{"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":["3847"],"full_dataset_link":["https://pax-db.org/dataset/3847/2413455250"],"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":["Data presented here are associated with the article: \"In-depth proteomic analysis of soybean (<i>Glycine max</i>) seeds during controlled deterioration treatment (CDT) reveals a shift in seed metabolism\" (Min et al., 2017) [1]. Seed deterioration is one of the major problems, affecting the seed quality, viability, and vigor in a negative manner. Here, we display the gel-based and gel-free proteomic data, associated with the CDT in soybean seeds. The present data was obtained from 2-DE, shotgun proteomic analysis (label-free quantitative proteomic analysis) using Q-Exactive, and gene ontology analysis associated with CDT in soybean seeds (Min et al., 2017) [1]."],"pubmed_title":["Gel-based and gel-free proteome data associated with controlled deterioration treatment of <i>Glycine max</i> seeds."],"pubmed_authors":["Min Cheol Woo CW, Lee Seo Hyun SH, Cheon Ye Eun YE, Han Won Young WY, Ko Jong Min JM, Kang Hang Won HW, Kim Yong Chul YC, Agrawal Ganesh Kumar GK, Rakwal Randeep R, Gupta Ravi R, Kim Sun Tae ST"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Gmax - Seed, iBAQ (Minetal,jproteomics2017)","description":"abundance based on iBAQ, Interaction consistency score: 9.7, Coverage: 7","dates":{"publication":"2017"},"accession":"2413455250","cross_references":{"pubmed":["29062869, 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