PXD064700-1

PXD064700 is an original dataset announced via ProteomeXchange.

Title	Impact of tissue fixation on the isolation and detection of human brain proteome (DIA-LC-HRMS)
Description	This study investigated the impact of tissue preservation methods on protein profiles analyzed by reversed-phase liquid chromatography-high-resolution mass spectrometry (LC-HRMS) using data-independent acquisition (DIA). We compared proteomic profiles from formalin-fixed, formalin-fixed and paraffin-embedded (FFPE), and fresh-frozen human brain tissues (cortex and hippocampus, n=6). Additionally, we evaluated an FFPE-specific commercial protein extraction kit (n=4). Formalin-fixed samples closely resembled fresh-frozen profiles, whereas FFPE samples exhibited greater deviations. A core set of 1,753 proteins was consistently detected across all sample preparation methods. A total of 35 proteins were identified exclusively in fresh-frozen samples but without functional enrichment. Quantitative comparisons to the proteome of fresh-frozen tissue revealed an underrepresentation of cellular processes, energy metabolism, signaling, and transport related to protein properties such as length, location, and hydrophobicity. In contrast, neuronal development and phagosome-related pathways were overrepresented in fixed tissues. In a pilot study comparing low (Braak 0-II, n=4) and high (Braak IV-VI, n=4) Alzheimer’s disease (AD) stages using formalin-fixed samples, we identified 12 potential protein biomarkers, primarily nucleosomal proteins and carboxypeptidase M (CPM). These findings suggest that formalin-fixed brain tissue provides reliable proteomic information, making it a valuable resource for neurodegenerative disease research.
HostingRepository	PRIDE
AnnounceDate	2026-03-17
AnnouncementXML	Submission_2026-03-17_12:28:50.865.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laura Plantera
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-05 12:59:18	ID requested
⏵ 1	2026-03-17 12:28:51	announced

10.1016/J.JPROT.2025.105589;

submitter keyword: Human brain

hippocampus

prefrontal cortex

formalin-fixed

FFPE

fresh-frozen

DIA

LC-HRMS

Alzheimer

Braak

Uta Ceglarek
contact affiliation	Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Faculty of Medicine, University of Leipzig, Leipzig, Germany
contact email	uta.ceglarek@medizin.uni-leipzig.de
lab head
Laura Plantera
contact affiliation	University of Leipzig, Medical Faculty
contact email	laura.plantera@medizin.uni-leipzig.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/2026/03/PXD064700

PRIDE project URI

• PRIDE
  1. PXD064700
     1. Label: PRIDE project
     2. Name: Impact of tissue fixation on the isolation and detection of human brain proteome (DIA-LC-HRMS)