PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering4565https://pax-db.org/dataset/4565/118632943mering@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.Wheat is a cereal grain and one of the world's major food crops. Recent advances in wheat genome sequencing are by now facilitating its genomic and proteomic analyses. However, little is known about possible differences in total protein levels of hexaploid versus tetraploid wheat cultivars, and also knowledge of phosphorylated wheat proteins is still limited. Here, we performed a detailed analysis of the proteome of seedling leaves from two hexaploid wheat cultivars (<i>Triticum aestivum</i> L. Pavon 76 and USU-Apogee) and one tetraploid wheat (<i>T. turgidum</i> ssp. <i>durum</i> cv. Senatore Cappelli). Our shotgun proteomics data revealed that, whereas we observed some significant differences, overall a high similarity between hexaploid and tetraploid varieties with respect to protein abundance was observed. In addition, already at the seedling stage, a small set of proteins was differential between the small (USU-Apogee) and larger hexaploid wheat cultivars (Pavon 76), which could potentially act as growth predictors. Finally, the phosphosites identified in this study can be retrieved from the in-house developed plant PTM-Viewer (bioinformatics.psb.ugent.be/webtools/ptm_viewer/), making this the first searchable repository for phosphorylated wheat proteins. This paves the way for further in depth, quantitative (phospho)proteome-wide differential analyses upon a specific trigger or environmental change.Proteome Profiling of Wheat Shoots from Different Cultivars.Vu Lam Dai LD, Verstraeten Inge I, Stes Elisabeth E, Van Bel Michiel M, Coppens Frederik F, Gevaert Kris K, De Smet Ive IAdd, 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, ratioTriticum durum, bread wheat, Durum Wheats, Durum, Triticum vulgare, Triticum aestivum8, Canadian hard winter wheat, Triticum spelta, Durum Wheat, Triticum sativum, Triticum turgidum, Triticum aestivam, total expressed protein, Triticum turgidum subsp. durum, common wheat., Triticum aestivum subsp. aestivum, wheat, Proteomes, Wheat, Tricum aestivum, Triticum aestivumshoot axis, GRO:0005300.Ghrfr, IPP2A2, posttranslational modification, determination, 2410041A17Rik, ACTG, ACTE, Pflanze, postnatal development, growth and development, protein, fs(1)M34, Tetraploids, csp2, Act5, viridiplantae, l(1)G0420, 5730420M11Rik, DmelCG12051, Personal, protein polypeptide chains, exact), HEL-176, CG4601, protein aggregate, Wheat, A, SET, C, Malted Grain, posttranslational amino acid modification, Grain, cyt5C, Genomes, DHO, TAF-I, hypoplasia, CG18572, proteins, broad., wheat, Tricum aestivum, common wheat, DmelCG4299, IGAAD, set, Tetraploidies, DmelCG10574, act 42A, Sprouted, Ac5C, Durum Wheat, CG4027, Triticum turgidum, ACT, Act, stage, phapii, v&#225stago (Spanish, l(1)G0330, wide/broad, Actin/BAP47, Triticum vulgare, CTE-II, AACT, CTE-IIa, StF-IT-1, act, Ach1, hBACH, Triticum turgidum subsp. durum, ACH1, lit, LACH1, act42A, GIG25, Plant Sprouts, Su(b), Alpha-1-antichymotrypsin His-Pro-less, AFFX-Dros-ACTIN_M_r_at, GIG24, DFNA26, actin, Seed, LACH, GAT, DFNA20, little, Seeds, Epistemology, DmelCG4027, HLA-DR-associated protein II, PTM, DI-2, growth pattern, non-developmental growth, I-2Dm, l(1)G0117, Triticum sativum, Dignity, Plant, Actin, whole genome, CG4299, beta-actin/Bap47, I-2PP1, l(1)G0486, l(1)G0245, Seedling, Grains, wide, actin5C, TAF-IBETA, l(1)G0009, ACTL3, Lach1, post-translational modification, CG17153, TAF-Ibeta, i2pp2a, BACH, Proteomes, Triticum aestivum, l(1)Ab, protein levels, Plant Sprout, Act5c, l(1)G0010, Respect, Peptidomics, developmental stage, number, ACT5C, Gene, CG12051, Serpin A3, Triticum aestivum subsp. aestivum, protein-containing complex, Bach, presence, PHAPII, l(1)G0025, polypeptide chain, reduced, Sprouted Seed, Gene Products, 芽生え、実生 (Japanese, Cell growth-inhibiting gene 24|25 protein, Malted, tiny, plantae, study, act5C, Triticum aestivum8, Triticum spelta, BRWS2, ipp2a2, Triticum aestivam, 2pp2a, posttranslational protein modification, CG10574, fs(1)829, Act42a, anon-EST:fe2D2, bread wheat, 2PP2A, 1700027G07Rik, taf-ibeta, DmelCG18572, Personal Respect, dSET, dSet, T11, Act-5C, Cte-II, small, l(1)G0177, Triticum durum, 42A, data, CPS, Malted Grains, DmelCG17153, protein complex, Proteins, igaad, dJ393D12.2, total expressed protein, Tetraploid, grain, Sprout, group, development, count in organism, CAD, native protein, natural protein, I-2PP2A, beta-actin, Canadian hard winter wheat, Protein, chemical analysis, Dm I-2, I2PP2A, M32055, Act42, ACTA3, Foods, l(1)G0079, Sprouts, underdeveloped, ensemble, Durum, PYR1, VSCM, postnatal growth, act 5C, post-translational amino acid modification, Protein Gene Products, Gene Proteins, dSET/TAF-Ibeta, Durum Wheats, 2610030F17Rik, Sprouted Seeds, Ssp, DRORUD, BAP47, assay, ACTSG, AA407739, growth, Bap47, Actin5C0falseTaestivum - Shoot, iBAQ (Vuetal,frontplantsci2017)abundance based on iBAQ, Interaction consistency score: 22.9, Coverage: 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