PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering9544https://pax-db.org/dataset/9544/3696013597mering@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.<h4>Purpose</h4>Endocervical mucus changes play a key role in regulating fertility throughout the menstrual cycle and in response to hormonal contraceptives. Non-human primates (NHP) provide the most translational animal model for reproductive tract studies, as they have hormonally-regulated menstrual cycles and mucus changes, similar to women.<h4>Experimental design</h4>We used TMT labelling and LC-LC/MS to compare the proteins found in the mucus of the rhesus macaque to the mucus of the human endocervix. Data are available via ProteomeXchange with identifier PXD021710.<h4>Results</h4>We found 3048 total proteins present in both rhesus mucus and human mucus, and of these, 57% showed a similar expression pattern. An even higher similarity occurred in the top 500 most prevalent proteins, with overlap in 341 (68%) proteins. Mucin MUC5B was the most highly expressed mucin protein (top 10 expressed proteins in both) but other key proteins related to mucus structure were present in both samples.<h4>Conclusions and clinical relevance</h4>We find that the mucus proteome of the endocervical mucus is highly conserved in NHP and women. This supports use of the NHP model system for studies of the endocervix and trials of novel fertility treatments targeting the cervix.Comparing endocervical mucus proteome of humans and rhesus macaques.Han Leo L, Park Daye D, Reddy Ashok A, Wilmarth Phillip A PA, Jensen Jeffrey T JTAdd, 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, ratiocervical canal of uterus, rhesus macaque, Rhesus Macaque, endocervical, Rhesus Macaques, cervical canal, Monkey, Man (Taxonomy), Macaque, Macaca mulatta lasiotas, Modern, endocervical canal, total expressed protein, rhesus monkeys, rhesus macaques, endocervix, Rhesus Monkeys, Macaca mulatta lasiota, cavity of cervix, Human, Chinese Rhesus Macaque, canal of the cervix, Homo sapiens, mucous, Modern Man, mucous layer, mucus, Cercopithecus mulatta, Rhesus., Rhesus monkey, extracellular proteinaceous gel, Chinese Rhesus Macaques, Rhesus Monkey, Rhesus, Chinese, Proteomes, Man, humansPalm Leaf Reaction, Fern Test, Palm-Leaf Reactions, Reactions, Mucus, cervix mucus, Cervix, Reaction, Palm-Leaf, Tests, Fern Tests, Palm-Leaf Reaction, Test, Cervical, Fern, Cervical Mucus.Experimental Designs, rhesus macaque, Research Technique, Canal, Problem Formulations, Adjustments, Macaque, Design, Error Sources, lobus nervosus neurohypophysis, rhesus monkeys, protein, Technic, Ectocervix, World Fertility Survey, AV085033, Fertility Preferences, Techniques, protein polypeptide chains, Tier, Roles, Below Replacement, Method, MUC-5B, mucous layer, Concepts, 10.5, Chinese Rhesus Macaques, protein aggregate, animal, Effect, IKKg, Fertility Surveys, 10.9, KEY, Key, Experimental Design, Geschlechtsorgan, Animalia, cervical canal of uterus, Group, Uterine Cervical Canals., Fertility Incentives, Cervical Canal, Rhesus Macaques, F, lobus posterior hypophysis, Monkey, Man (Taxonomy), DmelCG2328, Natural, Matched Group, Designs, Matched, Clinical Importance, Groups, proteins, V, External Os Cervix, Endocervix, neuro hypophysis, experimental design, cavity of cervix, caudal segment of uterus, posterior pituitary gland, Reporting, 2300002I04Rik, Role Concepts, posterior lobe of pituitary, Fertility Determinant, Research Techniques, Fertility Preference, Mucin, Primate, Differential Fertility, Primata, Data Reporting, Endometrial Cycle, Ovarian Cycle, Research Technic, Research Methodology, animalia, Modern, neural lobe, World Fertility Surveys, Contraceptives, Research Proposals, Rhesus Monkeys, Uterine, Girl, results, Significance, Research Proposal, Cervixes, neural lobe of pituitary gland, canal of the cervix, DmIKKgamma, organism, TPSG1, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Experimental, External Os of the Cervix, Role Concept, dIKK, Endocervical Canals, posterior lobe of pituitary gland, Uterine Cervical, Kenny, ectocervix, Role, VI, overlap, Technics, Problem Formulation, posterior pituitary, Problem, 20.35, cervical canal, whole organism, neck of uterus, Relevance, IKK-gamma, Preferences, human, Fertility Determinants, Formulations, organ system, cervix uteri, DmelCG16910, Agents, lobus posterior, Menstrual, Koerper, PRSS31, Surveys, eve2, Rhesus, External Os, Fecundability, TMT, Data Adjustments, Proteomes, Marital Fertility, CG2328, 14.10, Subfecundity, endocervical, human being, multi-cellular organism, conformation, Effects, Macaca mulatta lasiotas, pituitary gland neural lobe, Matched Groups, Importance, primate, Gene, Fertility, endocervix, Scoring Method, protein-containing complex, body system, dIKK-gamma, Human, uterine cervix, Adjustment, Determinant, Homo sapiens, polypeptide chain, Ovarian, Scoring Methods, mucous, DmIKK-gamma, Sources, A130042M24, Cycle, Girls, Ovarian Cycles, Gene Products, Survey, system, Preference, even, dmIKKgamma, World Fertility, Animal, IKK[[gamma]], Clinical Significance, Man, Technique, Fecundity, Contraceptive Effect, genital tract, Cycles, Methodology, anatomical systems, pattern, Clinical, Menstrual Cycles, Scoring, Research, Proposals, Cervical Canal of the Uterus, distribution, canalis cervicis uteri, infundibular process, metazoa, labeling, man, neural lobe of pituitary, Endocervical, Research Strategy, cervix, Endometrial, IKK, Below Replacement Fertility, reproductive tissue, Error Source, Rhesus monkey, Uterine Cervical Canal, genitalia, systemata genitalia, Fertility Incentive, Strategies, Chinese, Contraceptive, relational structural quality, thiol methyltransferase activity, Uterine Cervical Canals, posterior lobe, genital system, Contraceptive Effects, Rhesus Macaque, data, Endometrial Cycles, Women's Group, World, body, protein complex, posterior lobe of hypophysis, Women Groups, Proteins, endocervical canal, Endocervical Canal, total expressed protein, whole body, Formulation, reproductive tract, Woman, Concept, Chinese Rhesus Macaque, neurohypophysis, Research Strategies, IKKgamma, primates, lobus nervosus, native protein, natural protein, Metazoa, Protein, mucus, Cercopithecus mulatta, Natural Fertility, Eve, EVE, lobus posterior (glandula pituitaria), connected anatomical system, Determinants, Proposal, Methods, organa genitalia, Dmikkgamma, pituitary gland, cervix of uterus, Source, Uterine Cervix, mucin 5b, Women's Groups, l(2)46Ce, Research Designs, rhesus macaques, MG1, NHP, Research Technics, CG16910, Macaca mulatta lasiota, MUC9, l(2)46Cg, MUC5, Protein Gene Products, l(2)46CFj, Gene Proteins, l(2)46CFh, Data Adjustment, Differential, exocervix, Marital, Error, Data, l(2)46CFp, Cervix, Modern Man, animal reproductive system, extracellular proteinaceous gel, Rhesus Monkey, Strategy, E(eve), l(2)46CFg, Fertility Survey0falseMmulatta - Cervical mucus, iBAQ (Hanetal,proteomicsclinappl2021)abundance based on iBAQ, Interaction consistency score: 11.2, Coverage: 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