Mitochondria are essential organelles that regulate a wide range of cellular functions. Here, we have developed data-independent acquisition mass spectrometry (DIA-MS) strategy and have quantified 3648 proteins in 114 proteomes collected from the BXD genetic reference populations in five tissues: liver, heart, brain, brown adipose tissue (BAT) and quadriceps. Protein expression varied more significantly across tissues than across genetic backgrounds. Although we observed broad correlation between transcript and protein expression, genes in the same pathway may have striking difference in regulation on transcript and protein levels, for example the genes in the electron transport chain. We compared two fractions from each tissue, mitochondria and total tissue. By comparing these two fractions, we identified several dozen proteins as mitochondrial proteins, which have not been reported in the literature. Among them, we validated three proteins in mitochondria (MTAP, SOAT2 and IMPDH2), and one protein in the mitochondria-associated membrane (ABCC6). Our results have revealed the disrupted protein composition of complex V of the electron transport chain on protein level, but not on the transcript level. Furthermore, we confirmed UCP1 protein level as a better predictor for cold test response compared with its transcript level. These findings demonstrate the synergy of proteomics and genomics to study complex metabolic processes, and they provide a resource for further discovery and analysis of proteoforms and protein localization.


Y. Wu: None.

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