title: Translational Targeted Proteomics Profiling of Mitochondrial Energy Metabolic Pathways in Mouse and Human Samples.
abstract: Absolute measurements of protein abundance are important in the understanding of biological processes and the precise computational modeling of biological pathways. We developed targeted LC-MS/MS assays in the selected reaction monitoring (SRM) mode to quantify over 50 mitochondrial proteins in a single run. The targeted proteins cover the tricarboxylic acid cycle, fatty acid β-oxidation, oxidative phosphorylation, and the detoxification of reactive oxygen species. Assays used isotopically labeled concatemers as internal standards designed to target murine mitochondrial proteins and their human orthologues. Most assays were also suitable to quantify the corresponding protein orthologues in rats. After exclusion of peptides that did not pass the selection criteria, we arrived at SRM assays for 55 mouse, 52 human, and 51 rat proteins. These assays were optimized in isolated mitochondrial fractions from mouse and rat liver and cultured human fibroblasts and in total liver extracts from mouse, rat, and human. The developed proteomics approach is suitable for the quantification of proteins in the mitochondrial energy metabolic pathways in mice, rats, and humans as a basis for translational research. Initial data show that the assays have great potential for elucidating the adaptive response of human patients to mutations in mitochondrial proteins in a clinical setting.
authors.affiliation: Department of Pharmacy, Analytical Biochemistry, University of Groningen , 9713 AV, Groningen, The Netherlands.|Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.|Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Justina C
authors.initials: JC
authors.lastname: Wolters
authors.affiliation: Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.|Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Jolita
authors.initials: J
authors.lastname: Ciapaite
authors.affiliation: Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.|Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Karen
authors.initials: K
authors.lastname: van Eunen
authors.affiliation: Department of Laboratory Medicine, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Klary E
authors.initials: KE
authors.lastname: Niezen-Koning
authors.affiliation: Surgical Research Laboratory, Department of Surgery, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.|Section Hepato-Pancreato-Biliary Surgery and Liver Transplantation, Department of Surgery, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Alix
authors.initials: A
authors.lastname: Matton
authors.affiliation: Surgical Research Laboratory, Department of Surgery, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.|Section Hepato-Pancreato-Biliary Surgery and Liver Transplantation, Department of Surgery, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Porte
authors.affiliation: Department of Pharmacy, Analytical Biochemistry, University of Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Peter
authors.initials: P
authors.lastname: Horvatovich
authors.affiliation: Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.|Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Barbara M
authors.initials: BM
authors.lastname: Bakker
authors.affiliation: Department of Pharmacy, Analytical Biochemistry, University of Groningen , 9713 AV, Groningen, The Netherlands.|Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, University Medical Center Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Rainer
authors.initials: R
authors.lastname: Bischoff
authors.affiliation: Department of Pharmacy, Analytical Biochemistry, University of Groningen , 9713 AV, Groningen, The Netherlands.
authors.forename: Hjalmar P
authors.initials: HP
authors.lastname: Permentier
mesh_terms: D000818:Animals; D004734:Energy Metabolism; D005347:Fibroblasts / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008099:Liver / Q000737:chemistry / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D051379:Mice; D008928:Mitochondria / Q000378:metabolism*; D024101:Mitochondrial Proteins; D040901:Proteomics / Q000379:methods*; D051381:Rats; D053719:Tandem Mass Spectrometry; D057170:Translational Research, Biomedical / Q000379:methods*
chemical_list: D024101:Mitochondrial Proteins
keywords: absolute quantification; concatemer; mitochondrial energy metabolic pathways; selected reaction monitoring (SRM); targeted proteomics; translational proteomics