Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy

Post-translational modifications hugely increase the functional diversity of proteomes. Recent algorithms based on ultratolerant database searching are forging a path to unbiased analysis of peptide modifications by shotgun mass spectrometry. However, these approaches identify only one-half of the modified forms potentially detectable and do not map the modified residue. Moreover, tools for the quantitative analysis of peptide modifications are currently lacking. Here, we present a suite of algorithms that allows comprehensive identification of detectable modifications, pinpoints the modified residues, and enables their quantitative analysis through an integrated statistical model. These developments were used to characterize the impact of mitochondrial heteroplasmy on the proteome and on the modified peptidome in several tissues from 12-week-old mice. Our results reveal that heteroplasmy mainly affects cardiac tissue, inducing oxidative damage to proteins of the oxidative phosphorylation system, and provide a molecular mechanism explaining the structural and functional alterations produced in heart mitochondria. [Display omitted] •Algorithms for comprehensive identification of protein modifications by mass spectrometry•Modified site is located with 85% accuracy•Integrates quantitative analysis of the proteome and the modified peptidome•mtDNA heteroplasmy causes oxidative damage in heart OXPHOS proteins Bagwan et al. present a suite of algorithms for the unbiased identification and quantification of post-translational modifications and their site of modification by mass spectrometry. They illustrate its utility by showing that mitochondrial heteroplasmy in mice affects mainly the heart, inducing oxidative damage to proteins of the oxidative phosphorylation system.