PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering9606https://pax-db.org/dataset/9606/3913791442mering@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.Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly affected proteins. The adipocyte-secreted SERPINF1 and apolipoprotein APOF1 were most significantly regulated with fold changes of -16% and +37%, respectively (P < 10^-13), and the entire apolipoprotein family showed characteristic differential regulation. Clinical laboratory parameters are reflected in the plasma proteome, and eight plasma proteins correlated better with insulin resistance than the known marker adiponectin. Nearly all study participants benefited from weight loss regarding a ten-protein inflammation panel defined from the proteomics data. We conclude that plasma proteome profiling broadly evaluates and monitors intervention in metabolic diseases.Proteomics reveals the effects of sustained weight loss on the human plasma proteome.Geyer Philipp E PE, Wewer Albrechtsen Nicolai J NJ, Tyanova Stefka S, Grassl Niklas N, Iepsen Eva W EW, Lundgren Julie J, Madsbad Sten S, Holst Jens J JJ, Torekov Signe S SS, Mann Matthias MAdd, 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, ratioPlasma, Fresh, Weight Reductions, Fresh Frozen Plasmas, Fresh Frozen, portion of blood plasma, Blood Plasma, Weight Reduction, Frozen Plasma, human being, Man (Taxonomy), Fresh Frozen Plasma, Peptidomics, Blood, Modern, Reduction, total expressed protein, portion of plasma, Loss of weight, man, Plasmas, human, Human, Frozen Plasmas, blood plasm, Loss, Homo sapiens, Modern Man, Blood Plasmas, Weight, Proteomes., Weight Losses, Losses, Reductions, Man, plasmaPlasma, Fresh, Frozen Plasmas, Fresh Frozen Plasmas, Fresh Frozen, blood plasm, portion of blood plasma, Blood Plasma, Frozen Plasma, Fresh Frozen Plasma, Blood Plasmas, Blood, portion of plasma, Plasmas, plasma.Networks, Weight Reductions, Weight Reduction, Kinship, Inflammations, Laboratory, Ass-1, FON1, Feature, Blood, protein, Loss of weight, Body fails to respond to insulin, FLORAL ORGAN NUMBER 1, Adiposis, Social Controls, Obese, protein polypeptide chains, unspecified, AA408052, Weight Losses, SUP, fold, Life Cycle, Analysis, protein aggregate, Formal Social Controls, Family Life Cycle, ACDC, Mass Spectrum Analysis, average, Fresh Frozen Plasmas, Fresh Frozen, Thesaurismosis, Kinship Network, inflammatory response, Analyses, Metabolic disease, Bdr, proteins, Super protein, SURGICAL AND MEDICAL PROCEDURES, sp, SNAP-25, Social, ASS, Lipocytes, METABOLISM DISORDER NOS, Family Life Cycles, MD - Metabolic disorders, apM-1 Protein, plasma, Insulin Sensitivity, apolipoprotein, Frozen Plasma, wide/broad, obese, Normalcy, Procedure, Sdf3, Plasmas, Spectrum Analysis, Fat Cells, Spectroscopy, weight, Apolipoprotein, Weight, Obesity [Ambiguous], Obese (finding), Diseases, GENA70, NOS, laboratory, Individual, Filiation, Adipocyte, portion of blood plasma, METAB DIS, Spectrometry, Control, Adiposity, OBESITY NOS, PIG35, Controls, Features, fat cell, Life Cycles, ACRP30 Protein, wide, blood plasm, Health, Fat Cell, Cells, Unspecified disorder of metabolism, Fat, Regulation, Innate, Proteomes, ACRP30, FLORAL DEFECTIVE 10, Fresh, Regulations, protein levels, Inflammatory Response, Family Member, Metabolic Disease, Fresh Frozen Plasma, C1q and Collagen Domain Containing Protein, Peptidomics, lipophorin, obesity disease, PEDF, Gene, SUPERMAN, Network, broad, Spectrum Analyses, protein-containing complex, Normalcies, Intervention or Procedure, Obesity, Generalized metabolic disorder, IR, polypeptide chain, Insulin, Mass, Gene Products, metabolism disorder, Losses, Mass Spectroscopy, Normalities, study, Generalized metabolic disorder (disorder), Blood Plasma, disease of metabolism, interventionDescription, Research, Reduction, Interventional, inflammation, Overweight and obesity, Maintenances, AI195227, OI12, Pedfl, Mif1, Loss, Innate Inflammatory Response, Blood Plasmas, EPC-1, Lipocyte, Pedf, Sensitivity, Metabolic disorder, lipocyte, Characteristics, Kinship Networks, Family, Dmrs91, Intervention Strategies, Individual Health, Adipocyte Complement-Related Protein 30-kDa, data, Disease, Family Research, Adipose Most Abundant Gene Transcript 1, Formal Social Control, protein complex, Proteins, total expressed protein, Synaptosomal-associated 25 kDa protein, disorder of metabolism NOS (disorder), Cell, OI6, obesity, Family Members, Frozen Plasmas, adipose cell, Drug resistance to insulin (disorder), MS, Characteristic, native protein, natural protein, Social Control, disorder of metabolism NOS, Protein, Generalised metabolic disorder, Resistance, apM 1 Protein, adipocyte, Reductions, obesity disorder, Mass Spectrum Analyses, Obesity (disorder), Intervention, Plasma, Mass Spectrum, Metabolic disease (disorder), Metabolic disorders., Thesaurismoses, Metabolic, Normality, metabolic disease, Obesity NOS, ob, OB, portion of plasma, FLO10, HERP, GBP28, Protein Gene Products, Gene Proteins, Metabolic Diseases, Families, SNAP, Innate Inflammatory Responses, APM1, Adipocyte Complement Related Protein 30 kDa, regulation, Relatives0falseH.sapiens - Plasma, iBAQ (Geyeretal.,molsystbiol2016)abundance based on iBAQ, Interaction consistency score: 7.7, Coverage: 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