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Updated: Dec 30, 2025

Author Spotlight: Two-Step Tag-Free Isolation of Mitochondria for Improved Protein Discovery and Quantification
Published on: June 2, 2023
MMPdb and MitoPredictor: Tools for facilitating comparative analysis of animal mitochondrial proteomes
Viraj Muthye1, Gaurav Kandoi2, Dennis V Lavrov1
1Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, Iowa 50011, USA; Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, Iowa 50011, USA.
Abstract:
Data on experimentally-characterized animal mitochondrial proteomes (mt-proteomes) are limited to a few model organisms and are scattered across multiple databases, impeding a comparative analysis. We developed two resources to address these problems. First, we re-analyzed proteomic data from six species with experimentally characterized mt-proteomes: animals (Homo sapiens, Mus musculus, Caenorhabditis elegans, and Drosophila melanogaster), and outgroups (Acanthamoeba castellanii and Saccharomyces cerevisiae) and created the Metazoan Mitochondrial Proteome Database (MMPdb) to host the results. Second, we developed a novel pipeline, "MitoPredictor" that uses a Random Forest classifier to infer mitochondrial localization of proteins based on orthology, mitochondrial targeting signal prediction, and protein domain analyses. Both tools generate an R Shiny applet that can be used to visualize and interact with the results and can be used on a personal computer. MMPdb is also available online at https://mmpdb.eeob.iastate.edu/.
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