Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28049 Madrid, Spain.
Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28049 Madrid, Spain; CIBER Cardiovascular Diseases (CIBERCV), Madrid, Spain.
Cell Rep. 2018 Jun 19;23(12):3685-3697.e4. doi: 10.1016/j.celrep.2018.05.080.
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.
翻译后修饰极大地增加了蛋白质组的功能多样性。最近基于超宽容数据库搜索的算法正在为通过鸟枪法质谱对肽修饰进行无偏分析开辟一条道路。然而，这些方法仅能识别潜在可检测修饰形式的一半，且无法定位修饰残基。此外，目前缺乏用于肽修饰定量分析的工具。在此，我们提出了一套算法，该算法能够全面识别可检测的修饰，精确确定修饰残基，并通过综合统计模型对其进行定量分析。这些进展被用于表征线粒体异质性对12周龄小鼠多个组织中蛋白质组和修饰肽组的影响。我们的结果表明，异质性主要影响心脏组织，对氧化磷酸化系统的蛋白质造成氧化损伤，并提供了一种分子机制来解释心脏线粒体中产生的结构和功能改变。
