PAXDB

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http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2001000ProteomicsChristian von Mering3847https://pax-db.org/dataset/3847/2125262930mering@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.Tungsten (W) finds increasing application in military, aviation and household appliance industry, opening new paths into the environment. Since W shares certain chemical properties with the essential plant micronutrient molybdenum (Mo), it is proposed to inhibit enzymatic activity of molybdoenzymes [e.g., nitrate reductase (NR)] by replacing the Mo-ion bound to the co-factor. Recent studies suggest that W, much like other heavy metals, also exerts toxicity on its own. To create a comprehensive picture of tungsten stress, this study investigated the effects of W on growth and metabolism of soybean (Glycine max), depending on plant nitrogen regime [nitrate fed (N fed) vs. symbiotic N2 fixation (N fix)] by combining plant physiological data (biomass production, starch and nutrient content, N2 fixation, nitrate reductase activity) with root and nodule proteome data. Irrespective of N regime, NR activity and total N decreased with increasing W concentrations. Nodulation and therefore also N2 fixation strongly declined at high W concentrations, particularly in N fix plants. However, N2 fixation rate (g N fixed g-1 nodule dwt) remained unaffected by increasing W concentrations. Proteomic analysis revealed a strong decline in leghemoglobin and nitrogenase precursor levels (NifD), as well as an increase in abundance of proteins involved in secondary metabolism in N fix nodules. Taken together this indicates that, in contrast to the reported direct inhibition of NR, N2 fixation appears to be indirectly inhibited by a decrease in nitrogenase synthesis due to W induced changes in nodule oxygen levels of N fix plants. Besides N metabolism, plants exhibited a strong reduction of shoot (both N regimes) and root (N fed only) biomass, an imbalance in nutrient levels and a failure of carbon metabolic pathways accompanied by an accumulation of starch at high tungsten concentrations, independent of N-regime. Proteomic data (available via ProteomeXchange with identifier PXD010877) demonstrated that the response to high W concentrations was independent of nodule functionality and dominated by several peroxidases and other general stress related proteins. Based on an evaluation of several W responsive proteotypic peptides, we identified a set of protein markers of W stress and possible targets for improved stress tolerance.Molecular Mechanisms of Tungsten Toxicity Differ for Glycine max Depending on Nitrogen Regime.Preiner Julian J, Wienkoop Stefanie S, Weckwerth Wolfram W, Oburger Eva EAdd, 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, ratiosoybean, Soy Bean, cv. Wye, Soybeans, Wolfram, nitrogen, Stickstoff, nitrogeno., Phaseolus max, Soybean, Glycine max, N, Bean, soybeans, margin of safety, Soy Beans, Beans, toxic potential, 7N, azote, Soyshoot axis, GRO:0005300.biochemical pathways, Metabolic Networks, Networks, IPP2A2, Metabolic Process, Activity, ion, FON1, Metabolisms, Pflanze, postnatal development, Tertiary Sectors, Metabolic Concepts, Amylum, growth and development, protein, FLORAL ORGAN NUMBER 1, GRO:0005338, composed of, viridiplantae, secondary metabolite metabolism, SUB, 5730420M11Rik, nitrate(1-), Polypeptides, protein polypeptide chains, shoot axis, Abnormal retropulsion test, peptido, DmelCG12298, Carbon-12, oxigeno, SUP, Concepts, Impacts, SCRAMBLED, Environmental Impacts, Metabolism Concept, E948, protein aggregate, Phenomenon, Nutrient, present in fewer numbers in organism, KIF20A, multicellular organismal biosynthetic process, strong, nodule morphogenesis, C, SET, single-organism biosynthetic process, ostium, Oxidoreductase, peptides, Soybean, nitrite:acceptor oxidoreductase, TAF-I, catabolism, anabolism, N, O, Soy Beans, Oxygen-16, Bdr, Pathways, composition, metabolic process resulting in cell growth, plants, proteins, Super protein, sp, SNAP-25, DmelCG4299, Environmental Impact, Oxygen, IGAAD, set, Starch, decreased, [OO], DmelCG10574, Respiratory, climbing root (narrow), Carbon, Respiratory Nitrate Reductase, fish-eye disease, biotransformation, NO3(-), ostia, Catabolism, GRO:0005300, phapii, Soybeans, Pathway, Vanadium, Process, functional failure, Metal, Air Traffic, metabolism resulting in cell growth, land plants, STRUBBELIG, NO3, aerial root (narrow), StF-IT-1, Metabolic Network, foramina, alpha-lecithin cholesterol acyltransferase deficiency, Parachuting, metal elements, Soy Bean, T32E8.9, Vitreous, lymhpoid nodule, Quinol Nitrate Oxidoreductase, Ionen, Stickstoff, Sauerstoff, margin of safety, nitrate reductase (acceptor), GENA70, T32E8_9, secretion, secondary metabolism, failure, fixed, respiratory nitrate reductase activity, Amylomaize, parent ion, Disauerstoff, dioxygen, HLA-DR-associated protein II, growth pattern, DI-2, Phaseolus max, Respiratory Nitrate, non-developmental growth, 6C, content, I-2Dm, Control, Plant, root, CG4299, NITRATE REDUCTASE, metal element, I-2PP1, cv. Wye, Nitrate Reductase, Vitreous Carbon, higher plants, Sector, nitrogen, TAF-IBETA, precursor ion, NR1, AKL3L, carbonium, Micronutrient, root tubercle, TAF-Ibeta, Polypeptide, Nitrogenase, 7N, i2pp2a, Proteomes, Dioxygen, FLORAL DEFECTIVE 10, Traffic Control, AT1G11140, secondary metabolite metabolic process, Sectors, LCATA deficiency, nodule, Molybdenum-98, Processes, Amylomaize Starch, Gene, E-948, high weight, SUPERMAN, carbon, biosynthesis, 8O, Network, precursor, disfunctional, Metabolic Processes, AKL3L1, Cornstarch, protein-containing complex, PHAPII, CG12298, alpha-lecithin:cholesterol acyltransferase deficiency, reduced, resilient, Vanadium Nitrogenase, dioxygene, polypeptide chain, Air, subnumerary, Metabolism, tough, heavy, Gene Products, Imbalance, nitrate reductase 1, Metabolism Phenomena, Partial LCAT deficiency, dyslipoproteinemic corneal dystrophy, Industries, plantae, study, NITRATE REDUCTASE 1, Dinitrogenase, formation, AK6, iones, elemental metal, mei-1794, soybeans, nutrients, ipp2a2, Reduced ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing), Metabolic Concept, 2pp2a, decreased number, ions, CG10574, soybean, synthesis, Mif1, FED, Kohlenstoff, GNR1, 2PP2A, taf-ibeta, dSET, dSet, Beans, peptidos, toxic potential, SRF9, Soy, NITRATE ION, Macronutrient, molecular oxygen, Gene., nutrient, data, foramen, Oxygen 16, metals, degradation, protein complex, synthesize, Proteins, igaad, total expressed protein, nitrite:(acceptor) oxidoreductase, Synaptosomal-associated 25 kDa protein, defective, nitrite - acceptor oxidoreductase, compositionality, micronutrients, carbone, oxygen, Peptide, group, Impact, Concept, Metabolic Phenomena, all, STRUBBELIG-RECEPTOR FAMILY 9, Macronutrients, Secondary Metabolisms, carbono, Environmental, development, Quinol-Nitrate Oxidoreductase, Metabolism Concepts, Wolfram, Tertiary, Leghemoglobin A, native protein, natural protein, Keoflo, I-2PP2A, Protein, Dm I-2, Phenomena, proteomic analysis, I2PP2A, Nitrate, oxygene, metabolism, OXYGEN MOLECULE, Metabolic Pathways, Metabolic Phenomenon, Reductase, O2, multicellular organism metabolic process, biodegradation, Metabolic, ensemble, Ovoperoxidase, alpha-LCAT deficiency, Bean, Dub, postnatal growth, trace elements, FLO10, azote, AK3L1, nitrite - (acceptor) oxidoreductase, HERP, Molybdenum 98, nitrogeno, Carbon 12, Protein Gene Products, elemental metals, Gene Proteins, Secondary, dSET/TAF-Ibeta, single-organism metabolic process, 2610030F17Rik, [NO3](-), Ion, Biomasses, SNAP, opening, Glycine max, structure, Air Traffic Control, Environments, Metabolic Pathway, Tertiary Sector, Peptid, FIX, Quinol-Nitrate, responsive, E 948, AA407739, growth, T19D16.8, General activity, SCM, Anabolism1falseGmax - Shoot, iBAQ (Preineretal,frontplantsci2019)abundance based on iBAQ, Interaction consistency score: 7.6, Coverage: 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