PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering4081https://pax-db.org/dataset/4081/1164108207mering@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.Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces beta-caryophyllene and alpha-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells.Studies of a biochemical factory: tomato trichome deep expressed sequence tag sequencing and proteomics.Schilmiller Anthony L AL, Miner Dennis P DP, Larson Matthew M, McDowell Eric E, Gang David R DR, Wilkerson Curtis C, Last Robert L RLAdd, 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, ratiol(2)46CFj, 14.10, CG2328., l(2)46CFh, 20.35, F, l(2)46CFp, DmelCG2328, 10.5, eve2, l(2)46Ce, VI, Eve, even, EVE, V, E(eve), 10.9, l(2)46CFg, l(2)46CgPeptidomics., Indumentum, Solanum lycopersicum L., tomato, Solanum esculentum Dunal, Tomato, Lycopersicum esculentum, Lycopersicon esculentum, Expressed Sequence, Lycopersicon esculentum var. esculentum, Tomatoes, Solanum esculentum, Tags, setae (related), Solanum lycopersicum var. humboldtii, Indumentums, seta (related), Expressed, Sequence Tag, Lycopersicon lycopersicum, Trichome, ESTs, Expressed Sequence Tag, Solanum lycopersicon, Lycopersicon esculentum Mill., Sequence Tags, Tagplantae, organism, multi-cellular organism, whole organism, body, Lycopersicum, Koerper, Pflanze, Lycopersicon (Mill.) Seithe, Plant, whole body, animal, viridiplantae.biochemical pathways, IPP2A2, Metabolic Process, Materials, determination, RNA Sequence, Metabolic Concepts, Biochemical, Epidermic Cells, Probes, Tags, CG11121, 5730420M11Rik, primary metabolites, old, cDNA library construction, exact), Sesquiterpene, Trichome, Concepts, Scanning Transmission Electron Microscopy, Metabolism Concept, animal, Phenomenon, primary stem, CG18546, Sequence Tags, portion of tissue, SET, me75, TAF-I, tomato, catabolism, complementary DNA, Tissue, proteins, metabolic process resulting in cell growth, plants, Base Sequences, D17Mit170, SO, T1, DmelCG4299, IGAAD, set, DmelCG10574, Derivatives, Biochemical Concept, sample, Lycopersicon lycopersicum, cDNA Probes, biotransformation, Farnesanes, Expressed Sequence Tag, Nucleotide, Catabolism, So, Farnesene, phapii, Dissections, Process, metabolism resulting in cell growth, land plants, StF-IT-1, Expressed Sequence, Tl3, Tl2, anon-WO03070958.3, Electron Microscopy, organism, tissue portion, Genetic Materials, secretion, simple tissue, Biochemical Phenomenon, DNA Sequence, Genetic Material, farnesyl pyrophosphate, whole organism, HLA-DR-associated protein II, DI-2, I-2Dm, Plant, CG4299, Epidermic, 葉 (Japanese, Sesquiterpenoid, I-2PP1, metastatic, higher plants, TAF-IBETA, primary axis, Expressed, Material, metabolites, Base, Koerper, Cells, STEM, Cistron, TAF-Ibeta, Complementary DNA, DNA, Solanum lycopersicon, i2pp2a, Lycopersicon esculentum Mill., Nucleotide Sequence, Z)-isomer, Biochemical Process, multi-cellular organism, Peptidomics, Processes, secondary metabolites, Gene, stalk, Sesquiterpenoids, Sesquiterpene Derivatives, Metabolic Processes, Biochemical Concepts, Tomatoes, (E, PHAPII, DmelCG11121, Metabolism, E)-isomer, Gene Products, (Z, Low, Metabolism Phenomena, somda, Genetic, ipp2a2, 2pp2a, Metabolic Concept, Lycopersicon esculentum, Lycopersicon esculentum var. esculentum, CG10574, culm, 2PP2A, Indumentums, taf-ibeta, Sequence Tag, dSET, dSet, farnesylpyrophosphate, Biochemical Processes, species, Tag, Drl, RNA, data, farnesyl diphosphate, cou, degradation, body, Solanum esculentum Dunal, Tomato, axis, Nucleotide Sequences, Lycopersicum esculentum, Proteins, igaad, DmelCG31211, whole body, Scanning Transmission, Epidermal Cell, cDNA, Cistrons, Cell, Solanum esculentum, group, Mdu, Concept, Metabolic Phenomena, Sequences, Metabolism Concepts, Lr, Solanum lycopersicum var. humboldtii, native protein, pyrosequencing, I-2PP2A, Sequence, mda, chemical analysis, Protein, Dm I-2, I2PP2A, Phenomena, sequence, metabolism, ami, Metabolic Phenomenon, RNA Sequences, multicellular organism metabolic process, Indumentum, Farnesenes, biodegradation, ensemble, Metabolic, Solanum lycopersicum L., med, metabolite, CG14732, hoja (Spanish, sample population, primary structure of sequence macromolecule, Epidermic Cell., Protein Gene Products, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, single-organism metabolic process, Epidermal, ESTs, Bra, assay, DNA Sequences, AA407739, Anabolism0falseS.lycopersicum - Whole organism, SC (Schilmiller,plant_physiol,2010)abundance based on Spectral counting, Interaction consistency score: 10.5, Coverage: 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