PXD066598-1

PXD066598 is an original dataset announced via ProteomeXchange.

Title	Identification of differentially abundant proteins in glaucomatous and non-glaucomatous trabecular meshwork cell cultures using isobaric multiplexed quantitative proteomics
Description	Glaucoma trabecular meshwork (GTM) cells cultured in vitro retain many characteristics of their in situ phenotype. We used isobaric labeling quantitative proteomics to identify proteins that were differentially regulated between glaucomatous and age-matched non-glaucomatous TM (NTM) cells. NTM (n=5) and GTM cells (n=5) were grown to confluence, placed in serum-free media for 3 days, and scraped cells then were lysed by bead beating in 5% SDS. Equal amounts of protein were reduced, alkylated, and digested with trypsin and peptides were labeled with 18-plex tandem mass tags (TMTpro). After combining samples, they were fractionated on an Orbitrap Fusion mass spectrometer. Data was processed using the PAW/Comet pipeline and EdgeR with Benjami-Hochberg multiple correction testing (p<0.05). Pathway enrichment analysis was done. Western immunoblotting and immunofluorescence validations were performed. Analysis of the NTM and GTM biological replicates identified 206 proteins that were significantly up-regulated in GTM cells, 42 proteins that were down-regulated, with 5270 non-candidates. Interestingly, there were 18 proteins that were not detected in any of the NTM cell strains but produced abundant reporter ion intensities in GTM cells. Significant regulated pathways included the Wnt and TGFb pathways, protein degradation, actin cytoskeletal regulation, and nuclear proteins. Western immunoblotting studies agreed with the TMT data.
HostingRepository	PRIDE
AnnounceDate	2026-04-07
AnnouncementXML	Submission_2026-04-07_13:28:24.963.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Phillip Wilmarth
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-25 15:36:29	ID requested
⏵ 1	2026-04-07 13:28:25	announced

10.1038/s41598-026-44561-x;

Holden P, Sun YY, Zientek K, Wilmarth PA, Reddy AP, Keller KE, Isobaric quantitative proteomics reveals altered extracellular matrix, cytoskeletal, and degradation pathways in glaucomatous trabecular meshwork cells. Sci Rep, 16(1):(2026) [pubmed]

submitter keyword: isobaric labeling,Trabecular meshwork, glaucoma, mass spectrometry, human, cell culture, quantitative proteomics, extracellular matrix

Kate E. Keller, Ph.D.
contact affiliation	Department of Ophthalmology School of Medicine Oregon Health & Science University Portland, OR 97239 USA
contact email	gregorka@ohsu.edu
lab head
Phillip Wilmarth
contact affiliation	OHSU
contact email	wilmarth@ohsu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD066598
     1. Label: PRIDE project
     2. Name: Identification of differentially abundant proteins in glaucomatous and non-glaucomatous trabecular meshwork cell cultures using isobaric multiplexed quantitative proteomics