{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["3702"],"full_dataset_link":["https://pax-db.org/dataset/3702/2872091233"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses."],"pubmed_title":["Arabidopsis proteome and the mass spectral assay library."],"pubmed_authors":["Zhang Huoming H, Liu Pei P, Guo Tiannan T, Zhao Huayan H, Bensaddek Dalila D, Aebersold Ruedi R, Xiong Liming L"],"data_synonyms":["Add, 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, ratio"],"pubmed_title_synonyms":["measuring, Library., determination, Cresses, A., Arabidopsis thaliana, Mouse-ear Cress, thaliana, total expressed protein, FBN, A. thaliana, MASS, Mouse-ear Cresses, Mouse-ear, Cardaminopsis, ACMICD, OCTD, Arabidopsis, Arabidopsis thalianas, ECTOL1, scientific observation, A. thalianas, SSKS, chemical analysis, thalianas, Cress, MFS1, assay, Mouse ear, Arabidopses, GPHYSD2, Proteomes, WMS, WMS2, SGS"],"name_synonyms":["silique, GRO:0005250."],"pubmed_abstract_synonyms":["Agronomies, (+, CDF, Abszisinsaeure, multi-cellular organism, human being, determination, Peptidomics, Researchs, -)-Isomer, A., Pflanze, number, Proteogenomic Profiling, Gene, Agronomy, (7E, protein, Development, Spectrum Analyses, 514, protein-containing complex, Normalcies, (S)-(+)-abscisic acid, presence, (E, Cardaminopsis, viridiplantae, Human, peptide, Polypeptides, protein polypeptide chains, Arabidopsis thalianas, POF, peptido, Homo sapiens, polypeptide chain, A. thalianas, DmelCG1768, thalianas, Mass, HILDA, Gene Products, 2, (Z, AGAMOUS-like 61, Analysis, 6, protein aggregate, animal, Man, Mass Spectroscopy, DiA, Farming, plantae, Normalities, Mass Spectrum Analysis, ABA, average, 5-(1-hydroxy-2, Man (Taxonomy), l(2)k07135, peptides, Genomes, Analyses, Cresses, Research, C1, (S-(Z, Mouse-ear Cress, proteins, DIASP, man, Mouse-ear, DIA, Dia, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, 2-cis, Proteogenomic, Abscisic Acid, (+)-S-ABA, 38E.16, Abscisinsaeure, Abscissic Acid, Dia., Cress, peptidos, species, Mouse ear, DIA2, Arabidopses, Individual Health, Profiling, E)-(+-)-Isomer, data, (+)-(S)-ABA, Z)-(+, body, protein complex, acide abscissique, Modern, Desmoplastic astrocytoma of infancy, Arabidopsis thaliana, Proteins, acido abscisico, 4-trans-abscisic acid, total expressed protein, 9Z)-(6S)-6-hydroxy-3-oxo-11-apo-epsilon-caroten-11-oic acid, whole body, A. thaliana, Normalcy, CG1768, Abscisic acid, DRF2, Spectrum Analysis, Peptide, predicted, Spectroscopy, polypeptide, organism, count in organism, ms(2)04138, Desmoplastic infantile astrocytoma, MS, native protein, natural protein, E)-Isomer, (R)-Isomer, MLPLI, Protein, chemical analysis, Proteogenomic Research, Individual, Dias, E))-, Library, Mass Spectrum Analyses, 4-Pentadienoic acid, DDA, Mass Spectrum, 6-trimethyl-4-oxo-2-cyclohexen-1-yl)-3-methyl-, Epistemology, whole organism, Normality, POF2, F27C12_24, Proteogenomic Analysis, F27C12.24, Plant, Spectrometry, thaliana, whole genome, abscisic acid, Mouse-ear Cresses, human, Atlases, Protein Gene Products, Gene Proteins, Arabidopsis, Health, Agricultural, Abscissins, Modern Man, Koerper, DIANA, Peptid, Polypeptide, assay, Abscisic Acid Monoammonium Salt, Proteomes, abscisin II, Agricultural Development"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"A.thaliana - Silique, SC (Zhangetal,scidata2019)","description":"abundance based on Spectral counting, Interaction consistency score: 1.9, Coverage: 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