PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/494884207mering@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.The turnover of brain proteins is critical for organism survival, and its perturbations are linked to pathology. Nevertheless, protein lifetimes have been difficult to obtain in vivo. They are readily measured in vitro by feeding cells with isotopically labeled amino acids, followed by mass spectrometry analyses. In vivo proteins are generated from at least two sources: labeled amino acids from the diet, and non-labeled amino acids from the degradation of pre-existing proteins. This renders measurements difficult. Here we solved this problem rigorously with a workflow that combines mouse in vivo isotopic labeling, mass spectrometry, and mathematical modeling. We also established several independent approaches to test and validate the results. This enabled us to measure the accurate lifetimes of ~3500 brain proteins. The high precision of our data provided a large set of biologically significant observations, including pathway-, organelle-, organ-, or cell-specific effects, along with a comprehensive catalog of extremely long-lived proteins (ELLPs).Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions.Fornasiero Eugenio F EF, Mandad Sunit S, Wildhagen Hanna H, Alevra Mihai M, Rammner Burkhard B, Keihani Sarva S, Opazo Felipe F, Urban Inga I, Ischebeck Till T, Sakib M Sadman MS, Fard Maryam K MK, Kirli Koray K, Centeno Tonatiuh Pena TP, Vidal Ramon O RO, Rahman Raza-Ur RU, Benito Eva E, Fischer André A, Dennerlein Sven S, Rehling Peter P, Feussner Ivo I, Bonn Stefan S, Simons Mikael M, Urlaub Henning H, Rizzoli Silvio O SOAdd, 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, ratiothe brain, Mus musculus, suprasegmental structures, Laboratory, protein complex, Swiss, Subcellular, mice, Mus domesticus, Encephalon, Proteins, mouse, Swiss Mouse, Tissue, Gene, House Mice, Swiss Mice, proteins, protein, suprasegmental levels of nervous system, protein-containing complex, House Mouse, encephalon, mice C57BL/6xCBA/CaJ hybrid, domesticus, Mus muscaris, Laboratory Mice, Protein Gene Products, Gene Proteins, protein polypeptide chains, native protein, natural protein, polypeptide chain, House, Mus, Fraction, Subcellular Fraction, Fractions, Protein, Gene Products, Mus musculus domesticus, Mouse, synganglion, house mouse, protein aggregate, Mice, Laboratory Mouse, Subcellular.brain cortex, cortex of cerebral hemisphere, Allocortices, Cortex Cerebrus, Cerebral Cortices, Cortical, Paleocortex, Cortical Plates, Archipalliums, muscle, muscle element, Cortical Plate., cortical plate (CTXpl), cortical plate (areas), Cortex, Periallocortex, musculus, Periallocortices, Plate, pallium of the brain, Allocortex, Cortex Cerebri, cortex cerebri, Cerebral, cortex cerebralis, Archipallium, Paleocorticesbiochemical pathways, single-organism catabolic process, multicellular organismal catabolic process, CPD photolyase activity, IPP2A2, PhrB photolyase activity, Laboratory, Aminosaeure, Mus domesticus, Mbp1, Amino acid, protein, Organelle, pigmented epithelium, House Mouse, element, 5730420M11Rik, dmTAF[[II]]230, protein polypeptide chains, cellular degradation, 3, synganglion, NUP96, cytopathology, Analysis, protein aggregate, Work Flow, animal, myd, epithelium, Mass Spectrum Analysis, organ, SET, amino acids, TFIID TAF250, Analyses, TAF-I, cel, catabolism, long, pigmented retina, Mbp-1, Swiss Mice, proteins, suprasegmental levels of nervous system, DNA cyclobutane dipyrimidine photolyase activity, SUPPRESSOR OF AUXIN RESISTANCE 3, DmelCG4299, IGAAD, set, DmelCG10574, Pathologies, biotransformation, house mouse, close to, phapii, PRE, dTAF[[II]]230, suprasegmental structures, gyltl1b-b, Aminokarbonsaeure, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, mouse, TAF200, StF-IT-1, TAFII-250, TAF250/230, Spectrum Analysis, alpha-amino carboxylic acids, results, mice C57BL/6xCBA/CaJ hybrid, Spectroscopy, organism, Workflows, TAFII250, retinal pigment, MDDGA6, mKIAA0609, dipyrimidine photolyase (photosensitive), secretion, KIAA0609, retinal pigment layer, fg, Amino Acid, Acid, Mus musculus, breakdown, gyltl1b, whole organism, histopathology, HLA-DR-associated protein II, death rate, Amino acids, DI-2, mice, I-2Dm, Encephalon, Swiss Mouse, mdc1d, Spectrometry, expanded, CG4299, CG17603, TAF[[II]], domesticus, I-2PP1, MDC1D, phr A photolyase activity, DNA-photoreactivating enzyme, TAF-IBETA, enr, enlarged, Taf250, SR3-5, Koerper, Acids, Mouse, TAF-Ibeta, i2pp2a, Work Flows, TAF230, the brain, big, d230, multi-cellular organism, Aminocarbonsaeure, Gene, dTAFII250, alpha-amino acid, Spectrum Analyses, photoreactivating enzyme activity, protein-containing complex, EfW1, cellular catabolism, deoxyribodipyrimidine photolyase activity, froggy, PHAPII, Gyltl1a, large, polypeptide chain, House, dmTAF1, Taf230, Gene Products, Mass, Diets, Mus musculus domesticus, stratum pigmentosa retinae, Mice, Mass Spectroscopy, Catalogs, TAF250, Taf200, MOS3, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, dTAF[[II]]250, PRECOCIOUS, breakdown of chemical, Swiss, cell, MDDGB6, ipp2a2, F23A5.3, 2pp2a, Taf1p, labeling, LARGE, CG10574, BPFD#36, dTAF250, 2PP2A, taf-ibeta, time of survival, anatomical unit, great, body organ, dSET, dSet, species, TAF, F23A5_3, cellular breakdown, data, TAF[[II]]250, degradation, body, protein complex, Proteins, igaad, l(3)84Ab, whole body, alpha-amino acids, BG:DS00004.13, encephalon, Cell, Mus muscaris, group, dTAF230, near to, MODIFIER OF SNC1, MS, survival, native protein, natural protein, Mus, I-2PP2A, p230, Protein, Dm I-2, deoxyribonucleic photolyase activity, I2PP2A, TAF[[II]]250/230, TFIID, Mass Spectrum Analyses, breakdown of molecule, Taf[[II]]250, Mass Spectrum, RPE, TAF[[II]]230, biodegradation, ensemble, photolyase activity, Protein., Dietary, House Mice, TAF[II]250, Amino, p. pigmentosa retinae, Laboratory Mice, Protein Gene Products, Gene Proteins, dSET/TAF-Ibeta, breakdown of substance, 2610030F17Rik, DmelCG17603, approaches, vicinity of, deoxyribonucleate pyrimidine dimer lyase (photosensitive), biopsy, AA407739, Laboratory Mouse, TAF10falseM.musculus - Cerebral cortex, SC (Fornasieroetal,natcomm2018)abundance based on Spectral counting, Interaction consistency score: 8.0, Coverage: 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