PXD069877-1

PXD069877 is an original dataset announced via ProteomeXchange.

Title	An ultrasensitive spatial tissue proteomics workflow exceeding 100 proteomes per day
Description	Achieving high-resolution spatial tissue proteomes requires careful balancing and integration of optimized sample processing, chromatography, and MS acquisition. Here, we present an advanced cellenONE protocol for loss-reduced tissue processing and compare all Evosep ONE Whisper Zoom gradients (20, 40, 80, and 120 samples per day), along with three common DIA acquisition schemes on a timsUltra AIP mass spectrometer. We found that tissue type was as important as gradient length and sample amount in determining proteome coverage. Moreover, the benefit of increased tissue sampling was gradient- and dynamic range-dependent. Analyzing mouse liver, a high dynamic range tissue, over tenfold more tissue sampling led to only ~30% gain in protein identification for short gradients (120 SPD and 80 SPD). However, even the lowest tested tissue amount (0.04 nL, 40,000 µm3) yielded 3,200 reproducibly quantified proteins for the 120 SPD method. Longer gradients (40 SPD and 20 SPD) instead significantly benefited from more tissue sampling, quantifying over 7,500 proteins from 0.5 nL of tonsil T-cell niches. Finally, we applied our workflow to a rare squamous cell carcinoma of the oral cavity, uncovering disease-associated pathways and region-specific protein level changes. Our study demonstrates that more than 100 high-quality spatial tissue proteomes can be prepared and acquired daily, laying a strong foundation for cohort-size spatial tissue proteomics in translational research.
HostingRepository	PRIDE
AnnounceDate	2026-01-14
AnnouncementXML	Submission_2026-01-14_10:08:29.867.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fabian Coscia
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	No PTMs are included in the dataset
Instrument	timsUltra AIP

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-24 05:08:55	ID requested
⏵ 1	2026-01-14 10:08:30	announced

10.1016/J.MCPRO.2025.101489;

submitter keyword: None

Dr. Fabian
contact affiliation	Spatial Proteomics Lab, Max Delbrück Center für Molekulare Medizin, Berlin, Germany
contact email	fabian.coscia@mdc-berlin.de
lab head
Fabian Coscia
contact affiliation	Max Delbrück Center
contact email	fabian.coscia@mdc-berlin.de
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/2026/01/PXD069877

PRIDE project URI

• PRIDE
  1. PXD069877
     1. Label: PRIDE project
     2. Name: An ultrasensitive spatial tissue proteomics workflow exceeding 100 proteomes per day