PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering10116https://pax-db.org/dataset/10116/1991083093mering@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.Regulation of protein turnover allows cells to react to their environment and maintain homeostasis. Proteins can show different turnover rates in different tissue, but little is known about protein turnover in different brain cell types. We used dynamic SILAC to determine half-lives of over 5100 proteins in rat primary hippocampal cultures as well as in neuron-enriched and glia-enriched cultures ranging from <1 to >20 days. In contrast to synaptic proteins, membrane proteins were relatively shorter-lived and mitochondrial proteins were longer-lived compared to the population. Half-lives also correlate with protein functions and the dynamics of the complexes they are incorporated in. Proteins in glia possessed shorter half-lives than the same proteins in neurons. The presence of glia sped up or slowed down the turnover of neuronal proteins. Our results demonstrate that both the cell-type of origin as well as the nature of the extracellular environment have potent influences on protein turnover.Local and global influences on protein turnover in neurons and glia.Dörrbaum Aline R AR, Kochen Lisa L, Langer Julian D JD, Schuman Erin M EMAdd, 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, ratioSatellite Glia Cell, Bergmann Glial Cell, Nerve Cells, Satellite Glia Cells, Satellite, protein complex, Satellite Glia, Satellite Glias, Proteins, Nerve, Glial Cell, Gene, Satellite Glial, neuroglia, proteins, protein, Satellite Glial Cells, protein-containing complex, Satellite Glial Cell., Cell, Neuroglial Cell, Protein Gene Products, Glia Cells, Gene Proteins, Neuroglias, protein polypeptide chains, Bergmann, native protein, Glial Cells, natural protein, polypeptide chain, Neuroglial, Bergmann Glia Cells, Bergmann Glial, Glias, Protein, Cells, Bergmann Glia, Gene Products, Neuron, Glial, Glia Cell, protein aggregate, Nerve Cell, Bergmann Glial Cells, Neuroglial Cells, Bergmann Glia Cell, GliaSubiculums, Horn, hippocampus, Ammon's, Ammon, Propers, Hippocampal, Hippocampus Proper., Formations, Proper, Hippocampus Propers, Ammon's Horn, Ammon Horn, Hippocampal Formation, Cornu Ammonis, Subiculum, Hippocampal Formations, Ammons Horn, Formation, HippocampusIntegral Membrane Proteins, Ghrfr, Rat, Laboratory, Surface Proteins, A4, Norway Rat, protein, Membrane-Associated Proteins, Integral, Norway Rats, Social Controls, dmTAF[[II]]230, School-Age, protein polypeptide chains, rat, Mammals, Impacts, synganglion, Norway rat, Environmental Impacts, protein aggregate, Formal Social Controls, portion of tissue, TFIID TAF250, Satellite, cel, Surface, Tissue, proteins, inhibition of homeostatic process, suprasegmental levels of nervous system, Laboratory Rat, Social, Glia Cells, Environmental Impact, Bergmann Glia, homeostasis, Surface Protein, Membrane Associated Proteins, Nerve Cell, Membrane Protein, Bergmann Glia Cell, Satellite Glia Cell, dTAF[[II]]230, suprasegmental structures, TAF200, lit, Mitochondrial Protein, Rattus, TAFII-250, TAF250/230, Neuroglial Cell, results, TAFII250, Mus norvegicus, Rattus norwegicus, positive regulation of homeostatic process, School Age, tissue portion, simple tissue, little, Satellite Glial Cell, Cell Membrane Protein, Populations, Mitochondrial, Nerve Cells, Encephalon, Membrane-Associated, Control, neuroglia, Cell Membrane Proteins, Satellite Glial Cells, pulse SILAC, Controls, CG17603, TAF[[II]], rats, Neuroglias, DMDA, Taf250, SR3-5, Neuroglial, Cells, School-Age Population, Regulation, Glia, TAF230, Integral Membrane, the brain, Regulations, d230, nerve cell, norvegicus, Nerve, number, Gene, dTAFII250, protein-containing complex, EfW1, presence, TYPE, DAGA4, dynamic SILAC, Rattus sp. strain Wistar, Rats, polypeptide chain, dmTAF1, Taf230, Membrane-Associated Protein, Glias, Gene Products, Glial, Glia Cell, Rattus rattiscus, MAM, SCG3, TAF250, brown rat, Cell Membrane, School-Age Populations, Taf200, dTAF[[II]]250, Rattus norvegicus, cell, Satellite Glias, Satellite Glial, Taf1p, Population, dTAF250, Bergmann, Glial Cells, Bergmann Glia Cells, negative regulation of homeostatic process, Neuron, School Age Population, TAF, Rattus norvegicus8, Autoregulation, Gene., TAF[[II]]250, Formal Social Control, protein complex, Proteins, l(3)84Ab, Cell Surface, Cell Surface Protein, BG:DS00004.13, encephalon, Cell, LGMD2C, Impact, dTAF230, Environmental, count in organism, native protein, natural protein, Social Control, p230, Bergmann Glial, Laboratory Rats, Protein, Membrane Proteins, TAF[[II]]250/230, TFIID, regulation of homeostatic process, Bergmann Glial Cells, Neuroglial Cells, Cell Surface Proteins, Membrane Associated Protein, Taf[[II]]250, Bergmann Glial Cell, TAF[[II]]230, Satellite Glia Cells, DMDA1, Satellite Glia, Glial Cell, TAF[II]250, Membrane, School Age Populations, Protein Gene Products, Gene Proteins, extracellular, activation of homeostatic process, DmelCG17603, Integral Membrane Protein, neuronal cell, SCARMD2, pulsed SILAC, Environments, regulation, Norway, TAF1, Gunn rats0falseR.norvegicus - Hippocampal formation, SC (Doerrbaumetal,elife2018)abundance based on Spectral counting, Interaction consistency score: 15.1, Coverage: 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