PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering10116https://pax-db.org/dataset/10116/3360659913mering@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.Highly aggressively proliferating immortalized (HAPI) microglial cells have been used as an in vitro model for investigating key microglial functions including inflammatory, neurotoxic, and phagocytic activities. Through the use of offline strong cation-exchange fractionation followed by inline reversed-phase chromatographic separation and tandem mass spectrometric analysis on a hybrid linear ion trap-Orbitrap instrument, the HAPI microglial proteome was characterized to a depth of 3006 unique protein groups. Upon bioinformatic analysis of the HAPI proteome data set, enrichment was observed for processes relevant to microglial function including those associated with immune system response. This study marks the most comprehensive reference data set generated to date for the rat microglial proteome.Proteomic analysis of rat microglia establishes a high-confidence reference data set of over 3000 proteins.Bell-Temin Harris H, Barber David S DS, Zhang Ping P, Liu Bin B, Stevens Stanley M SMAdd, 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, ratiobrown rat, MF.microglia.CNS, microglial cell, Rat, Rattus norvegicus, norvegicus, Data Set, Hortega cell, Laboratory, Protein., Microglial Cell, brain-resident macrophage, Proteins, Norway Rat, Gene, proteins, Rattus, rats, Norway Rats, microgliocyte, microglia, Cell, Laboratory Rat, Microglial, Protein Gene Products, Gene Proteins, rat, Rattus sp. strain Wistar, Mus norvegicus, Rats, Rattus norwegicus, native protein, Mammals, Laboratory Rats, Protein, proteomic analysis, Gene Products, Norway rat, brain macrophage, hortega cells, Norway, Rattus rattiscus, Microglias, Microglial Cells, Rattus norvegicus8, Gunn ratsMicroglial, Peptidomics., MF.microglia.CNS, microglial cell, Hortega cell, Microglial Cell, brain-resident macrophage, brain macrophage, hortega cells, Microglias, microgliocyte, Microglial Cells, microglia, CellKation, Hybrids, Rat, Immune Systems, norvegicus, determination, Laboratory, cation, instrument configuration, FBN, Gene, Norway Rat, protein, protein-containing complex, Norway Rats, dIKK-gamma, hardware, Microglial, protrusion, protein polypeptide chains, rat, Rattus sp. strain Wistar, Rats, resilient, polypeptide chain, ECTOL1, Mammals, DmIKK-gamma, tough, responsivity, Gene Products, Norway rat, dmIKKgamma, Rattus rattiscus, IKK[[gamma]], protein aggregate, Microglias, Separated, IKKg, WMS, KEY, Key, brown rat, strong, reactivity, study, Divorced, Rattus norvegicus, Microglial Cell, HardwareType, Divorces, proteins, Chimeras, Laboratory Rat, OCTD, cations, Immune, IKK, Cation, GPHYSD2, SGS, Rattus norvegicus8, anatomical protrusion, Data Set, protein complex, Proteins, Kationen, total expressed protein, function, Rattus, backward, Cell, cationes, ACMICD, IKKgamma, DmIKKgamma, Mus norvegicus, Hybrid, native protein, Rattus norwegicus, natural protein, dIKK, Laboratory Rats, chemical analysis, Protein, Systems, Proteomes., Kenny, MFS1, WMS2, Separation, instrument, Dmikkgamma, System, Separations, IKK-gamma, MASS, CG16910, rats, Protein Gene Products, Gene Proteins, DmelCG16910, spine, SSKS, assay, Norway, response, Proteomes, Microglial Cells, reversed, Gunn rats0falseR.norvegicus - Microglial cell, SC (Bell-temin,proteomics,2012)abundance based on Spectral counting, Interaction consistency score: 20.2, Coverage: 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