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

Smith AC, Robinson AJ - Mol. Cell Proteomics (2009)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB20XY, United Kingdom.

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.

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The cumulative increase in the number of (i) proteins reported as mitochondrial (gray bars) and (ii) publications (black line) over the last 10 years using the 33 publications on mitochondrial localization included in MitoMiner. Protein redundancy was removed by using HomoloGene to merge orthologs and duplicate proteins. The number of transmembrane proteins (dark gray) as annotated in UniProt that have been found is about 20% of the total (light gray).
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f7: The cumulative increase in the number of (i) proteins reported as mitochondrial (gray bars) and (ii) publications (black line) over the last 10 years using the 33 publications on mitochondrial localization included in MitoMiner. Protein redundancy was removed by using HomoloGene to merge orthologs and duplicate proteins. The number of transmembrane proteins (dark gray) as annotated in UniProt that have been found is about 20% of the total (light gray).

Mentions: To assess progress in determining the mitochondrial proteome, we used MitoMiner to find the annual growth in data and publications on the mitochondrial localization of proteins from the 33 publications. The increase in the number of proteins (evaluated as HomoloGene clusters) reported in the publications closely matched the growth in the number of publications (Fig. 7). By 2008, the total number of proteins reported across all species was 3672. In 2008, the increase in the number of mitochondrial proteins was 220, although Pagliarini et al. (6) had published a study that identified about 1100 mitochondrial proteins. The proportion of proteins with experimental evidence of mitochondrial localization that had the “transmembrane” keyword in their UniProt entry increased from 18% in 2002 to 21% in 2008. Of the 3672 proteins, 1506 (41%) had been annotated as mitochondrial by either the Gene Ontology or UniProt, 1326 (36%) had not been annotated as mitochondrial but had been annotated in another subcellular location, and 840 (23%) had no annotation for subcellular localization.


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

Smith AC, Robinson AJ - Mol. Cell Proteomics (2009)

The cumulative increase in the number of (i) proteins reported as mitochondrial (gray bars) and (ii) publications (black line) over the last 10 years using the 33 publications on mitochondrial localization included in MitoMiner. Protein redundancy was removed by using HomoloGene to merge orthologs and duplicate proteins. The number of transmembrane proteins (dark gray) as annotated in UniProt that have been found is about 20% of the total (light gray).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2690483&req=5

f7: The cumulative increase in the number of (i) proteins reported as mitochondrial (gray bars) and (ii) publications (black line) over the last 10 years using the 33 publications on mitochondrial localization included in MitoMiner. Protein redundancy was removed by using HomoloGene to merge orthologs and duplicate proteins. The number of transmembrane proteins (dark gray) as annotated in UniProt that have been found is about 20% of the total (light gray).
Mentions: To assess progress in determining the mitochondrial proteome, we used MitoMiner to find the annual growth in data and publications on the mitochondrial localization of proteins from the 33 publications. The increase in the number of proteins (evaluated as HomoloGene clusters) reported in the publications closely matched the growth in the number of publications (Fig. 7). By 2008, the total number of proteins reported across all species was 3672. In 2008, the increase in the number of mitochondrial proteins was 220, although Pagliarini et al. (6) had published a study that identified about 1100 mitochondrial proteins. The proportion of proteins with experimental evidence of mitochondrial localization that had the “transmembrane” keyword in their UniProt entry increased from 18% in 2002 to 21% in 2008. Of the 3672 proteins, 1506 (41%) had been annotated as mitochondrial by either the Gene Ontology or UniProt, 1326 (36%) had not been annotated as mitochondrial but had been annotated in another subcellular location, and 840 (23%) had no annotation for subcellular localization.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB20XY, United Kingdom.

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.

Show MeSH