PXD005972 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-02-27 02:04:10 | ID requested | |
⏵ 1 | 2018-03-26 00:30:31 | announced | |
Publication List
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] |
Keyword List
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 |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD005972
- Label: PRIDE project
- Name: Angiogenic and Immunologic Proteins Identified by Deep Proteomic Profiling of Human Choroidal and Retinal Vascular Endothelial Cells