PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/1029310712mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.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.Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling.Kislinger Thomas T, Cox Brian B, Kannan Anitha A, Chung Clement C, Hu Pingzhao P, Ignatchenko Alexandr A, Scott Michelle S MS, Gramolini Anthony O AO, Morris Quaid Q, Hallett Michael T MT, Rossant Janet J, Hughes Timothy R TR, Frey Brendan B, Emili Andrew AAdd, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratiopeptides, protein complex, Proteins, Gene, proteins, protein, protein-containing complex, Peptide, Protein Gene Products, Gene Proteins, polypeptide, peptide, Polypeptides, protein polypeptide chains, native protein, peptido, natural protein, polypeptide chain, Protein, Gene Products, Peptid, peptidos, Polypeptide, protein aggregate, count.organ, Mus musculus, Laboratory Mice., Laboratory, protein complex, Swiss, mice, Mus domesticus, Proteins, mouse, Swiss Mouse, Gene, House Mice, Swiss Mice, proteins, protein, Organelle, protein-containing complex, House Mouse, mice C57BL/6xCBA/CaJ hybrid, element, domesticus, Mus muscaris, Protein Gene Products, Gene Proteins, protein polypeptide chains, native protein, natural protein, polypeptide chain, House, Mus, anatomical unit, body organ, Protein, Gene Products, Mus musculus domesticus, Mouse, house mouse, protein aggregate, Mice, Laboratory Mousedorsal tube, vertebrate heart, dTAF[[II]]230, TAF[[II]]250, d230, Herz, protein complex, Proteins, TAF200, adult heart, branchial heart, Gene, l(3)84Ab, dTAFII250, Hearts, protein, BG:DS00004.13, TAFII-250, protein-containing complex, TAF250/230, EfW1, Peptide, Cell, dTAF230, polypeptide, peptide, dmTAF[[II]]230, circulatory vessel, Polypeptides, protein polypeptide chains, chambered heart, TAFII250, native protein, peptido, count, natural protein, polypeptide chain, dmTAF1, Taf230, p230, heart, Protein, Gene Products, TAF[[II]]250/230, TFIID, cardium, protein aggregate, TAF250, Taf[[II]]250, Taf200, dTAF[[II]]250, TAF[[II]]230, peptides, TFIID TAF250, cel, heart or heart like organ, cell, Taf1p, proteins, TAF[II]250, muscle, cardiac structure, CG17603, TAF[[II]], muscle element, Protein Gene Products, Gene Proteins, dTAF250, cardiac pump, DmelCG17603, TAF1., Taf250, SR3-5, musculus, Peptid, peptidos, Polypeptide, TAF, TAF230the brain, noyau atomique, Herz, Procedures, Tandem, Laboratory, Mus domesticus, nucleocapsid, placenta (Spanish, mouse <Mus musculus>, Gene, adult heart, branchial heart, Kern, protein, Organelle, protein-containing complex, Mass Spectrometry Mass Spectrometry, composed of, Mitochondrial Contractions, Atomkern, House Mouse, jecur, Membrane Tissues, circulatory vessel, protein polypeptide chains, Techniques, exact), polypeptide chain, House, parenchyma of lung, Method, Messenger, Gene Products, Mitochondrion, lung, Studies, establishment and maintenance of position, Mus musculus domesticus, mammals, synganglion, establishment and maintenance of substrate location, protein aggregate, nucleo atomico, placenta, neoplasm, Mice, Technique, Non Polyadenylated, Phenomenography, nuclei, portion of tissue, nucleus atomi, Tissues, Microsome, heart or heart like organ, Swiss, MS2, Contraction, nucleo, noyau, Polyadenylated Messenger, Mammalia., Tissue, iecur, messenger RNA, composition, Swiss Mice, Mass Spectrometry, proteins, procedures, suprasegmental levels of nervous system, cardiac structure, 胎座 (Japanese, Study, portion of placenta tissue (exact), cardiac pump, template RNA, Methodological Studies, nucleus, Normal, house mouse, eutherian placenta, reniculate kidney, Membrane Tissue, dorsal tube, vertebrate heart, establishment and maintenance of substance location, RNA, suprasegmental structures, placentas (exact, pulmo, Polyadenylated, protein complex, plural), Placentas, Mammal, Proteins, mouse, lung parenchyma, Messenger RNA, Hearts, compositionality, Procedure, encephalon, mice C57BL/6xCBA/CaJ hybrid, Mus muscaris, Contractions, single organism localization, chambered heart, native protein, placentae (exact, natural protein, Mus, Poly(A)+ mRNA, Protein, heart, core, tissue portion, INSDC_feature:mRNA, establishment and maintenance of localization, simple tissue, cardium, laboratory, techniques, Polyadenylated RNA, tandem MS, neoplasms, Polyadenylated Messenger RNA, Mus musculus, Mitochondrial, Poly(A)+ RNA, Non Polyadenylated mRNA, protein_coding_transcript, mRNA, Poly(A) Tail, MS/MS, mice, content, Encephalon, allantoic placenta, Swiss Mouse, Non-Polyadenylated, House Mice, Mass Spectrometry-Mass Spectrometry, Methodological, single-organism localization, Membrane, Methodological Study, Non-Polyadenylated mRNA, domesticus, Laboratory Mice, Protein Gene Products, Mitochondrial Contraction, Gene Proteins, Livers, Kidneys, mitochondria, localisation, pulmonary, structure, Placentomes, Cytosols, Placentome, Mammalia, Lungs, Mouse, Polyadenylated mRNA, Laboratory Mouse, Poly(A) RNA, Proteomes, Placentoma, methodology, establishment and maintenance of cellular component location0falseM.musculus - Heart, Protein peptide count (Kislinger,cell,2006)abundance based on Protein peptide count, Interaction consistency score: 2.5, Coverage: 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