PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering3847https://pax-db.org/dataset/3847/2413455250mering@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.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].Gel-based and gel-free proteome data associated with controlled deterioration treatment of <i>Glycine max</i> seeds.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 ST0falseGmax - Seed, iBAQ (Minetal,jproteomics2017)abundance based on iBAQ, Interaction consistency score: 9.7, Coverage: 72017241345525029062869, 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