Dataset Information

Variation in the Mitochondrial Proteome: Quantifying and Localizing Proteins Across Five Tissues in Mice. Mouse BXD, 8 Strains by 5 Metabolic Tissues (BAT, Liver, Heart, Quadriceps, Brain) by 2 fractions (Mitochondria and Total Cell)

ABSTRACT: We used 8 strains the BXD mouse genetic reference population, including parents C57BL/6J and DBA/2J, to study the proteome of the heart, whole brain, liver, quadriceps, and brown adipose tissue (BAT) across 8 different genotypes. For each sample, we examined the proteome of the mitochondria, as well as the whole cell fraction (including mitochondria). Later, we supplemented this study with an additional 19 strains of BXD mouse, with one strain overlapping, in the BAT for both whole cell and mitochondrial extract to examine tissue-specific hypotheses generated from the original set of 8 strains. All together, these data allowed us to (1) examine proteome expression of the mitochondria, (2) examine differences in proteome expression across tissue, (3) examine differences in proteome expression across strain, and (4) examine all three of the preceding factors simultaneously against one-another. This allowed us to uncover several proteins which are expressed in the mitochondria but are not reported as such in the literature, of which we validated a few by traditional staining techniques. Furthermore, we compare our proteome data against transcriptome data gathered in the same individual mice. We observe (1) that differences in expression of genes involved in oxidative phosphorylation are far more tissue-dependent at the protein level than the transcript level, and (2) and we observe that the phenotypic relationship between BAT and thermogenesis is far more evident at the protein expression data than it is from the transcript expression. Together, these data provide two conclusions: (1) next-gen mass spectrometry proteomics techniques can identify organelle localizations that were not evident from other techniques (perhaps particularly those proteins which are expressed both inside and outside the mitochondria); and (2) proteome and transcriptome data are complimentary, and proteome data may help us find and test new hypotheses even for physiological pathways which have been well studied at the genetic and transcriptomic levels.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Quadriceps, Heart, Brain, Brown Adipose Tissue, Liver

SUBMITTER: Evan Williams

LAB HEAD: Ruedi Aebersold

PROVIDER: PXD005044 | Pride | 2018-06-29

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Complete5TissueSWATHLibrary_final.TraML	Other
	Complete5TissueSWATHLibrary_spectrast2tsv.tsv	Tabular
	TOT_ywu_K141123_001a_SW_BAT_BXD_C57.zip	Other
	TOT_ywu_K141123_002a_SW_BAT_BXD_DBA.zip	Other
	TOT_ywu_K141123_003a_SW_BAT_BXD45.zip	Other

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Publications

Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population.

Williams Evan G EG Wu Yibo Y Wolski Witold W Kim Jun Yong JY Lan Jiayi J Hasan Moaraj M Halter Christian C Jha Pooja P Ryu Dongryeol D Auwerx Johan J Aebersold Ruedi R

Molecular & cellular proteomics : MCP 20180626 9

We have used SWATH mass spectrometry to quantify 3648 proteins across 76 proteomes collected from genetically diverse BXD mouse strains in two fractions (mitochondria and total cell) from five tissues: liver, quadriceps, heart, brain, and brown adipose (BAT). Across tissues, expression covariation between genes' proteins and transcripts-measured in the same individuals-broadly aligned. Covariation was however far stronger in certain subsets than others: only 8% of transcripts in the lowest expre ...[more]

PMID: 29945935

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