MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data.

TitleMitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data.
Publication TypeJournal Article
Year of Publication2009
AuthorsSmith, AC, Robinson, AJ
JournalMol Cell Proteomics
Volume8
Issue6
Pagination1324-37
Date Published2009 Jun
ISSN1535-9484
KeywordsDatabases, Protein, Humans, Mitochondria, Proteomics, User-Computer Interface
Abstract

Mitochondria are a vital component of eukaryotic cells with functions that extend beyond energy production to include metabolism, signaling, cell growth, and apoptosis. Their dysfunction is implicated in a large number of metabolic, degenerative, and age-related human diseases. Therefore, it is important to characterize and understand the mitochondrion. Many experiments have attempted to define the mitochondrial proteome, resulting in large and complex data sets that are difficult to analyze. To address this, we developed a new public resource for the storage and investigation of this mitochondrial proteomics data, called MitoMiner, that uses a model to describe the proteomics data and associated biological information. The proteomics data of 33 publications from both mass spectrometry and green fluorescent protein tagging experiments were imported and integrated with protein annotation from UniProt and genome projects, metabolic pathway data from Kyoto Encyclopedia of Genes and Genomes, homology relationships from HomoloGene, and disease information from Online Mendelian Inheritance in Man. We demonstrate the strengths of MitoMiner by investigating these data sets and show that the number of different mitochondrial proteins that have been reported is about 3700, although the number of proteins common to both animals and yeast is about 1400, and membrane proteins appear to be underrepresented. Furthermore analysis indicated that enzymes of some cytosolic metabolic pathways are regularly detected in mitochondrial proteomics experiments, suggesting that they are associated with the outside of the outer mitochondrial membrane. The data and advanced capabilities of MitoMiner provide a framework for further mitochondrial analysis and future systems level modeling of mitochondrial physiology.

DOI10.1074/mcp.M800373-MCP200
Alternate JournalMol. Cell Proteomics
Citation Key10.1074/mcp.M800373-MCP200
PubMed ID19208617
PubMed Central IDPMC2690483
Grant ListMC_U105674181 / / Medical Research Council / United Kingdom
/ / Medical Research Council / United Kingdom