Human Proteinpedia enables sharing of human protein data

Nature Biotechnology (Impact Factor: 41.51). 03/2008; 26(2):164-7. DOI: 10.1038/nbt0208-164
Source: PubMed


Proteomic technologies, such as yeast twohybrid, mass spectrometry (MS), protein/ peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories. Even more difficult is the annotation and display of pertinent information in the context of the corresponding proteins. Wikipedia, an online encyclopedia that anyone can edit, has already proven quite successful1 and can be used as a model for sharing biological data. However, the need for experimental evidence, data standardization and ownership of data creates scientific obstacles.

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Available from: Petra Zürbig, Oct 14, 2015
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    • "We carried out a bioinformatics analysis of subcellular localization, molecular function and biological processes by searching the identified proteins against the manually curated Human Protein Reference Database (HPRD; and Human Proteinpedia ( [63-65]. Of the 1,205 proteins identified in this study, 599 proteins possess signal peptides and 318 proteins are reported to be localized in extracellular compartment. "
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    ABSTRACT: Background:The vitreous humor is a transparent, gelatinous mass whose main constituent is water. It plays an important role in providing metabolic nutrient requirements of the lens, coordinating eye growth and providing support to the retina. It is in close proximity to the retina and reflects many of the changes occurring in this tissue. The biochemical changes occurring in the vitreous could provide a better understanding about the pathophysiological processes that occur in vitreoretinopathy. In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry. Results:The vitreous humor was subjected to multiple fractionation techniques followed by LC-MS/ MS analysis. We identified 1,205 proteins, 682 of which have not been described previously in the vitreous humor. Most proteins were localized to the extracellular space (24%), cytoplasm (20%) or plasma membrane (14%). Classification based on molecular function showed that 27% had catalytic activity, 10% structural activity, 10% binding activity, 4% cell and 4% transporter activity. Categorization for biological processes showed 28% participate in metabolism, 20% in cell communication and 13% in cell growth. The data have been deposited to the ProteomeXchange with identifier PXD000957. Conclusion: This large catalog of vitreous proteins should facilitate biomedical research into pathological conditions of the eye including diabetic retinopathy, retinal detachment and cataract. Keywords: retina, SCX chromatography, OFFGEL electrophoresis, Proteome Discoverer, secreted proteins, protein biomarkers, body fluid proteomics
    Clinical Proteomics 05/2014; 11(1). DOI:10.1186/1559-0275-11-29
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    • "The MO3.13 proteome was classified according to the Human Proteome Reference Database ( [16]. Keratin subunits were discarded of the MO3.13 dataset due to the potential of contamination during the proteomic workflow. "
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    ABSTRACT: Myelination of the central nervous system is performed by oligodendrocytes, which have been implicated in brain disorders such as multiple sclerosis and schizophrenia. We have used the human oligodendroglial cell line MO3.13 to establish an oligodendrocyte reference proteome database. Proteins were pre-fractionationated by SDS-PAGE and after in-gel digestion subjected to nano-flow liquid chromatography mass spectrometry (nLC-MS/MS) analysis. Approximately 11,600 unique peptides were identified and, after stringent filtering, resulted in 2,290 proteins representing 9 distinct biological processes and various molecular classes and functions. Oligodendrocyte-specific proteins such as MBP and CNP as well as proteins involved in multiple sclerosis and schizophrenia were also identified and are discussed. Proteins of this dataset have also been classified according to their chromosomal origin for providing useful data to the chromosome-centric human proteome project (C-HPP). Given the importance of oligodendrocytes in the etiology of demyelinating and oligodendrogial disorders, the MO3.13 proteome database will provide a valuable resource. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD000263. This article is protected by copyright. All rights reserved.
    Proteomics 12/2013; 13(23-24). DOI:10.1002/pmic.201300201 · 3.81 Impact Factor
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    • "GO analysis was carried out using Human Protein Reference Database (HPRD: [52] and Human Proteinpedia [58] which are GO compliant databases. Pathway analyses were carried out using Ingenuity Pathways Analysis (IPA) software version 7.1 available at "
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    ABSTRACT: The ciliary body is the circumferential muscular tissue located just behind the iris in the anterior chamber of the eye. It plays a pivotal role in the production of aqueous humor, maintenance of the lens zonules and accommodation by changing the shape of the crystalline lens. The ciliary body is the major target of drugs against glaucoma as its inhibition leads to a drop in intraocular pressure. A molecular study of the ciliary body could provide a better understanding about the pathophysiological processes that occur in glaucoma. Thus far, no large-scale proteomic investigation has been reported for the human ciliary body. In this study, we have carried out an in-depth LC-MS/MS-based proteomic analysis of normal human ciliary body and have identified 2,815 proteins. We identified a number of proteins that were previously not described in the ciliary body including importin 5 (IPO5), atlastin-2 (ATL2), B-cell receptor associated protein 29 (BCAP29), basigin (BSG), calpain-1 (CAPN1), copine 6 (CPNE6), fibulin 1 (FBLN1) and galectin 1 (LGALS1). We compared the plasma proteome with the ciliary body proteome and found that the large majority of proteins in the ciliary body were also detectable in the plasma while 896 proteins were unique to the ciliary body. We also classified proteins using pathway enrichment analysis and found most of proteins associated with ubiquitin pathway, EIF2 signaling, glycolysis and gluconeogenesis. More than 95% of the identified proteins have not been previously described in the ciliary body proteome. This is the largest catalogue of proteins reported thus far in the ciliary body that should provide new insights into our understanding of the factors involved in maintaining the secretion of aqueous humor. The identification of these proteins will aid in understanding various eye diseases of the anterior segment such as glaucoma and presbyopia.
    Clinical Proteomics 08/2013; 10(1):9. DOI:10.1186/1559-0275-10-9
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