PXD071205-1

PXD071205 is an original dataset announced via ProteomeXchange.

Title	LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients - Optimized Astral dataset
Description	Recent advancements in liquid chromatography-mass spectrometry (LC-MS) have increasingly focused on high-throughput workflows, leveraging rapid chromatographic gradients and minimal sample input to maximize proteome coverage from limited material. This shift is particularly driven by the rise of single-cell proteomics, where sensitivity and reproducibility are critical. Building on our previous benchmark dataset (PXD028735), we now present an expanded study utilizing the latest generation of LC-MS platforms optimized for high-throughput proteomics. This study features shorter LC gradients and lower sample input to address the growing need for rapid and sensitive proteome analysis. Using a standardized hybrid proteome mixture with defined ratios of Human, Yeast, and E. coli, we generated a comprehensive Data-Dependent and Data-Independent Acquisition (DDA/DIA) dataset across multiple state-of-the-art LC-MS platforms. The updated dataset incorporates the latest acquisition methodologies and extends coverage across an even broader range of data formats, including enhanced ion mobility-enabled and scanning quadrupole-based acquisitions. Our results providea detailed assessment of the impact of technological advancements and demonstrate how shortening LC gradients influence proteome coverage, quantitative precision, and data consistency across instruments
HostingRepository	PRIDE
AnnounceDate	2026-02-03
AnnouncementXML	Submission_2026-02-03_03:45:04.630.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD071205
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Bart Van Puyvelde
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Escherichia coli; NCBI TaxID: NEWT:562; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-25 11:57:44	ID requested
⏵ 1	2026-02-03 03:45:05	announced

10.6019/PXD071205;

submitter keyword: Orbitrap Astral, LFQ, HYE

Maarten Dhaenens
contact affiliation	ProGenTomics, Laboratory of Pharmaceutical Biotechnology,Ghent University
contact email	maarten.dhaenens@ugent.be
lab head
Bart Van Puyvelde
contact affiliation	Ghent University
contact email	bart.vanpuyvelde@ugent.be
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD071205

PRIDE project URI

• PRIDE
  1. PXD071205
     1. Label: PRIDE project
     2. Name: LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients - Optimized Astral dataset