PXD077556-1

PXD077556 is an original dataset announced via ProteomeXchange.

Title	Ultra-sensitive cohort data analysis for Orbitrap Astral based single-cell proteomics
Description	Orbitrap Astral mass spectrometry driven data-independent acquisition (DIA) strategy enables deep profiling in shotgun proteomics and is increasingly adopted in single-cell proteomics (SCP). However, the high proportion of missing values reported by existing DIA software remains a bottleneck for sensitive SCP analysis. Here, we present ApuQuant, an Orbitrap Astral DIA data analysis software that performs cohort-level re-identification and quantification. In ApuQuant, we apply a contrastive learning model to Match Between Run (MBR) analysis and introduce a false discovery rate estimation algorithm to rule out false MBR results across runs within a cohort. Compared with DIA-NN and Spectronaut, ApuQuant reduced missing values from 43.45%–50.82% to nearly 1% on a technical-replicate dataset, thereby enabling ultra-sensitive data analysis. Further validation on additional datasets demonstrated that this improvement was achieved without increasing false positive results. Finally, ApuQuant was applied to an A549-single-cell proteomics dataset and showed a 39.99% increase in protein identifications, illustrating a more comprehensive characterization of proteomic heterogeneity at single-cell resolution.
HostingRepository	iProX
AnnounceDate	2026-04-23
AnnouncementXML	Submission_2026-04-23_19:17:48.178.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yuzhuo Gu
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2026-04-23 19:17:28	ID requested
⏵ 1	2026-04-23 19:17:48	announced

Dataset with its publication pending

submitter keyword: single-cell proteomics, data-independent acquisition, Orbitrap Astral mass spectrometry

Chao Liu
contact affiliation	Beihang University
contact email	liuchaobuaa@buaa.edu.cn
lab head
Yuzhuo Gu
contact affiliation	Beihang University
contact email	yuzhuogu@buaa.edu.cn
dataset submitter

iProX dataset URI