{"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":["9606"],"full_dataset_link":["https://pax-db.org/dataset/9606/4132152676"],"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 quadrupole Orbitrap mass spectrometer (Q Exactive) made a powerful proteomics instrument available in a benchtop format. It significantly boosted the number of proteins analyzable per hour and has now evolved into a proteomics analysis workhorse for many laboratories. Here we describe the Q Exactive Plus and Q Exactive HF mass spectrometers, which feature several innovations in comparison to the original Q Exactive instrument. A low-resolution pre-filter has been implemented within the injection flatapole, preventing unwanted ions from entering deep into the system, and thereby increasing its robustness. A new segmented quadrupole, with higher fidelity of isolation efficiency over a wide range of isolation windows, provides an almost 2-fold improvement of transmission at narrow isolation widths. Additionally, the Q Exactive HF has a compact Orbitrap analyzer, leading to higher field strength and almost doubling the resolution at the same transient times. With its very fast isolation and fragmentation capabilities, the instrument achieves overall cycle times of 1 s for a top 15 to 20 higher energy collisional dissociation method. We demonstrate the identification of 5000 proteins in standard 90-min gradients of tryptic digests of mammalian cell lysate, an increase of over 40% for detected peptides and over 20% for detected proteins. Additionally, we tested the instrument on peptide phosphorylation enriched samples, for which an improvement of up to 60% class I sites was observed."],"pubmed_title":["The Q Exactive HF, a Benchtop mass spectrometer with a pre-filter, high-performance quadrupole and an ultra-high-field Orbitrap analyzer."],"pubmed_authors":["Scheltema Richard Alexander RA, Hauschild Jan-Peter JP, Lange Oliver O, Hornburg Daniel D, Denisov Eduard E, Damoc Eugen E, Kuehn Andreas A, Makarov Alexander A, 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":["PRE, CPD photolyase activity, MOS3, RPE, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, PhrB photolyase activity, PRECOCIOUS, photolyase activity, developmental field, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, analyzer., pigmented retina, F23A5.3, future organ, photoreactivating enzyme activity, pigmented epithelium, DNA cyclobutane dipyrimidine photolyase activity, deoxyribodipyrimidine photolyase activity, SUPPRESSOR OF AUXIN RESISTANCE 3, p. pigmentosa retinae, phr A photolyase activity, organ field, MODIFIER OF SNC1, DNA-photoreactivating enzyme, retinal pigment, deoxyribonucleic photolyase activity, dipyrimidine photolyase (photosensitive), 3, deoxyribonucleate pyrimidine dimer lyase (photosensitive), stratum pigmentosa retinae, field, NUP96, epithelium, retinal pigment layer, F23A5_3"],"name_synonyms":["Line, Cell Lines, Cell., Cell, Lines"],"pubmed_abstract_synonyms":["CPD photolyase activity, cycline, PhrB photolyase activity, ion, determination, Peptidomics, Laboratory, Ass-1, Feature, DmcyclinE, fond, instrument configuration, STK10, FBN, Gene, cycE, photoreactivating enzyme activity, CycEI, pigmented epithelium, body system, Migrant Workers, l(2)br37, phosphorylation, deoxyribodipyrimidine photolyase activity, CG7826, hardware, CYCLE, Productivity, cdi7, peptide, Polypeptides, organ field, Ccne, cyclinE, peptido, isolation, ECTOL1, Injection, AA408052, Gene Products, Cdi7, CDI7, CG7835, fold, CG42273, 3, system, Min, stratum pigmentosa retinae, field, Low, NUP96, epithelium, Injectables, WMS, DmelCG42273, me75, MOS3, anatomical systems, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, CYCE, Migrant Worker, peptides, PRECOCIOUS, iones, DmelCG3938, developmental field, CyclE, Transients, Nonmigrant, pigmented retina, F23A5.3, 3938, min, HardwareType, Nonmigrants, mAPC, proteins, purification, analyzer, Worker, DmcycE, ions, Transient, D17Mit170, T1, DNA cyclobutane dipyrimidine photolyase activity, Fast, SUPPRESSOR OF AUXIN RESISTANCE 3, OCTD, AI047805, Injectable, isolation and purification, ASS, Squatter, l(2)k05007, dm-cycE, lysate, h, ATP:Fas-activated serine/threonine protein phosphotransferase activity, Squatters, peptidos, Characteristics, GPHYSD2, F23A5_3, FAST, SGS, PRE, DYRK1, cou, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, Proteins, Dmel_CG7826, Phosphorylations, FASTK, future organ, Tl3, Cyc E, br37, Tl2, Peptide, ACMICD, polypeptide, MODIFIER OF SNC1, Lr, Characteristic, l(2)k02514, native protein, DmCycE, BG:DS07108.3, retinal pigment, Ionen, Dm1, Migrant, Protein, chemical analysis, deoxyribonucleic photolyase activity, Nomad, dipyrimidine photolyase (photosensitive), MFS1, phosphorylation enrichment, Workers, Dyrk1, CyeE, connected anatomical system, l(2)05206, class., retinal pigment layer, Migrants and Transients, Dmel_CG7835, WMS2, Mnb, MNB, AU020952, RPE, l(2)k02602, instrument, photolyase activity, CC1, l(2)35Dd, MASS, AW124434, Features, p. pigmentosa retinae, ME-IV, Protein Gene Products, organ system, Gene Proteins, D-CycE, phr A photolyase activity, DNA-photoreactivating enzyme, l35Dd, socioeconomic factors, Ion, Activation Method, Nomads, SSKS, Bra, Migrants, Peptid, deoxyribonucleate pyrimidine dimer lyase (photosensitive), assay, Polypeptide, CG3938"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"H.sapiens - Cell line, SC (Scheltemaetal,molcellproteomics,2014)","description":"abundance based on Spectral counting, Interaction consistency score: 19.1, Coverage: 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