PXD063161

PXD063161 is an original dataset announced via ProteomeXchange.

Title	Proteomic Profiling of Cerebrospinal Fluid in Adult Rats with Compromised Lymphatic Drainage Using DIA-PASEF
Description	The glymphatic system’s outflow of “dirty” brain fluids collects in the meningeal lymphatic vessels, which drain via lymphatic collectors primarily to the deep cervical lymph nodes (dcLN). It is unclear, however, whether lymphatic dcLN drainage is a prerequisite for normal cerebral homeostasis. Here, we applied proteomic profiling of cerebrospinal fluid (CSF) using Data-Dependent Acquisition (DDA) and Data-Independent Acquisition Parallel Accumulation–Serial Fragmentation (DIA PASEF) approaches to characterize the CSF obtained from 3-month-old young rats. The study included two sets of samples: Sham (n=5) and Cauterized dcLN (n=4). For spectral library generation, 20% of each digested sample was pooled and analyzed using timsTOF Pro2 in DDA PASEF mode. Following bottom-up analysis, enrichment analysis using Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) identified several pathways indicative of a damaging phenotype and cellular stress-related neurodegeneration. The CSF proteomic analysis revealed cellular stress in the form of low-grade inflammation and up-regulation of pathways associated with neurodegeneration in young rats with lymphatic drainage impairment. Our findings illuminate the brain’s age-dependent adaptive mechanisms to chronic mechanical stress and underscore the urgency of developing targeted therapies for lymphatic dysfunction.
HostingRepository	PRIDE
AnnounceDate	2025-07-04
AnnouncementXML	Submission_2025-07-04_08:32:50.868.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	ZOHAIB KHAN
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	No PTMs are included in the dataset
Instrument	autoflex

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-21 14:52:20	ID requested
⏵ 1	2025-07-04 08:32:51	announced

Dataset with its publication pending

submitter keyword: Cauterized,RAT, DIA-PASEF

LAURA SANTAMBROGIO
contact affiliation	Weill Cornell Medicine, New York, USA
contact email	las4011@med.cornell.edu
lab head
ZOHAIB KHAN
contact affiliation	WEILL CORNELL MEDICINE
contact email	znk4001@med.cornell.edu
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/2025/07/PXD063161

PRIDE project URI

• PRIDE
  1. PXD063161
     1. Label: PRIDE project
     2. Name: Proteomic Profiling of Cerebrospinal Fluid in Adult Rats with Compromised Lymphatic Drainage Using DIA-PASEF