Translational Targeted Proteomics Profiling of Mitochondrial Energy Metabolic Pathways in Mouse and Human Samples

Justina C. Wolters, Jolita Ciapaite, Karen Van Eunen, Klary E. Niezen-Koning, Alix Matton, Robert J. Porte, Peter Horvatovich, Barbara M. Bakker, Rainer Bischoff, Hjalmar P. Permentier*

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


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.

Original languageEnglish
Pages (from-to)3204-3213
Number of pages10
JournalJournal of Proteome Research
Issue number9
Publication statusPublished - 2 Sept 2016
Externally publishedYes


  • absolute quantification
  • concatemer
  • mitochondrial energy metabolic pathways
  • selected reaction monitoring (SRM)
  • targeted proteomics
  • translational proteomics


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