PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering9544https://pax-db.org/dataset/9544/859666168mering@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.Though the rhesus monkey is one of the most valuable non-human primate animal models for various human diseases because of its manageable size and genetic and proteomic similarities with humans, proteomic research using rhesus monkeys still remains challenging due to the lack of a complete protein sequence database and effective strategy. To investigate the most effective and high-throughput proteomic strategy, comparative data analysis was performed employing various protein databases and search engines. The UniProt databases of monkey, human, bovine, rat and mouse were used for the comparative analysis and also a universal database with all protein sequences from all available species was tested. At the same time, de novo sequencing was compared to the SEQUEST search algorithm to identify an optimal work flow for monkey proteomics. Employing the most effective strategy, proteomic profiling of monkey organs identified 3,481 proteins at 0.5% FDR from 9 male and 10 female tissues in an automated, high-throughput manner. Data are available via ProteomeXchange with identifier PXD001972. Based on the success of this alternative interpretation of MS data, the list of proteins identified from 12 organs of male and female subjects will benefit future rhesus monkey proteome research.A draft map of rhesus monkey tissue proteome for biomedical research.Lee Jin-Gyun JG, McKinney Kimberly Q KQ, Lee Yong-Yook YY, Chung Hae-Na HN, Pavlopoulos Antonis J AJ, Jung Kook Y KY, Kim Woong-Ki WK, Kuroda Marcelo J MJ, Han David K DK, Hwang Sunil SAdd, 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, ratiorhesus macaque, Rhesus Macaque, MUTYH-Associated Polyposis, Macaque, methionine aminopeptidase activity, Macaca mulatta lasiotas, MYH-associated polyposis, autosomal recessive familial adenomatous polyposis, Maps, total expressed protein, rhesus monkeys, Rhesus Monkeys, Biomedical, Chinese Rhesus Macaque, Investigative Medicine, Experimental, Investigative, Cercopithecus mulatta, tissue portion, 2, Chinese Rhesus Macaques, simple tissue, Medical, familial adenomatous polyposis, Investigational, MAP, peptidase M activity, autosomal recessive, adenomas, portion of tissue, RUTBC3, rabGAPLP, L-methionine aminopeptidase activity, Rhesus Macaques, Monkey, Research, familial adenomatous polyposis 2, Experimental Medicine, Tissue, RabGAP-5, rhesus macaques, MYH-Associated Polyposis, Macaca mulatta lasiota, RABGAP5, autosomal recessive multiple colorectal adenomas, RUSC3, multiple colorectal, Medical Research., Investigational Medicine, Medicine, Rhesus monkey, MAP syndrome, Rhesus Monkey, Rhesus, Chinese, Proteomes, FAP2, colorectal adenomatous polyposisBrodmann's, Brodmann Area 8, Lobe, Eye Fields, Lobus Frontalis., Area 8, Frontal Cortex, Cortex, Supplementary Eye Fields, Brodmann, Frontal region, Brodmann's Area 8, Brodmanns Area 8, frontal cortex, frontal neocortex, Frontal Eye Field, Eye Field, Frontal, Supplementary, Frontal Lobes, Supplementary Eye Field, Frontal Eye Fields, Frontal Corticesrhesus macaque, dairy cow, Rat, Macaque, Activity, Monkeys, determination, Laboratory, Mus domesticus, rhesus monkeys, Norway Rat, protein, Norway Rats, House Mouse, Long Term, protein polypeptide chains, rat, Tier, DSmurf, diseases, Mammals, Chinese Rhesus Macaques, diseases and disorders, Norway rat, Analysis, Research Activity, protein aggregate, Work Flow, animal, Laboratory Research, Effect, male, Animalia, Priorities, human disease, Rhesus Macaques, Monkey, Man (Taxonomy), Analyses, Bos bovis, Tissue, Swiss Mice, proteins, Futurology, Laboratory Rat, genetic, Bos Tauurus, oxen, Smurf, Homo sapiens disease, domestic cow, Research Priority, house mouse, Primate, Long-Term Effects, Primata, CG4943, D-smurf, Predictions and Projections, animalia, Anthropoidea, Modern, familial, mouse, Longterm Effect, Research Priorities, Rhesus Monkeys, Rattus, Lack, female, mice C57BL/6xCBA/CaJ hybrid, organism, Mus norvegicus, Workflows, Rattus norwegicus, Algorithm, Old World monkeys, Diseases, monkeys, Research and Development, Mus musculus, whole organism, DmelCG4943, maleate, mice, Swiss Mouse, rats, human, domesticus, Activities, disease, data analysis, Koerper, Rhesus, inherited genetic, Mouse, bovine, Proteomes, Work Flows, humans, other disease, human being, multi-cellular organism, norvegicus, Macaca mulatta lasiotas, Effects, Peptidomics, dSmurf1, primate, Gene, protein-containing complex, Human, Rattus sp. strain Wistar, Rats, Homo sapiens, polypeptide chain, cattle, House, Gene Products, disease or disorder, Mus musculus domesticus, Projections and Predictions, Animal, Rattus rattiscus, Mice, Man, brown rat, Rattus norvegicus, Research, New World monkeys, Longterm, Swiss, metazoa, Long-Term, man, Research Activities., non-neoplastic, d-smurf, data processing, Rhesus monkey, disorder, Long-Term Effect, Development and Research, species, Chinese, constitutitional genetic, Rattus norvegicus8, Rhesus Macaque, monkey, data, cow, female human body, body, protein complex, Males, Proteins, disorders, total expressed protein, whole body, medical condition, Dsmurf, Mus muscaris, Chinese Rhesus Macaque, dSmurf, primates, Priority, native protein, natural protein, Mus, Bos primigenius taurus, Smurf ubiquitin ligase, Laboratory Rats, Metazoa, Protein, chemical analysis, Long Term Effects, Cercopithecus mulatta, Research Activities, sequence, condition, domestic cattle, Data Base, rhesus macaques, House Mice, Macaca mulatta lasiota, primary structure of sequence macromolecule, Longterm Effects, Laboratory Mice, Protein Gene Products, male human body, Gene Proteins, ox, Data, Modern Man, Anthropoids, Rhesus Monkey, Norway, assay, Future, hereditary, Laboratory Mouse, Data Analyses, Females, Gunn rats0falseMmulatta - Frontal cortex, SC (Leeetal,plosone.2015)abundance based on Spectral counting, Interaction consistency score: 5.4, Coverage: 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