{"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":["4513"],"full_dataset_link":["https://pax-db.org/dataset/4513/2107721590"],"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":["Meiosis is a highly dynamic and precisely regulated process of cell division, leading to the production of haploid gametes from one diploid parental cell. In the crop plant barley (<i>Hordeum vulgare</i>), male meiosis occurs in anthers, in specialized cells called meiocytes. Barley meiotic tissue is scarce and not easily accessible, making meiosis study a challenging task. We describe here a new micro-proteomics workflow that allows sensitive and reproducible genome-wide label-free proteomic analysis of individual staged barley anthers. This micro-proteomic approach detects more than 4,000 proteins from such small amounts of material as two individual anthers, covering a dynamic range of protein relative abundance levels across five orders of magnitude. We applied our micro-proteomics workflow to investigate the proteome of the developing barley anther containing pollen mother cells in the early stages of meiosis and we successfully identified 57 known and putative meiosis-related proteins. Meiotic proteins identified in our study were found to be key players of many steps and processes in early prophase such as: chromosome condensation, synapsis, DNA double-strand breaks or crossover formation. Considering the small amount of starting material, this work demonstrates an important technological advance in plant proteomics and can be applied for proteomic examination of many size-limited plant specimens. Moreover, it is the first insight into the proteome of individual barley anther at early meiosis. The proteomic data have been deposited to the ProteomeXchange with the accession number PXD010887."],"pubmed_title":["Application of a Sensitive and Reproducible Label-Free Proteomic Approach to Explore the Proteome of Individual Meiotic-Phase Barley Anthers."],"pubmed_authors":["Lewandowska Dominika D, Zhang Runxuan R, Colas Isabelle I, Uzrek Nicola N, Waugh Robbie R"],"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":["allergic reaction, Barley, two-rowed barley, Hordeum vulgare, barley, sensitive, label, domesticated barley., total expressed protein, Hordeum vulgare L., sensitivity, Proteomes, Horedum vulgare, free"],"name_synonyms":["Zea anther (narrow)., Poaceae anther (narrow)"],"pubmed_abstract_synonyms":["Plant Male, Male, Pflanze, LUC7A, Phases, protein, Pollen, Divisions, viridiplantae, dmTAF[[II]]230, protein polypeptide chains, exact), Work Flow, protein aggregate, Fs(3)Hor, IKKg, KEY, Key, Diploid Cells, portion of tissue, DmelCG2684, thymus nucleic acid, Grain, M Phases, TFIID TAF250, Genomes, cel, M, Tissue, hypoplasia, proteins, NTef2, free, Division Phase, allergic reaction, K2p3.1, homologous chromosome separation at meiosis I, 花粉 (Japanese, Double-Stranded DNA, Haploid, Hordeum vulgare L., deoxyribonucleic acids, DNAn, Diploid, Haploidies, male nuclear division, dTAF[[II]]230, anatomical protrusion, wide/broad, Meiotic M Phase, Male Gametophytes, CROP, Crop, TAF200, Double-Stranded, TAFII-250, TAF250/230, Cell Divisions, Male Gametophyte, Fs(3)Sz11, (Deoxyribonucleotide)n+m, DmIKKgamma, TAFII250, Workflows, TBAK1, Chromosomal Synapsis, dIKK, Kenny, tissue portion, Gamete, Synapsis, simple tissue, desoxyribose nucleic acid, Meiotic M Phases, synapsis, PPH4, craw, Zea anther (narrow), CREAP-1, IKK-gamma, Plant, whole genome, CG17603, chromosomal pairing, Haploid Cell, TAF[[II]], early, wide, Grains, Plant Male Gametes, DmelCG16910, Taf250, spine, SR3-5, label, Horka, Cells, ds DNA, CG2684, Fs(3)Horka, DNA, TASK-1, Proteomes, Work Flows, TAF230, pollen grain, hLuc7A, formation of chiasmata, meiosis, chromosomal synapsis, d230, Pollen Grain, DNS, DNA condensation, (Deoxyribonucleotide)n, Peptidomics, Chromosome Pairings, number, Gene, dTAFII250, broad, protein-containing complex, Male Gametes, EfW1, presence, dIKK-gamma, Deoxyribonucleic acids, protrusion, two-rowed barley, reduced, polypeptide chain, Deoxyribonucleic Acid, dmTAF1, Taf230, sensitive, DmIKK-gamma, Gene Products, DmF2, tiny, dmIKKgamma, IKK[[gamma]], sensitivity, RGD1307981, TAF250, plantae, Gametes, lod, meiotic homologous chromosome separation, study, Taf200, Pollen Grains, Plant Microspores, dTAF[[II]]250, Microspores, Diploids, polen (Spanish, Cell Division Phase, cell, resolution of meiotic joint molecules as recombinants, Gametophytes, Double Stranded, Taf1p, Meioses, Cell Division, Deoxyribonucleic acid, Division, crossover biosynthesis, Barley, dTAF250, Hordeum vulgare, Meiotic, male generative cell, IKK, Plant Male Gamete, (Deoxyribonucleotide)m, TAF, Poaceae anther (narrow), Plant Microspore, small, Haploid Cells, homologous chromosome pairing at meiosis, male meiosis, data, TAF[[II]]250, OAT1, protein complex, DNAn+1, OA48-18, Proteins, total expressed protein, l(3)84Ab, Gametophyte, BG:DS00004.13, Male Gamete, crossover formation, Cell, Chromosomal, dTAF230, TASK, IKKgamma, count in organism, pollen grain (exact), Prophases, native protein, natural protein, p230, Protein, proteomic analysis, TAF[[II]]250/230, eukaryotic chromosome condensation, TFIID, CRA, ds-DNA, M Phase, domesticated barley, Taf[[II]]250, Phase, Meiotic M, TAF[[II]]230, underdeveloped, Dmikkgamma, TAF[II]250, Lds, CG16910, cardinality., Protein Gene Products, Gene Proteins, DmelCG17603, barley, Haploids, Diploid Cell, nuclear chromosome condensation, Desoxyribonukleinsaeure, Diploidies, Microspore, Horedum vulgare, TAF1"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Hvulgare - Anther, iBAQ (Lewandowskaetal,frontplantsci2019)","description":"abundance based on iBAQ, Interaction consistency score: 8.3, Coverage: 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