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PXD005044 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleVariation 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)
DescriptionWe 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterEvan Williams
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListNo PTMs are included in the dataset
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02016-09-27 03:34:50ID requested
12018-06-29 00:42:31announced
Publication List
Williams EG, Wu Y, Wolski W, Kim JY, Lan J, Hasan M, Halter C, Jha P, Ryu D, Auwerx J, Aebersold R, Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population. Mol Cell Proteomics, 17(9):1766-1777(2018) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: BXD Mouse, BAT, Liver, Heart, Brain, Quadriceps, Mitochondria
Contact List
Ruedi Aebersold
contact affiliationInstitue of Molecular Systems Biology ETH Zurich, Switzerland
contact emailaebersold@imsb.ethz.ch
lab head
Evan Williams
contact affiliationETH Zurich
contact emailevangw@gmail.com
dataset submitter
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