{"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":["10090"],"full_dataset_link":["https://pax-db.org/dataset/10090/1779616615"],"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":["Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated liquid chromatography system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high tandem MS frequencies. The new reflectron and detector improve resolving power compared with the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) and accurate fold change determination in spike-in experiments in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originating from different tissues. Finally, after high pH reversed-phase fractionation we identified 9515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in single measurements of cerebellum-the highest proteome coverage reported with a QTOF instrument so far."],"pubmed_title":["The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics."],"pubmed_authors":["Beck Scarlet S, Michalski Annette A, Raether Oliver O, Lubeck Markus M, Kaspar Stephanie S, Goedecke Niels N, Baessmann Carsten C, Hornburg Daniel D, Meier Florian F, Paron Igor I, Kulak Nils A NA, Cox Juergen J, 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"],"pubmed_title_synonyms":["instrument configuration, Peptidomics., HardwareType, TOF, instrument, hardware"],"name_synonyms":["epencephalon-1, Parencephalon, parencephalon, Cerebella., corpus cerebelli, infratentorial region, Cerebellums, muscle, Parencephalons, Corpus Cerebelli, musculus, muscle element"],"pubmed_abstract_synonyms":["apparatus, corpus cerebelli, ion, determination, leg, epencephalon-1, instrument configuration, LFQ, Capillary, l(1)AA33, peptide, dmTAF[[II]]230, Polypeptides, Personal, devices, peptido, Beds, Line, 1, Extracts, 2, Min, Analysis, Work Flow, WMS, DmelCG42273, Diploid Cells, Mass Spectrum Analysis, Psychological, appliances, peptides, TFIID TAF250, Analyses, cel, Tissue, min, crumb, Saccharomyes cerevisiae, HardwareType, mAPC, proteins, Saccharomyces uvarum var. melibiosus, Sinusoidal Bed, Social, Bed, AI047805, Parencephalon, infratentorial region, l(1)B2/13.1, RUN, Run, Saccharomyces capensis, anatomical tube, ppm, RCB0007, blood capillary, Social Power, Haploid, brewer's yeast, Diploid, SIMPLE, GPHYSD2, Haploidies, SGS, Power, Sinusoid, Tube, dTAF[[II]]230, l(1)LB9, CG6383, Inlet, Liquid Chromatography, TAF200, Dmel_CG7826, Th, Sinusoids, Psychological Powers, TAFII-250, TAF250/230, Spectrum Analysis, Cerebella, AA33, ACMICD, Spectroscopy, TUBE, TAFII250, Workflows, Ionen, Dm1, PIG7, Inlets, Dmel_CG7835, Lines, Mnb, MNB, Yeast, Parencephalons, instrument, MS/MS, Spectrometry, MASS, AW124434, CG17603, TAF[[II]], Haploid Cell, organ system, Complex Extract, parencephalon, Cerebellums, Taf250, SR3-5, duct, Cells, Polypeptide, E430016J11Rik, Powers, Proteomes, l(3)S050920, Work Flows, TAF230, Crbs, Hybrids, Psychological Power, CG1849, d230, Extract, Peptidomics, Professional Power, FBN, instruments, Gene, baker's yeast, dTAFII250, far, Spectrum Analyses, thomson, Ximpact, EfW1, body system, Saccharomyces italicus, CG7826, Crude Extracts, hardware, mass-to-charge ratio, Crude, Crude Extract, Complex Mixture, Crumbs, TOF, dmTAF1, ECTOL1, Taf230, yeast, Mass, Gene Products, CG7835, Capillary Bed, CG42273, system, Mass Spectroscopy, lager beer yeast, TAF250, Taf200, Mixtures, CT19912, 0509/20, anatomical systems, dTAF[[II]]250, Diploids, 2310061K05Rik, cell, iones, MS2, Sinusoidal Beds, Runt, Complex, HeLa, 1384/04, Taf1p, ions, Chimeras, OCTD, dTAF250, Candida robusta, 10^[-6], peptidos, TAF, LB5, l(3)j1B5, TP53I7, Haploid Cells, data, DYRK1, TAF[[II]]250, Mixture, Proteins, DmelCG1849, Cell Lines, total expressed protein, l(3)84Ab, BG:DS00004.13, Mischung, Rnt, impact-a, Peptide, Cell, Saccaromyces cerevisiae, dTAF230, l(3)07207, lLB5, polypeptide, Sccharomyces cerevisiae, MS, capillary vessel, Hybrid, native protein, equipment, p230, Protein, chemical analysis, AI551343, TAF[[II]]250/230, TFIID, CRB, Crb, MFS1, Professional, Dyrk1, connected anatomical system, Sinusoidal, l(3)S058104, dJ142L7.2, Mass Spectrum Analyses, tandem MS, WMS2, DmelCG6383., Saccharomyces oviformis, Taf[[II]]250, AU020952, Mass Spectrum, TAF[[II]]230, Corpus Cerebelli, CC1, TAF[II]250, l(1)19Ea, ME-IV, Protein Gene Products, P235, Gene Proteins, Personal Power, DmelCG17603, Capillary Beds, Ion, Haploids, Diploid Cell, SSKS, Power (Psychology), Peptid, assay, Diploidies, Bay, RWDD5, Complex Extracts, TAF1"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"M.musculus - Cerebellum, iBAQ (Becketal.,molcellproteomics2015)","description":"abundance based on iBAQ, Interaction consistency score: 19.7, Coverage: 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