{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["89462"],"full_dataset_link":["https://pax-db.org/dataset/89462/2599551988"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["The study aimed to describe the Bubalus bubalis seminal plasma proteome using a label-free shotgun UDMS<sup>E</sup> approach. A total of 859 nonredundant proteins were identified across five biological replicates with stringent identification. Proteins specifically related to sperm maturation and protection, capacitation, fertilization and metabolic activity were detected in the buffalo seminal fluid. In conclusion, we provide a comprehensive proteomic profile of buffalo seminal plasma, which establishes a foundation for further studies designed to understand regulation of sperm function and discovery of novel biomarkers for fertility. MS data are available in the ProteomeXchange with identifier PXD003728."],"pubmed_title":["Label-free proteome of water buffalo (Bubalus bubalis) seminal plasma."],"pubmed_authors":["Brito Mayara F MF, Auler Patrícia A PA, Tavares Guilherme C GC, Rezende Cristiana P CP, Almeida Gabriel M F GMF, Pereira Felipe L FL, Leal Carlos A G CAG, Moura Arlindo de Alencar AA, Figueiredo Henrique C P HCP, Henry Marc M"],"data_synonyms":["Add, 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, ratio"],"pubmed_title_synonyms":["Water, Bubalus arnee, Plasma, Bubalus bubalus, male genital secretion, Bos bubalis, domestic water buffalo, Water Buffalo, Bubalis bubalis, Bubalis arnee bubalis, prostate fluid, Bubalus, river buffalo, total expressed protein, milt, free, Bubalus arnee bubalis, Buffalo, water buffalo, Water Buffaloes, seminal fluid, prostatic fluid, Seminal Plasma, male genital fluid., label, Syncerus, Proteomes, Seminal"],"name_synonyms":["seminal fluid, male genital secretion, prostatic fluid, milt, sperm, ejaculate., prostate fluid, male genital fluid"],"pubmed_abstract_synonyms":["Regulations, Bubalus bubalus, Bos bubalis, Conceptions, Subfecundity, Sperm, Biological Markers, Viral Marker, Polyspermic Fertilization, Surrogate Endpoints, Activity, Clinical Markers, Laboratory, prostate fluid, FON1, Clinical Marker, Biochemical, Gene, Endpoint, Fertility, SUPERMAN, milt, FLORAL ORGAN NUMBER 1, Serum, Foundation, Y-Chromosome-Bearing Sperm, Social Controls, Surrogate End Points, World Fertility Survey, Delayed Fertilizations, Surrogate Markers, Fertility Preferences, Laboratory Markers, Determinant, Biological, Below Replacement, SUP, Gene Products, Spermatozoon, Survey, Preference, World Fertility, Y Bearing Sperm, Formal Social Controls, Polyspermic, Fertility Surveys, Fecundity, Spermatozoa Maturation, X-Chromosome-Bearing Sperm, study, sperm cell, Biomarker, male genital secretion, Fertility Incentives, X-Bearing, domestic water buffalo, Clinical, Bubalis arnee bubalis, Natural, Biological Marker, Bdr, proteins, X-Bearing Sperms, Super protein, free, male genital fluid, sp, SNAP-25, X-Chromosome-Bearing Sperms, water buffalo, Social, prostatic fluid, Mif1, Y Chromosome Bearing Sperm, Maturation of Spermatozoa, Maturation, Immunologic Markers, Immune, Markers, Delayed Fertilization, Y-Bearing Sperm, sperm, X Chromosome Bearing Sperm, data., Viral Markers, Y-Chromosome-Bearing Sperms, Below Replacement Fertility, Fertility Determinant, Fertility Preference, SPERM, Fertility Incentive, Immunologic Marker, Differential Fertility, Biologic, ejaculate, Y-Chromosome-Bearing, X-Bearing Sperm, Viral, Bubalis bubalis, Polyspermic Fertilizations, Surrogate Endpoint, Formal Social Control, World, Proteins, Serum Markers, World Fertility Surveys, river buffalo, total expressed protein, End Point, Biochemical Markers, Synaptosomal-associated 25 kDa protein, function, Biologic Marker, spermatozoon, Immune Marker, Seminal Plasma, native protein, Conception, Social Control, Marker, Surrogate End Point, Protein, Natural Fertility, GENA70, Determinants, Y-Bearing, Biologic Markers, Bubalus arnee, Plasma, X-Chromosome-Bearing, Serum Marker, End Points, Surrogate, Endpoints, Control, FLO10, Immunologic, Controls, Laboratory Marker, HERP, spermatozoid, Bubalus arnee bubalis, X Bearing Sperm, Preferences, Surrogate Marker, Fertility Determinants, Protein Gene Products, seminal fluid, Gene Proteins, Delayed, Fertilization, Y-Bearing Sperms, Differential, Marital, Biochemical Marker, label, syngamy, SNAP, Fertilizations, Sperms, Surveys, regulation, Fecundability, Regulation, Seminal, Proteomes, General activity, Fertility Survey, FLORAL DEFECTIVE 10, Immune Markers, Marital Fertility"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Bbubalis - Seminal fluid, iBAQ (Britoetal,reproddomestanim2018)","description":"abundance based on iBAQ, Interaction consistency score: 0.8, Coverage: 1","dates":{"publication":"2018"},"accession":"2599551988","cross_references":{"pubmed":["29888513"],"uniprot":["89462.XP_006058682.1","89462.XP_006063990.1","89462.XP_006053811.1","89462.XP_006071638.1","89462.XP_006042170.1","89462.XP_006077300.1","89462.XP_006051119.1","89462.XP_006042923.1","89462.XP_006065839.1","89462.XP_006054058.1","89462.XP_006077643.1","89462.XP_006069092.1","89462.XP_006076530.1","89462.XP_006063184.1","89462.XP_006070209.1","89462.XP_006077455.1","89462.XP_006052314.1","89462.XP_006046104.1","89462.XP_006042264.1","89462.XP_006080693.1","89462.XP_006061090.1","89462.XP_006059324.1","89462.XP_006051454.1","89462.XP_006057645.1","89462.XP_006063049.1","89462.XP_006048131.1","89462.XP_006058792.1","89462.XP_006060938.1","89462.XP_006063388.1","89462.XP_006065751.1","89462.XP_006043252.1","89462.XP_006077003.1","89462.XP_006058253.1","89462.XP_006062029.1","89462.XP_006052157.1","89462.XP_006046734.1","89462.XP_006055725.1","89462.XP_006047390.1","89462.XP_006045255.1","89462.XP_006046159.1","89462.XP_006048192.1","89462.XP_006042233.1","89462.XP_006043597.1","89462.XP_006079523.1","89462.XP_006080872.1","89462.XP_006075148.1","89462.XP_006054867.1","89462.XP_006077688.1","89462.XP_006063897.1","89462.XP_006059969.1","89462.XP_006056632.1","89462.XP_006067524.1","89462.XP_006067395.1","89462.XP_006077264.1","89462.XP_006073133.1","89462.XP_006053677.1","89462.XP_006040351.1","89462.XP_006056492.1","89462.XP_006041235.1","89462.XP_006041942.1","89462.XP_006070478.1","89462.XP_006068858.1","89462.XP_006045573.1","89462.XP_006060443.1","89462.XP_006073663.1","89462.XP_006070644.1","89462.XP_006062854.1","89462.XP_006065646.1","89462.XP_006070357.1","89462.XP_006046257.1","89462.XP_006046299.1","89462.XP_006063368.1","89462.XP_006080720.1","89462.XP_006052555.1","89462.XP_006066420.1","89462.XP_006065698.1","89462.XP_006050061.1","89462.XP_006081046.1","89462.XP_006062860.1","89462.XP_006067041.1","89462.XP_006042816.1","89462.XP_006047622.1","89462.XP_006042334.1","89462.XP_006049426.1","89462.XP_006055783.1","89462.XP_006065099.1","89462.XP_006049700.1","89462.XP_006046198.1","89462.XP_006052795.1","89462.XP_006042420.1","89462.XP_006057345.1","89462.XP_006041949.1","89462.XP_006060379.1","89462.XP_006067825.1","89462.XP_006051456.1","89462.XP_006045039.1","89462.XP_006058427.1","89462.XP_006047698.1","89462.XP_006067328.1","89462.XP_006070893.1","89462.XP_006041616.1","89462.XP_006073013.1","89462.XP_006060609.1","89462.XP_006048328.1","89462.XP_006073624.1","89462.XP_006045164.1","89462.XP_006063028.1","89462.XP_006045767.1","89462.XP_006078222.1","89462.XP_006055293.1","89462.XP_006051806.1","89462.XP_006055805.1","89462.XP_006056975.1","89462.XP_006046520.1","89462.XP_006065547.1","89462.XP_006074465.1","89462.XP_006069425.1","89462.XP_006070946.1","89462.XP_006044367.1","89462.XP_006058681.1","89462.XP_006063725.1","89462.XP_006063702.1","89462.XP_006062656.1","89462.XP_006047932.1","89462.XP_006050985.1","89462.XP_006047770.1","89462.XP_006051329.1","89462.XP_006050706.1","89462.XP_006050936.1","89462.XP_006052879.1","89462.XP_006062558.1","89462.XP_006060831.1","89462.XP_006078066.1","89462.XP_006075487.1","89462.XP_006055569.1","89462.XP_006075750.1","89462.XP_006048404.1","89462.XP_006066622.1","89462.XP_006040625.1","89462.XP_006065912.1","89462.XP_006052961.1","89462.XP_006073260.1","89462.XP_006044210.1","89462.XP_006045325.1","89462.XP_006050017.1","89462.XP_006062856.1","89462.XP_006062451.1","89462.XP_006046920.1","89462.XP_006077708.1","89462.XP_006046028.1","89462.XP_006062107.1","89462.XP_006042870.1","89462.XP_006070359.1","89462.XP_006042628.1","89462.XP_006048099.1","89462.XP_006077961.1","89462.XP_006077867.1","89462.XP_006065164.1"]}}