{"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"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["4932"],"full_dataset_link":["https://pax-db.org/dataset/4932/469118354"],"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":["Mass spectrometry is a powerful technology for the analysis of large numbers of endogenous proteins. However, the analytical challenges associated with comprehensive identification and relative quantification of cellular proteomes have so far appeared to be insurmountable. Here, using advances in computational proteomics, instrument performance and sample preparation strategies, we compare protein levels of essentially all endogenous proteins in haploid yeast cells to their diploid counterparts. Our analysis spans more than four orders of magnitude in protein abundance with no discrimination against membrane or low level regulatory proteins. Stable-isotope labelling by amino acids in cell culture (SILAC) quantification was very accurate across the proteome, as demonstrated by one-to-one ratios of most yeast proteins. Key members of the pheromone pathway were specific to haploid yeast but others were unaltered, suggesting an efficient control mechanism of the mating response. Several retrotransposon-associated proteins were specific to haploid yeast. Gene ontology analysis pinpointed a significant change for cell wall components in agreement with geometrical considerations: diploid cells have twice the volume but not twice the surface area of haploid cells. Transcriptome levels agreed poorly with proteome changes overall. However, after filtering out low confidence microarray measurements, messenger RNA changes and SILAC ratios correlated very well for pheromone pathway components. Systems-wide, precise quantification directly at the protein level opens up new perspectives in post-genomics and systems biology."],"pubmed_title":["Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast."],"pubmed_authors":["de Godoy Lyris M F LM, Olsen Jesper V JV, Cox Jürgen J, Nielsen Michael L ML, Hubner Nina C NC, Fröhlich Florian F, Walther Tobias C TC, Mann Matthias 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"],"description_synonyms":["data, data., MS/MS, tandem MS, MS2"],"pubmed_title_synonyms":["Saccharomyces oviformis, Haploid Cells, Yeast, Diploids, lager beer yeast., FBN, total expressed protein, Saccharomyes cerevisiae, baker's yeast, MASS, Saccharomyces uvarum var. melibiosus, Haploid Cell, Cell, Saccharomyces italicus, Saccaromyces cerevisiae, ACMICD, OCTD, Sccharomyces cerevisiae, Candida robusta, Saccharomyces capensis, ECTOL1, Haploids, Diploid Cell, SSKS, Cells, yeast, MFS1, Haploid, Diploidies, brewer's yeast, Diploid, GPHYSD2, Haploidies, Proteomes, WMS, WMS2, SGS, Diploid Cells"],"name_synonyms":["organism, data, whole body, multi-cellular organism, whole organism, animal, data., body, MS/MS, tandem MS, MS2, Koerper"],"pubmed_abstract_synonyms":["Gene Ontology Projects, determination, Allelochemical, Aminosaeure, instrument configuration, Mbp1, Amino acid, Gene Expression Profile, protein, Profiles, prevention, DmelCG6383, Membrane Tissues, protein polypeptide chains, responsivity, Project, Analysis, protein aggregate, myd, prevention and control, Non Polyadenylated, IKKg, KEY, Key, integumentum commune, Diploid Cells, Mass Spectrum Analysis, Cell Walls, me75, cell fusion, amino acids, reference sample, Analyses, Biology, Polyadenylated Messenger, Comparative Genomics, membrane region, Tissue, crumb, Mbp-1, HardwareType, Saccharomyes cerevisiae, proteins, Ectohormones, Saccharomyces uvarum var. melibiosus, D17Mit170, Signatures, T1, preventive measures, Saccharomyces capensis, Expression Signature, Transcriptomes, Haploid, brewer's yeast, associated, Diploid, Haploidies, Synomones, Membrane Tissue, preventive therapy, Genomics, wide/broad, external covering of organism, CG6383, gyltl1b-b, Polyadenylated, Aminokarbonsaeure, Comparative, Arts, Expression Profiles, integral to membrane, organism surface, Functional Genomics, membranous organ component, Tl3, Tl2, Spectrum Analysis, alpha-amino carboxylic acids, Spectroscopy, Gene Expression, DmIKKgamma, Pheromone, dIKK, MDDGA6, mKIAA0609, Expression Signatures, Kenny, Ontology Projects, KIAA0609, Expression Profile, Culture Technique, Semiochemicals, Transcriptome Profiles, Polyadenylated Messenger RNA, fg, Amino Acid, Acid, Gene Ontologies, Yeast, Ontology, Industrial, membrane of organ, Non Polyadenylated mRNA, gyltl1b, Industrial Arts, Ontologies, protein_coding_transcript, Amino acids, Projects, instrument, mdc1d, IKK-gamma, Spectrometry, expanded, Haploid Cell, Non-Polyadenylated mRNA, MDC1D, wide, DmelCG16910, enr, enlarged, integumentary system, Cells, Cell Cultures, microarray, Acids, dermal system, Proteomes, l(3)S050920, Poly(A) RNA, Crbs, big, protein levels, Systems., Peptidomics, Transcriptome Profile, Allomone, mating, Aminocarbonsaeure, Gene, baker's yeast, far, Spectrum Analyses, alpha-amino acid, broad, protein-containing complex, Saccharomyces italicus, dIKK-gamma, Gene Ontology Project, froggy, Gene Ontology, Gyltl1a, hardware, large, surface, Structural, Crumbs, polypeptide chain, Messenger, integral component of membrane, DmIKK-gamma, yeast, Mass, Gene Products, Functional, Low, dmIKKgamma, IKK[[gamma]], Cell Culture, Mass Spectroscopy, lager beer yeast, Walls, reactivity, CT19912, 0509/20, Diploids, Tissues, MDDGB6, Allelochemicals, Profile, 1384/04, messenger RNA, LARGE, labeling, Semiochemical, Cell Culture Technique, BPFD#36, template RNA, Candida robusta, IKK, great, region of membrane, Allomones, Kairomones, l(3)j1B5, Controlled, Haploid Cells, membrane, Controlling, RNA, Culture Techniques, Transcriptome, cou, protein complex, Proteins, total expressed protein, Messenger RNA, alpha-amino acids, Cell, Saccaromyces cerevisiae, l(3)07207, whole transcriptome, Sccharomyces cerevisiae, Isotope, IKKgamma, MS, Lr, native protein, natural protein, Poly(A)+ mRNA, Kairomone, chemical analysis, Protein, Gene Expression Signatures, whole membrane, INSDC_feature:mRNA, CRB, Crb, Gene Expression Signature, Polyadenylated RNA, l(3)S058104, Mass Spectrum Analyses, Saccharomyces oviformis, Ontology Project, Mass Spectrum, Wall, transmembrane, Poly(A)+ RNA, mRNA, Poly(A) Tail, Dmikkgamma, body surface, prophylaxis, Non-Polyadenylated, Membrane, Amino, CG16910, Protein Gene Products, Gene Proteins, control, Haploids, Gene Expression Profiles, Diploid Cell, Bra, Structural Genomics, assay, Diploidies, response, Signature, Polyadenylated mRNA"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"S.cerevisiae - Whole organism, Ms/ms abundance data, SILAC normalized data (De_godoy,nature,2008)","description":"abundance based on SILAC normalized data, MS/MS abundance data, Interaction consistency score: 15.7, Coverage: 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