40.6%~43.3% by data-dependent acquisition (DDA) to 87.0%~94.5% by TAIMS. As a result, TAIMS substantially enhanced the accuracy of cross-link site localization and mitigated sensitivity loss in cross-link identification from large database searches. Enhanced identification sensitivity of TAIMS is further evidenced by its capacity to recover genuine cross-link identifications from data that would typically be discarded. On cross-linked E. coli lysate, 10.5% of the inclusion-list entries generated from unidentified cross-link-spectrum matches gained identity through TAIMS, of which 65.5% turned out to be linear peptides and 19.0% being cross-links, including 10 inter-molecular cross-links missed entirely by DDA. Overall, TAIMS increased high-confidence cross-link identifications by 52.9%~131.3%. Additionally, we demonstrate that TAIMS is a general method for identification of low-abundance, post-translationally modified peptides. On a mouse brain sample, TAIMS increased the number of phosphopeptides identified with accurate phosphosite assignment by 67%. These findings indicate that TAIMS holds broad applicability in proteomics.
HostingRepository	iProX
AnnounceDate	2026-06-28
AnnouncementXML	Submission_2026-07-16_01:06:54.769.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mengqiu Dong
SpeciesList	scientific name: Bos taurus; NCBI TaxID: 9913; scientific name: artificial sequences; NCBI TaxID: 81077; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932; scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	phosphorylated residue
Instrument	Q Exactive HF; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-30 00:32:12	ID requested
⏵ 1	2026-07-16 01:06:55	announced

Dataset with its publication pending

submitter keyword: CXMS, Targeted mass spectrometry, tAIMS, Spectral quality, Identification accuracy, Identification sensitivity, Cross-link site localization, Phosphorylation localization

Mengqiu Dong
contact affiliation	National Institute of Biological Sciences, Beijing
contact email	dongmengqiu@nibs.ac.cn
lab head
Mengqiu Dong
contact affiliation	National Institute of Biological Sciences, Beijing
contact email	adalaiti@nibs.ac.cn
dataset submitter

iProX dataset URI