title: Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling.
abstract: Organs and organelles represent core biological systems in mammals, but the diversity in protein composition remains unclear. Here, we combine subcellular fractionation with exhaustive tandem mass spectrometry-based shotgun sequencing to examine the protein content of four major organellar compartments (cytosol, membranes [microsomes], mitochondria, and nuclei) in six organs (brain, heart, kidney, liver, lung, and placenta) of the laboratory mouse, Mus musculus. Using rigorous statistical filtering and machine-learning methods, the subcellular localization of 3274 of the 4768 proteins identified was determined with high confidence, including 1503 previously uncharacterized factors, while tissue selectivity was evaluated by comparison to previously reported mRNA expression patterns. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal.
authors.affiliation: Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada.
authors.forename: Thomas
authors.initials: T
authors.lastname: Kislinger
authors.forename: Brian
authors.initials: B
authors.lastname: Cox
authors.forename: Anitha
authors.initials: A
authors.lastname: Kannan
authors.forename: Clement
authors.initials: C
authors.lastname: Chung
authors.forename: Pingzhao
authors.initials: P
authors.lastname: Hu
authors.forename: Alexandr
authors.initials: A
authors.lastname: Ignatchenko
authors.forename: Michelle S
authors.initials: MS
authors.lastname: Scott
authors.forename: Anthony O
authors.initials: AO
authors.lastname: Gramolini
authors.forename: Quaid
authors.initials: Q
authors.lastname: Morris
authors.forename: Michael T
authors.initials: MT
authors.lastname: Hallett
authors.forename: Janet
authors.initials: J
authors.lastname: Rossant
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Hughes
authors.forename: Brendan
authors.initials: B
authors.lastname: Frey
authors.forename: Andrew
authors.initials: A
authors.lastname: Emili
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D049452:Green Fluorescent Proteins / Q000378:metabolism; D051379:Mice; D008861:Microsomes / Q000378:metabolism; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism; D009928:Organ Specificity; D015388:Organelles / Q000378:metabolism*; D021381:Protein Transport; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D040901:Proteomics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D011506:Proteins; D012333:RNA, Messenger; D049452:Green Fluorescent Proteins