PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering3847https://pax-db.org/dataset/3847/265037373mering@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.Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported to date from soybean seeds. Comparative protein profiles of Saedanbaek and Daewon led to the identification of 2200 and 924 differential proteins in mature and filling stages seeds, respectively. Functional annotation of the differential proteins revealed enrichment of proteins related to major metabolism including amino acid, major carbohydrate, and lipid metabolism. In parallel, analysis of free amino acids and fatty acids in the filling stages showed higher contents of all the amino acids in the Saedanbaek while the fatty acids contents were found to be higher in the Daewon. Taken together, these results provide new insights into proteome changes during filling stages in soybean seeds. Moreover, results reported here also provide a framework for systemic and large-scale dissection of seed proteome for the seeds rich in SSPs by two-way pre-fractionation combined with TMT-based quantitative proteome analysis.In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of <i>Glycine max</i> Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis.Min Cheol Woo CW, Park Joonho J, Bae Jin Woo JW, Agrawal Ganesh Kumar GK, Rakwal Randeep R, Kim Youngsoo Y, Yang Pingfang P, Kim Sun Tae ST, Gupta Ravi RAdd, 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, ratioIGO, 14.1, IGL1, VPREB2, AGM2, IGL5, IGVPB., IGLJ14.1, CD179b, IGLLElaiosomes, Soybeans, sulfate, Sulfate dianion, cou, Proteins, number, Gene, sulphate, Tl3, Tl2, presence, SO4(2-), Soy Bean, Sulfate(2-), Inorganic Sulfates, TPSG1, count in organism, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Lr, native protein, tetraoxosulfate(2-), Embryos, Protein, Gene Products, tetraoxosulfate(VI), Low, Sulfate anion(2-), Seed, Elaiosome, study, Embryo, Diaspore, me75, [SO4](2-), tetraoxidosulfate(2-), Phaseolus max, Soybean, Sulfates, SULFATE ION, Bean, soybeans, Soy Beans, proteomic analysis., Plant, Plant Embryo, Plant Zygote, Zygote, proteins, Plant Embryos, D17Mit170, T1, Sulfuric acid ion(2-), Protein Gene Products, soybean, Gene Proteins, cv. Wye, Plant Zygotes, Diaspores, Glycine max, PRSS31, Bra, Zygotes, Beans, TMT, Sulfate, Soy, Inorganic, thiol methyltransferase activity, sulphate ionElaiosomes, Embryo, seed, Diaspore, Plant Zygotes, Diaspores, Embryos, pyrene (narrow)., Zygotes, Plant, Plant Embryo, Plant Zygote, Zygote, Seed, Elaiosome, GRO:0005339, Plant Embryosbiochemical pathways, acido graso, CPD photolyase activity, scale tissue, Metabolic Process, acidos grasos, PhrB photolyase activity, determination, Aminosaeure, Metabolic Concepts, Mbp1, Amino acid, hydrates de carbone, protein, Progress Reports, GRO:0005339, pigmented epithelium, glucide, carbohydrates, Polypeptides, protein polypeptide chains, peptido, SChöPF-Schulz-Passarge syndrome, Storage Protein, Summary Report, glucido, CG9063, Concepts, Saturated Fatty Acids, 3, Esterified Fatty Acid, NUP96, Analysis, Metabolism Concept, Elaiosome, protein aggregate, myd, Phenomenon, epithelium, Summary Reports, Esterified, Mass Spectrum Analysis, hypodontia, seed, SSPS, OODD, me75, Kohlenhydrate, amino acids, peptides, Analyses, Progress Report, Soybean, proportionality to, catabolism, plant peltate hair, Esterified Fatty, Soy Beans, Aliphatic, pigmented retina, chemical analysis., Plant Embryo, Mbp-1, proteins, metabolic process resulting in cell growth, Seed Storage, BcDNA:GH03694, D17Mit170, free, T1, DNA cyclobutane dipyrimidine photolyase activity, SUPPRESSOR OF AUXIN RESISTANCE 3, Storage Proteins, Progress, Aliphatic Acids, Field Reports, Diaspores, biotransformation, Catabolism, DmelCG9063, Dissections, Soybeans, PRE, Process, gyltl1b-b, Aminokarbonsaeure, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, metabolism resulting in cell growth, saccharides, Palmoplantar hyperkeratosis - cystic eyelids - hypodontia - hypotrichosis, Fettsaeuren, Tl3, Tl2, Spectrum Analysis, alpha-amino carboxylic acids, results, Spectroscopy, Soy Bean, TPSG1, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Investigative Report, retinal pigment, MDDGA6, mKIAA0609, Lipid, eccrine tumours with ectodermal dysplasia, dipyrimidine photolyase (photosensitive), secretion, Seed, KIAA0609, retinal pigment layer, Kohlenhydrat, saccharidum, fg, Amino Acid, Acid, Diaspore, Fatty Acid, gyltl1b, Saturated Fatty Acid, Amino acids, Phaseolus max, BcDNAGH03694, Eccrine tumors-ectodermal dysplasia, mdc1d, proportionality, Field, Spectrometry, Plant, expanded, Aliphatic Acid, Plant Zygote, rate, carbohidratos, 3L6, cv. Wye, MDC1D, carbohidrato, phr A photolyase activity, fatty acids, Health, Report, DNA-photoreactivating enzyme, enr, enlarged, rich, PRSS31, Acids, Polypeptide, a carbohydrate, glucidos, TMT, Proteomes, Saturated Fatty, big, STHAG4, Esterified Fatty Acids, Health Resource, Peptidomics, Processes, carbohydrate, peltate hair, number, Aminocarbonsaeure, saccharide, Gene, Spectrum Analyses, alpha-amino acid, photoreactivating enzyme activity, Metabolic Processes, protein-containing complex, presence, froggy, deoxyribodipyrimidine photolyase activity, Gyltl1a, and hypotrichosis, eccrine tumors with ectodermal dysplasia, large, Investigative, polypeptide chain, acides gras, Metabolism, Mass, Gene Products, stratum pigmentosa retinae, Low, Metabolism Phenomena, Resources, Mass Spectroscopy, Fatty Acids, proportion, MOS3, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, lipid metabolism, PRECOCIOUS, MDDGB6, soybeans, F23A5.3, Metabolic Concept, Zygote, LARGE, soybean, BPFD#36, Keratosis palmoplantaris - cystic eyelids - hypodontia - hypotrichosis, great, Zygotes, Beans, peptidos, Investigative Reports, Chromatographies, Soy, F23A5_3, thiol methyltransferase activity, Elaiosomes, Seed Storage Protein, Saturated, Palmoplantar keratoderma - cystic eyelids - hypodontia - hypotrichosis, cou, degradation, protein complex, Proteins, total expressed protein, alpha-amino acids, keratosis palmoplantaris with cystic eyelids, Peptide, Concept, Metabolic Phenomena, Metabolism Concepts, Fettsaeure, count in organism, SCHOPF-Schulz-Passarge syndrome, MODIFIER OF SNC1, MS, Lr, Resource, native protein, natural protein, Embryos, Protein, Research Reports, chemical analysis, deoxyribonucleic photolyase activity, Phenomena, scales, glucides, metabolism, Mass Spectrum Analyses, Metabolic Phenomenon, Mass Spectrum, Embryo, multicellular organism metabolic process, RPE, biodegradation, scale, Metabolic, photolyase activity, Bean, acide gras, Amino, Plant Embryos, Carbohydrate, p. pigmentosa retinae, Protein Gene Products, Gene Proteins, single-organism metabolic process, Reports, Plant Zygotes, Glycine max, cardinality, quotient, Bra, Peptid, deoxyribonucleate pyrimidine dimer lyase (photosensitive), assay, Summary, Field Report, pyrene (narrow), Anabolism0falseGmax - Seed, iBAQ (Minetal,cells2020)abundance based on iBAQ, Interaction consistency score: 14.1, Coverage: 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