Dataset Information

Identification of differentially abundant proteins in glaucomatous and non-glaucomatous trabecular meshwork cell cultures using isobaric multiplexed quantitative proteomics

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Eye, Trabecular Meshwork Cell

DISEASE(S): Glaucoma

SUBMITTER: Phillip Wilmarth

LAB HEAD: Kate E. Keller, Ph.D.

PROVIDER: PXD066598 | Pride | 2026-04-07

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	KELL-1212_HumanCells_TMT18_2DRPRP_50ug_PSRtrapPSRcol_140m_17pc_20230707_OT_filtered.ms2	Other
	KELL-1212_HumanCells_TMT18_2DRPRP_50ug_PSRtrapPSRcol_140m_17pc_20230707_OT_filtered.sqt	Other
	KELL-1212_HumanCells_TMT18_2DRPRP_50ug_PSRtrapPSRcol_140m_17pc_20230707_OT_filtered.txt	Txt
	KELL-1212_HumanCells_TMT18_2DRPRP_50ug_PSRtrapPSRcol_140m_20pc_20230707_OT.raw	Raw
	KELL-1212_HumanCells_TMT18_2DRPRP_50ug_PSRtrapPSRcol_140m_20pc_20230707_OT_filtered.ms2	Other

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Publications

Isobaric quantitative proteomics reveals altered extracellular matrix, cytoskeletal, and degradation pathways in glaucomatous trabecular meshwork cells.

Holden Paul P Sun Ying Ying YY Zientek Keith K Wilmarth Phillip A PA Reddy Ashok P AP Keller Kate E KE

Scientific reports 20260318 1

PMID: 41851243

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