PXD005044-1

PXD005044 is an original dataset announced via ProteomeXchange.

Title	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)
Description	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.
HostingRepository	PRIDE
AnnounceDate	2018-06-29
AnnouncementXML	Submission_2018-06-29_00:42:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Evan Williams
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2016-09-27 03:34:50	ID requested
⏵ 1	2018-06-29 00:42:31	announced

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]

curator keyword: Biological

submitter keyword: BXD Mouse, BAT, Liver, Heart, Brain, Quadriceps, Mitochondria

Ruedi Aebersold
contact affiliation	Institue of Molecular Systems Biology ETH Zurich, Switzerland
contact email	aebersold@imsb.ethz.ch
lab head
Evan Williams
contact affiliation	ETH Zurich
contact email	evangw@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD005044
     1. Label: PRIDE project
     2. Name: 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)