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Hegedűs T, Chaubey PM, Várady G, Szabó E, Sarankó H, Hofstetter L, Roschitzki B, Stieger B, Sarkadi B. Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav056. [PMID: 26078478 PMCID: PMC4480073 DOI: 10.1093/database/bav056] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/12/2015] [Indexed: 12/31/2022]
Abstract
Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies-the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics.
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Affiliation(s)
- Tamás Hegedűs
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Pururawa Mayank Chaubey
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - György Várady
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Edit Szabó
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Hajnalka Sarankó
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lia Hofstetter
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Bernd Roschitzki
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Bruno Stieger
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Balázs Sarkadi
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary, Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Raemistrasse 100, CH-8091 Zurich, Switzerland, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary and Functional Genomics Center Zurich, University of Zurich, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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