PXD005972

PXD005972 is an original dataset announced via ProteomeXchange.

Title	Angiogenic and Immunologic Proteins Identified by Deep Proteomic Profiling of Human Choroidal and Retinal Vascular Endothelial Cells
Description	PURPOSE Diseases that involve choroidal or retinal endothelial vascular cells are leading causes of vision loss: age-related macular degeneration, retinal ischemic vasculopathies and non-infectious posterior uveitis. Proteins differentially expressed by these endothelial cell populations are potential drug targets. We used deep proteomics to define the molecular phenotype of human choroidal and retinal endothelial cells at the protein level. METHODS Choroidal and retinal endothelial cells were separately isolated from 5 human eye pairs by selection on CD31. Total protein was extracted and digested, and peptide fractions were analysed by reverse-phase liquid chromatography tandem mass spectrometry. Peptide sequences were assigned to fragment ion spectra and proteins were inferred using public protein databases. Protein abundance was determined by spectral counting. Protein expression in choroidal versus retinal endothelial cells was compared using edgeR package in R, and annotation enrichment analysis was performed. RESULTS Human choroidal or retinal endothelial cells expressed 5042 non-redundant proteins. Setting the false discovery rate at 5%, 498 proteins (14.4%) of 3454 quantifiable proteins with minimum mean spectral counts of 2.5 were differentially expressed between cell populations. Choroidal and retinal endothelial cells were enriched in angiogenic proteins, and retinal endothelial cells were also enriched in immunologic proteins. CONCLUSIONS This work demonstrates the protein heterogeneity of human choroidal and retinal vascular endothelial cells and provides multiple candidates for further study as novel treatments or drug targets for posterior eye diseases.
HostingRepository	PRIDE
AnnounceDate	2018-03-26
AnnouncementXML	Submission_2018-03-26_00:30:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Justine Smith
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2017-02-27 02:04:10	ID requested
⏵ 1	2018-03-26 00:30:31	announced

Smith JR, David LL, Appukuttan B, Wilmarth PA, Angiogenic and Immunologic Proteins Identified by Deep Proteomic Profiling of Human Retinal and Choroidal Vascular Endothelial Cells: Potential Targets for New Biologic Drugs. Am J Ophthalmol, 193():197-229(2018) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Proteomics, MudPIT, tandem mass spectrometry, linear ion trap, spectral counting, protein expression, human, cell culture, retina, choroid, endothelial cells

Justine R. Smith
contact affiliation	Eye & Vison Health, Flinders University School of Medicine Flinders Medical Center Flinders University Australia
contact email	justine.smith@flinders.edu.au
lab head
Justine Smith
contact affiliation	Flinders University
contact email	justine.smith@flinders.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005972
     1. Label: PRIDE project
     2. Name: Angiogenic and Immunologic Proteins Identified by Deep Proteomic Profiling of Human Choroidal and Retinal Vascular Endothelial Cells