PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering392499https://pax-db.org/dataset/392499/3783339007mering@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.Chlorinated congeners of dibenzo-p-dioxin and dibenzofuran are widely dispersed pollutants that can be treated using microorganisms, such as the Sphingomonas wittichii RW1 bacterium, able to transform some of them into non-toxic substances. The enzymes of the upper pathway for dibenzo-p-dioxin degradation in S. wittichii RW1 have been biochemically and genetically characterized, but its genome sequence indicated the existence of a tremendous potential for aromatic compound transformation, with 56 ring-hydroxylating dioxygenase subunits, 34 extradiol dioxygenases and 40 hydrolases. To further characterize this enzymatic arsenal, new methodological approaches should be employed. Here, a large shotgun proteomic survey was performed on cells grown on dibenzofuran, dibenzo-p-dioxin and 2-chlorodibenzo-p-dioxin, and compared with growth on acetate. Changes in the proteome were monitored over time. In total, 502 proteins were observed and quantified using a label-free mass spectrometry-based approach; all data were deposited to the ProteomeXchange (PXD000403). Our results confirmed the roles of the dioxin dioxygenase DxnA1A2, trihydroxybiphenyl dioxygenase DbfB, meta-cleavage product hydrolase DxnB and reductase RedA2, and corroborated the proposed involvement of the Swit_3046 dioxygenase and DxnB2 hydrolase. Trends across substrates and over the course of growth do not support concerted pathway regulation and suggest the involvement of an additional hydrolase and several TonB-dependent receptors.Shotgun proteomics suggests involvement of additional enzymes in dioxin degradation by Sphingomonas wittichii RW1.Hartmann Erica M EM, Armengaud Jean JAdd, 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, ratiobiochemical pathways, single-organism catabolic process, multicellular organismal catabolic process, dioxine, cellular breakdown, Sphingomonas wittichii strain RW1, breakdown, TCDD, enzymes, biodegradation, degradation, Peptidomics, breakdown of chemical, Biocatalysts, catabolism, enzyme activity, tetradioxin, cellular catabolism, Sphingomonas wittichii str. RW1, Sphingomonas sp. RW1, breakdown of substance, Enzyme, 8-Tetrachlorodibenzo-p-dioxin, Biocatalyst, 2, cellular degradation, biotransformation, 3, secretion, Sphingomonas wittichii DSM 6014., PCDD 48, Dioxin, 7, 8-Tetrachlorodibenzodioxin, Tetrachlorodibenzodioxin, breakdown of moleculePRO1048, 2610524E03Rik, Koerper., organism, multi-cellular organism, whole organism, D1Bwg0491e, body, RW1, Neg, whole body, mKIAA0257, CC28, YR-23, animalaromatische Verbindungen, big, Regulations, aromatic molecular entity, Esters, Effects, Biocatalysts, postnatal development, ethanoate, Mbp1, cleavage, Gene, toxic substances, RING, growth and development, Spectrum Analyses, dRing, froggy, Long Term, Social Controls, Gyltl1a, dring, Hydrolase, large, Azetat, Gene Products, Mass, dRING, Analysis, myd, Effect, Formal Social Controls, Mass Spectroscopy, Ding, Mass Spectrum Analysis, enzymes, poisons, Genomes, Analyses, Longterm, p-dioxin, MDDGB6, Acetic Acid, Mbp-1, LARGE, proteins, dRING1, Long-Term, T16H5_60, free, CH3-COO(-), Social, BPFD#36, Enzyme, forecasting, Acetic Acids, great, dibenzo-p-dioxin catabolism, Neg, toxic agents, dibenzo-p-dioxin degradation, Long-Term Effect, Ring, CG5595, YR-23, Long-Term Effects, close to, aromatics, data, Dring, gyltl1b-b, Formal Social Control, RW1, dibenzo-p-dioxin breakdown, ACETATE ION, DRING, Proteins, Longterm Effect, total expressed protein, poisonous substances, ion(1-), Acetic Acid Esters, enzyme activity, Spectrum Analysis, Cell, results, Sphingomonas wittichii DSM 6014, PRO1048, futurology, Sphingomonas sp. RW1, Dioxygenase, near to, Spectroscopy, development, dRing1, RING1, poisonous substance, MS, native protein, Social Control, T16H5.60, Acetate, MDDGA6, mKIAA0609, Long Term Effects, Protein, sequence, Hydrolase., Ring/Sce, CC28, KIAA0609, Ethanoat, Mass Spectrum Analyses, fg, Sphingomonas wittichii strain RW1, Mass Spectrum, DmelCG5595, Acetic, gyltl1b, poisonous agents, D1Bwg0491e, growth pattern, non-developmental growth, Rnf2, toxic agent, mdc1d, postnatal growth, toxic substance, expanded, Spectrometry, Control, whole genome, mKIAA0257, Controls, primary structure of sequence macromolecule, Longterm Effects, 2610524E03Rik, Protein Gene Products, Sphingomonas wittichii str. RW1, Gene Proteins, MDC1D, enr, aromatic compounds, enlarged, approaches, label, vicinity of, Biocatalyst, Sce/dRing, MeCO2 anion, SCE, Acids, regulation, acetic acid, poisonous agent, growth, Regulation, Proteomes0falseSwittichii RW1 - Whole organism, NSAF (Hartmannetal,environmentmicrobiology2013)abundance based on NSAF, Interaction consistency score: 4.2, Coverage: 62013378333900724118890PUR7_SPHWWA5V5K1_SPHWWA5V614_SPHWWA5V4R6_SPHWWA5VCK0_SPHWWA5V284_SPHWWG6PI_SPHWWA5V9Q4_SPHWWA5V3F2_SPHWWA5VDE9_SPHWWA5V3A5_SPHWWA5V3E5_SPHWWENO_SPHWWRL16_SPHWWA5VAF1_SPHWWA5V2H4_SPHWWA5VA39_SPHWWA5V2T5_SPHWWA5VB77_SPHWWA5V661_SPHWWA5V8X4_SPHWWRL10_SPHWWA5VDK4_SPHWWA5V8R3_SPHWWA5V3R3_SPHWWA5V9X2_SPHWWA5V5S7_SPHWWA5V875_SPHWWA5V4R1_SPHWWA5V5U7_SPHWWA5VB17_SPHWWA5VFY0_SPHWWA5VFT8_SPHWWA5V4C9_SPHWWILVC_SPHWWA5V8U7_SPHWWA5V394_SPHWWRS2_SPHWWA5V642_SPHWWA5V5X9_SPHWWA5VFV2_SPHWWA5VD54_SPHWWA5VB11_SPHWWA5VAP1_SPHWWA5V5E6_SPHWWA5VDA4_SPHWWA5V8M1_SPHWWEFTS_SPHWWA5V5U6_SPHWWA5V2W7_SPHWWRL3_SPHWWA5V2J5_SPHWWA5VBX6_SPHWWA5VGN7_SPHWWA5VDN6_SPHWWA5V3S5_SPHWWA5V921_SPHWWA5VDK9_SPHWWA5V8R8_SPHWWA5VF35_SPHWWTATA_SPHWWA5V8U6_SPHWWA5VB12_SPHWWRL15_SPHWWA5VCZ8_SPHWWA5VC90_SPHWWRL9_SPHWWA5V4K4_SPHWWA5VAU4_SPHWWRS7_SPHWWSYL_SPHWWA5V2V6_SPHWWA5VCE7_SPHWWA5V3D1_SPHWWA5V3H1_SPHWWCH10_SPHWWA5VAH0_SPHWWA5VB76_SPHWWA5V2A0_SPHWWMDH_SPHWWA5V2H3_SPHWWA5V8T2_SPHWWA5VEU6_SPHWWA5VF66_SPHWWA5V2G0_SPHWWA5VBX4_SPHWWA5VB26_SPHWWA5VG31_SPHWWA5VC91_SPHWWA5V6F6_SPHWWA5VG47_SPHWWA5VA18_SPHWWMSCL_SPHWWA5VFG4_SPHWWA5VAU3_SPHWWA5V5U8_SPHWWA5VG24_SPHWWRS8_SPHWWA5V5J8_SPHWWGATB_SPHWWA5VD17_SPHWWA5V600_SPHWWRL25_SPHWWA5VFI7_SPHWWA5VFQ7_SPHWWA5VAZ0_SPHWWA5V9Y6_SPHWWA5VAS9_SPHWWA5VA72_SPHWWATPG_SPHWWNDK_SPHWWA5V4R7_SPHWWA5V945_SPHWWA5VD97_SPHWWRL17_SPHWWA5VAK9_SPHWWA5V3L6_SPHWWA5V3Q4_SPHWWA5VBW7_SPHWWRL22_SPHWWA5V3W1_SPHWWA5V3F9_SPHWWCH60_SPHWWRL6_SPHWWA5V8N4_SPHWWA5VFX9_SPHWWA5VDD7_SPHWWA5V5Y2_SPHWWA5V8X7_SPHWWA5V616_SPHWWA5V3A7_SPHWWA5VB05_SPHWWA5VCV4_SPHWWA5V3D3_SPHWWA5VAU1_SPHWWA5V262_SPHWWA5VF67_SPHWWA5VF71_SPHWWA5V7Z8_SPHWWA5VDB4_SPHWWA5VFF7_SPHWWA5V8V4_SPHWWA5V9X1_SPHWWA5VEY1_SPHWWA5VG49_SPHWWA5V3E0_SPHWWA5V2H5_SPHWWGLYA_SPHWWGATA_SPHWWA5V3M0_SPHWWA5VCC6_SPHWWA5V5I3_SPHWWA5V2I2_SPHWWA5VAI8_SPHWWA5VB32_SPHWWA5V5L0_SPHWWSUCC_SPHWWA5VAU0_SPHWWA5V4R5_SPHWWRL5_SPHWWA5V9J3_SPHWWA5V808_SPHWWA5VFF6_SPHWWGPMA_SPHWWA5VC09_SPHWWA5VGG6_SPHWWA5VF38_SPHWWA5VG30_SPHWWA5VEX5_SPHWWA5V2H6_SPHWWA5VG48_SPHWWSYV_SPHWWA5V5X7_SPHWWA5V4V9_SPHWWA5V644_SPHWWA5V9J4_SPHWWRL19_SPHWWRL1_SPHWWA5V9Q7_SPHWWA5VC98_SPHWWA5VCE3_SPHWWA5V2T2_SPHWWA5V9R4_SPHWWA5VCS9_SPHWWA5V8U9_SPHWWA5V4L3_SPHWWA5VDB9_SPHWWA5V9F4_SPHWWA5V949_SPHWWA5VCJ6_SPHWWRL7_SPHWWTAL_SPHWWA5VAU2_SPHWWA5V7M0_SPHWWA5VDS7_SPHWWA5VBW0_SPHWWA5VC00_SPHWWA5V586_SPHWWDNAK_SPHWWA5VBX2_SPHWWA5V6F4_SPHWWA5V5M4_SPHWWA5VAD4_SPHWWA5VC72_SPHWWA5VA64_SPHWWA5VGP3_SPHWWA5V594_SPHWWA5V2E5_SPHWWIF2_SPHWWRL14_SPHWWA5VAS8_SPHWWGRPE_SPHWWA5VAG2_SPHWWA5V9S2_SPHWWA5VDL3_SPHWWA5VGE1_SPHWWA5VEX7_SPHWWA5V5F6_SPHWWA5V3H0_SPHWWA5V8W3_SPHWWA5V5U5_SPHWWA5V9Q6_SPHWWA5V3D0_SPHWWA5V603_SPHWWA5V931_SPHWWRS16_SPHWWA5V643_SPHWWA5VCD6_SPHWWA5V4R3_SPHWWA5V3B4_SPHWWA5VAT9_SPHWWA5VCW3_SPHWWACCA_SPHWWA5V2T3_SPHWWRL2_SPHWWASSY_SPHWWA5V3E9_SPHWWA5VA58_SPHWWA5VDF5_SPHWWA5VCB7_SPHWWA5VBY4_SPHWWA5V5X0_SPHWWA5VC81_SPHWWA5V2E3_SPHWWA5VBW4_SPHWWA5V3Z7_SPHWWA5V4R2_SPHWWA5VFT7_SPHWWA5VEW6_SPHWWRPOA_SPHWWA5VF76_SPHWWA5V5X3_SPHWWA5VB93_SPHWWA5VB73_SPHWWRS3_SPHWWA5V3E4_SPHWWA5VAT0_SPHWWA5VB70_SPHWWA5V2U3_SPHWWRS5_SPHWWA5VA32_SPHWWA5VCJ7_SPHWWA5VC24_SPHWWA5V9J8_SPHWWA5VAG9_SPHWWA5V2W6_SPHWWA5VBY7_SPHWWA5V797_SPHWWCLPX_SPHWWRPOC_SPHWWA5V5V9_SPHWWSYA_SPHWWTIG_SPHWWA5VA33_SPHWWA5V970_SPHWWA5VFK3_SPHWWMETK_SPHWWA5V299_SPHWWA5V5G6_SPHWWA5VDI3_SPHWWA5VB71_SPHWWA5VAV1_SPHWWA5V6F1_SPHWWA5VCD9_SPHWWA5VB21_SPHWWATPA_SPHWWA5V2E2_SPHWWA5V8U4_SPHWWDAPA_SPHWWA5V3E7_SPHWWA5V5M3_SPHWWRL11_SPHWWRS18_SPHWWA5VEL4_SPHWWA5V9P6_SPHWWA5VBY6_SPHWWA5V2J2_SPHWWA5V9Z9_SPHWWARLY_SPHWWSYP_SPHWWRPOB_SPHWWA5VBA5_SPHWWA5VBW2_SPHWWRS19_SPHWWA5V8R5_SPHWWA5V657_SPHWWATPB_SPHWWPNP_SPHWWRS4_SPHWWA5VDK5_SPHWWPGK_SPHWW