{"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":1,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["9606"],"full_dataset_link":["https://pax-db.org/dataset/9606/1305695320"],"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":["LC-MS/MS is the most commonly used technique for the identification and characterization of proteins. The efficiency of the electrospray process is a critical factor in LC-MS/MS. Despite the benefits associated with very low flow rates for the ionization efficiency, most LC-MS/MS platforms are operated at relatively high flow rates. The purpose of this work was to develop a nano LC system operable at a flow rate of 20 nL/min, applicable for routine analysis in proteomics laboratories. Peptide separation was performed with an analytical column packed with 2 μm porous chromatographic beads, a length of 25 cm and an inner diameter (i.d.) of 25 μm. Practical usability, reproducibility, and overall performance of the system were evaluated with a tryptic peptide mixture generated from HeLa cells. Using 100 ng of sample, we identified on average 3721 protein groups based on 25,699 peptides. We demonstrate that the number of peptides identified with this system increases with decreasing flow rates. Probing the sensitivity of the set-up we analyzed only 10 ng of the sample, identifying an average number of 2042 protein groups based on 11 424 peptides. All MS data have been deposited in the ProteomeXchange with identifier PXD000396 (http://proteomecentral.proteomexchange.org/dataset/PXD000396)."],"pubmed_title":["Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up."],"pubmed_authors":["Köcher Thomas T, Pichler Peter P, De Pra Mauro M, Rieux Laurent L, Swart Remco R, Mechtler Karl K"],"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":["HeLa, RCB0007."],"pubmed_title_synonyms":["phapii, IPP2A2, single-organism developmental process, Tandem, postnatal development, igaad, StF-IT-1, growth and development, Mass Spectrometry Mass Spectrometry, PHAPII, group, 5730420M11Rik, development, I-2PP2A, Dm I-2, I2PP2A, tandem MS, SET, HLA-DR-associated protein II, i2pp2a., ensemble, DI-2, TAF-I, MS/MS, MS2, I-2Dm, ipp2a2, postnatal growth, 2pp2a, Mass Spectrometry, Mass Spectrometry-Mass Spectrometry, CG4299, CG10574, DmelCG4299, I-2PP1, IGAAD, set, dSET/TAF-Ibeta, 2610030F17Rik, TAF-IBETA, 2PP2A, DmelCG10574, taf-ibeta, dSET, dSet, TAF-Ibeta, Chromatographies, AA407739, growth"],"name_synonyms":["Line, HeLa, Peptidomics., Cell Lines, RCB0007, Cell, Lines"],"pubmed_abstract_synonyms":["liquid chromatography tandem mass spectroscopy, IPP2A2, Procedures, determination, Peptidomics, Laboratory, AI461847, number, Gene, protein, protein-containing complex, body system, CG7826, PHAPII, LC-MS-MS, Productivity, protrusion, 5730420M11Rik, peptide, Polypeptides, Techniques, method, protein polypeptide chains, peptido, polypeptide chain, Method, sensitive, method used in an experiment, LC-MSMS, Studies, Gene Products, CG7835, CG42273, system, Min, Pgi, protein aggregate, Gpi-1, Separated, Technique, sensitivity, DmelCG42273, average, SET, Divorced, anatomical systems, LCMSMS, peptides, TAF-I, Gpi-1r, Nlk, Gpi-1s, HeLa, ipp2a2, Phi, Gpi-1t, min, 2pp2a, mAPC, proteins, Divorces, CG10574, AI047805, DmelCG4299, Study, allergic reaction, IGAAD, set, 2PP2A, Methodological Studies, column, DmelCG10574, taf-ibeta, sample, dSET, dSet, Sensitivity, peptidos, NK/GPI, LC-MS2, Data Set., phapii, Gpi, DYRK1, data, anatomical protrusion, protein complex, Proteins, LC-MS/MS, igaad, Dmel_CG7826, StF-IT-1, Mischung, Procedure, MF, Amf, Peptide, Cell, group, polypeptide, LC/MS/MS, native protein, HeLa Cell, mOC-X, Dm1, natural protein, I-2PP2A, low flow, Protein, chemical analysis, Dm I-2, I2PP2A, Dyrk1, NK|GPI, connected anatomical system, Dmel_CG7835, NK, Mnb, MNB, AU020952, Separation, Org, ORG, HLA-DR-associated protein II, ensemble, DI-2, I-2Dm, Separations, CC1, Specificity, Gpi1-r, Gpi1-s, Methodological, CG4299, high flow, AW124434, Gpi1-t, Methodological Study, sample population, ME-IV, plan specification, Protein Gene Products, organ system, I-2PP1, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, TAF-IBETA, Specificity and Sensitivity, spine, liquid chromatography-tandem mass spectroscopy, Cells, cardinality, liquid chromatography tandem mass spectrometry, Peptid, TAF-Ibeta, assay, Polypeptide, AA407739, i2pp2a, Bglap-rs1, Gpi1s"],"citation_count":["1"],"additional_accession":[]},"is_claimable":false,"name":"H.sapiens - Cell line, Hela, SC (Kocher,proteomics,2014)","description":"abundance based on Spectral counting, hela, Interaction consistency score: 22.0, Coverage: 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