PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering4577https://pax-db.org/dataset/4577/1441245021mering@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.We performed large-scale, quantitative analyses of the maize (Zea mays) leaf proteome and phosphoproteome at four developmental stages. Exploiting the developmental gradient of maize leaves, we analyzed protein and phosphoprotein abundance as maize leaves transition from proliferative cell division to differentiation to cell expansion and compared these developing zones to one another and the mature leaf blade. Comparison of the proteomes and phosphoproteomes suggests a key role for posttranslational regulation in developmental transitions. Analysis of proteins with cell wall- and hormone-related functions illustrates the utility of the data set and provides further insight into maize leaf development. We compare phosphorylation sites identified here to those previously identified in Arabidopsis thaliana. We also discuss instances where comparison of phosphorylated and unmodified peptides from a particular protein indicates tissue-specific phosphorylation. For example, comparison of unmodified and phosphorylated forms of PINFORMED1 (PIN1) suggests a tissue-specific difference in phosphorylation, which correlates with changes in PIN1 polarization in epidermal cells during development. Together, our data provide insights into regulatory processes underlying maize leaf development and provide a community resource cataloging the abundance and phosphorylation status of thousands of maize proteins at four leaf developmental stages.Parallel proteomic and phosphoproteomic analyses of successive stages of maize leaf development.Facette Michelle R MR, Shen Zhouxin Z, Björnsdóttir Fjola R FR, Briggs Steven P SP, Smith Laurie G LGAdd, 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, ratioZea mays mays, Indian Corn, Zea mays subsp. sacharata, Zea mays var. japonica, Zea mays subsp. amylacea, corn, Zea mays var. sacharata, Corn, Maize, Teosinte, maize, Indian corn, Zea mays subsp. ramosa, Zea mays subsp. ceratina, Zea mays subsp. everta, Zea mays var. mays, Zea mays subsp. tunicata, Zea ramosa, Zea, Indian., Zea mays subsp. indurataexact)., exact), hoja (Spanish, 葉 (JapaneseForms, scale tissue, Zea mays var. japonica, AIPC, single-organism developmental process, determination, A., postnatal development, Mbp1, Phases, growth and development, protein, Epidermic Cells, Divisions, phosphorylation, Arabis thaliana, Social Controls, F6D5_2, Polypeptides, protein polypeptide chains, Arabidopsis thalianas, exact), peptido, PDZK3, Roles, A. thalianas, F6D5.2, Concepts, Zea mays subsp. tunicata, protein aggregate, myd, Formal Social Controls, IKKg, KEY, Key, maize <Zea mays>, Cell Walls, portion of tissue, M Phases, peptides, Hormone Receptor, M, non-developmental growth of a unicellular organism, plant peltate hair, Indian corn, Mouse-ear Cress, Tissue, Mbp-1, proteins, metabolic process resulting in cell growth, Phosphoprotein, Mouse-ear, endocrine, Social, Division Phase, reaction, Role Concepts, cellular growth, Zea, Arabidopses, Zea mays subsp. indurata, ARABIDOPSIS THALIANA PIN-FORMED 1, Zea mays subsp. amylacea, anatomical protrusion, Data Set, gyltl1b-b, metabolism resulting in cell growth, UBL5, A. thaliana, Receptor Agonists, Cell Divisions, ubl5, DmIKKgamma, Role Concept, dIKK, MDDGA6, Teosinte, mKIAA0609, non-developmental cell growth, Zea mays subsp. everta, Kenny, Role, tissue portion, Arabidopsis thaliana (thale cress), simple tissue, KIAA0609, Zea mays mays, fg, Zea mays subsp. sacharata, gyltl1b, mdc1d, IKK-gamma, expanded, Control, Controls, Epidermic, 葉 (Japanese, MDC1D, Arabidopsis, DmelCG16910, enr, enlarged, spine, Community Resource, leaf blade, Cells, Zea ramosa, Polypeptide, Indian, Regulation, Proteomes, pin1a, Community, PIN-FORMED 1, big, Regulations, pin1, peltate hair, Zea mays subsp. ceratina, number, Gene, DOD, protein-containing complex, presence, dIKK-gamma, froggy, Gyltl1a, Hormone, protrusion, large, polypeptide chain, DmIKK-gamma, Gene Products, thalianas, dmIKKgamma, CG17051, IKK[[gamma]], dod, Agonists, Walls, exact)., hormones, Cell Division Phase, Maize, growth of cell, Cresses, MDDGB6, D9Bwg1161e, LARGE, Cell Division, Hormone Receptor Agonists, Division, BPFD#36, PAPIN, thale-cress, IKK, great, maize, Zea mays subsp. ramosa, Cress, peptidos, Mouse ear, Pin1, PIN1, data, corn, PTF1, Formal Social Control, Arbisopsis thaliana, protein complex, Proteins, Arabidopsis thaliana, Phosphorylations, total expressed protein, Epidermal Cell, Cell, Peptide, Concept, Indian Corn, development, cell expansion, IKKgamma, count in organism, Zea mays var. sacharata, native protein, Resource, natural protein, Social Control, Protein, chemical analysis, phosphorylation enrichment, scales, M Phase, ATPIN1, thale cress, mouse-ear cress, Phase, Wall, scale, DmelCG17051, Dmikkgamma, 0610025L01Rik, postnatal growth, thaliana, CG16910, Mouse-ear Cresses, hoja (Spanish, phosphorylated protein, Protein Gene Products, Gene Proteins, Corn, Epidermal, Epidermic Cell, Zea mays var. mays, Peptid, regulation, Prot/PhosRes+, assay, growth0falseZ.mays - Leaf, Mature, SC (Facette,plantcell,2013)abundance based on Spectral counting, mature, Interaction consistency score: 8.2, Coverage: 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