MitoP2: the mitochondrial proteome database--now including mouse data

Prokisch, Holger; Andréoli, Christophe; Ahting, Uwe; Heiß, Kirsten; Ruepp, Andreas; Scharfe, Curt; Meitinger, Thomas

doi:10.1093/nar/gkj127

Cited by 89 publications

(90 citation statements)

References 41 publications

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“…The combined CITP/CZE and CIEF dataset was compared to the mitochondrial protein reference set of the MitoP2-database [58] containing a list of 731 mouse mitochondrial proteins. Distinct proteins (553 out of 2191; or 2082 nonredundant proteins) presented in this study overlapped with the MitoP2-database, corresponding to 76% mouse mitochondrial proteome coverage.…”

Section: Resultsmentioning

confidence: 99%

Application of capillary isotachophoresis‐based multidimensional separations coupled with electrospray ionization‐tandem mass spectrometry for characterization of mouse brain mitochondrial proteome

et al. 2008

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By employing a capillary ITP (CITP)/CZE-based proteomic technology, a total of 1795 distinct mouse Swiss-Prot protein entries (or 1705 nonredundant proteins) are identified from synaptic mitochondria isolated from mouse brain. The ultrahigh resolving power of CITP/CZE is evidenced by the large number of distinct peptide identifications measured from each CITP fraction together with the low peptide fraction overlapping among identified peptides. The degree of peptide overlapping among CITP fractions is even lower than that achieved using combined CIEF/nano-RP LC separations for the analysis of the same mitochondrial sample. When evaluating the protein sequence coverage by the number of distinct peptides mapping to each mitochondrial protein identification, CITP/CZE similarly achieves superior performance with 1041 proteins (58%) having 3 or more distinct peptides, 233 (13%) having 2 distinct peptides, and 521 (29%) having a single distinct peptide. The reproducibility of protein identifications is found to be around 86% by comparing proteins identified from repeated runs of the same mitochondrial sample. The analysis of the mouse mitochondrial proteome by two CITP/CZE runs results in the detection of 2095 distinct mouse Swiss-Prot protein entries (or 1992 nonredundant proteins), corresponding to 59% coverage of the updated Maestro mitochondrial reference set. The collective analysis from combined CITP/CZE and CIEF-based proteomic studies yields the identification of 2191 distinct mitochondrial protein entries (or 2082 nonredundant proteins), corresponding to 76% coverage of the MitoP2-database reference set.

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Section: Resultsmentioning

confidence: 99%

Application of capillary isotachophoresis‐based multidimensional separations coupled with electrospray ionization‐tandem mass spectrometry for characterization of mouse brain mitochondrial proteome

et al. 2008

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“…Based on the number of publications in PubMed, lipid rafts and/or caveolae have been an extremely popular subcellular domain for proteomic investigations (10), equivalent perhaps to mitochondria (46) and certainly more so than phagosomes (47). Prior to the advent of proteomics, rafts were considered to be exclusive to the plasma membrane and membranes immediately up-and downstream of the plasmalemma (i.e., late Golgi/trans-Golgi network and endosomes/phagosomes).…”

Section: Discussionmentioning

confidence: 99%

Mitochondria do not contain lipid rafts, and lipid rafts do not contain mitochondrial proteins

Zheng

Berg

Foster

2009

Journal of Lipid Research

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Lipid rafts are membrane microdomains involved in many cellular functions, including transduction of cellular signals and cell entry by pathogens. Lipid rafts can be enriched biochemically by extraction in a nonionic detergent at low temperature, followed by floatation on a sucrose density gradient. Previous proteomic studies of such detergentresistant membranes (DRMs) are in disagreement about the presence of mitochondrial proteins in raft components. Here, we approach the status of mitochondrial proteins in DRM preparations by employing stable isotope labeling by amino acids in cell culture to evaluate the composition of differentially purified subcellular fractions as well as highresolution linear density gradients. Our data demonstrate that F 1 /F 0 ATPase subunits, voltage-dependent anion selective channels, and other mitochondrial proteins are at best partially copurifying contaminants of raft preparations.

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“…Despite the great expectations raised by this original method, current knowledge on the evolution of the mitochondrial proteome makes it advisable to use this with caution, since most of the mitochondrial proteins do not originate from the alpha-proteobacteria, and a considerable fraction of proteins derived from this bacterial group have a nonmitochondrial localization (25,26). Nevertheless, the presence of homologs in Rickettsia prowazekii is still used, in combination with other lines of evidence, as indicative for mitochondrial localization (9,51).…”

Section: Identifying the Complete Repertoire Of Mitochondrial Proteinsmentioning

confidence: 99%

“…Such an approach is used by the MitoP2 mitochondrial proteome database (51). This server integrates data from computational prediction and subcellular proteomics techniques, but also results from other experiments that might be indicative of mitochondrial localization.…”

Section: Identifying the Complete Repertoire Of Mitochondrial Proteinsmentioning

confidence: 99%

Computational approaches for the prediction of protein function in the mitochondrion

Gabaldón

2006

American Journal of Physiology-Cell Physiology

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Gabaldó n, Toni. Computational approaches for the prediction of protein function in the mitochondrion. Am J Physiol Cell Physiol 291: C1121-C1128, 2006. First published July 26, 2006 doi:10.1152/ajpcell.00225.2006.-Understanding a complex biological system, such as the mitochondrion, requires the identification of the complete repertoire of proteins targeted to the organelle, the characterization of these, and finally, the elucidation of the functional and physical interactions that occur within the mitochondrion. In the last decade, significant developments have contributed to increase our understanding of the mitochondrion, and among these, computational research has played a significant role. Not only general bioinformatics tools have been applied in the context of the mitochondrion, but also some computational techniques have been specifically developed to address problems that arose from within the mitochondrial research field. In this review the contribution of bioinformatics to mitochondrial biology is addressed through a survey of current computational methods that can be applied to predict which proteins will be localized to the mitochondrion and to unravel their functional interactions. genomic context; proteome THE DETAIL AND ACCURACY with which we can model the systemlevel properties of the mitochondrion relies substantially on how comprehensive our knowledge is about its individual components and their corresponding interactions. In recent years, great progress has been achieved toward the identification of the complete set of proteins that perform their functions inside the mitochondrion, the so-called mitochondrial proteome. For instance, advances in subcellular proteomics have allowed the isolation of 615 proteins from human heart mitochondria (60), and the combination of experimental research with genomics and sequence analyses has expanded the set of mitochondrial proteins to nearly a thousand (13). Nevertheless, despite these efforts, a substantial fraction of the human mitochondrial proteome, estimated to contain about 1500 proteins (37), remains still unidentified. Moreover, a large fraction of the identified proteins have unknown functions, and for many of the rest the knowledge of their biological roles is just general.During the last decade, the concourse of computational biology in mitochondrial research has been essential. For instance, bioinformatics tools have been widely used for predicting which proteins are targeted to the mitochondrion and for identifying their functional homologs. More recently, a number of novel computational techniques that integrate different sources of data and unravel new functional interactions among proteins have been developed (24). These techniques, known as context-based function prediction methods, are increasingly being used in the context of the mitochondrial proteome and have proven especially useful for the identification of novel disease genes. Here I survey the most prominent computational biology methods that are used in the field of mitochondr...

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MitoP2: the mitochondrial proteome database--now including mouse data

Cited by 89 publications

References 41 publications

Application of capillary isotachophoresis‐based multidimensional separations coupled with electrospray ionization‐tandem mass spectrometry for characterization of mouse brain mitochondrial proteome

Application of capillary isotachophoresis‐based multidimensional separations coupled with electrospray ionization‐tandem mass spectrometry for characterization of mouse brain mitochondrial proteome

Mitochondria do not contain lipid rafts, and lipid rafts do not contain mitochondrial proteins

Computational approaches for the prediction of protein function in the mitochondrion

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