MassIVE MSV000081764

Imported Reanalysis Dataset Public PXD000787

A proteomic map of the human aqueous humor

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Description

The aqueous humor is a colourless, transparent fluid that fills the anterior chamber of the eye. It has an important role to play in maintaining the intraocular pressure of the eye and providing nourishment to avascular structures such as the lens and cornea. It is also essential for providing a clear path for the entry and exit of light from the eye and maintaining the refractive power of the eye. In this study, 250 samples of aqueous humor were collected from patients undergoing cataract surgery. The samples were pooled, divided into aliquots and subjected to ingel digestion, insolution digestion followed by strong cation exchange chromatography and basic reverse phase liquid chromatography fractionation. MS/MS analysis was carried out on a Fourier transform LTQ-Orbitrap velos mass spectrometer and the data were searched with the search algorithms Mascot, SEQUEST and X!Tandem against the NCBI RefSeq human protein database. We have identified 818 proteins of which 447 have been identified for the first time. Proteins such as sorbitol dehydrogenase, filensin and phakinin were some of the novel proteins identified in this study. Classification of proteins based on domain information yielded 304 proteins with signal peptides, 46 proteins with transmembrane domain and 75 proteins with both signal peptide and transmembrane domains. Our study provides a detailed profile of the human aqueous humor. The results from this study of aqueous proteins should help facilitate research into pathological conditions of the eye such as glaucoma, myopia, cataract and uveitis. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Human ; Eye ; Aqueous humor ; humor ; LC-MS/MS ; Trypsin ; bRPLC ; InGel ; SCX

Contact

Principal Investigators:
(in alphabetical order) 		Akhilesh Pandey, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA, N/A
Submitting User: ccms

Publications

Murthy KR, Rajagopalan P, Pinto SM, Advani J, Murthy PR, Goel R, Subbannayya Y, Balakrishnan L, Dash M, Anil AK, Manda SS, Nirujogi RS, Kelkar DS, Sathe GJ, Dey G, Chatterjee A, Gowda H, Chakravarti S, Shankar S, Sahasrabuddhe NA, Nair B, Somani BL, Prasad TS, Pandey A.
Proteomics of human aqueous humor.
OMICS. 2015 May;19(5):283-93.

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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.