{"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":["83332"],"full_dataset_link":["https://pax-db.org/dataset/83332/2118471723"],"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":["Research advancing our understanding of Mycobacterium tuberculosis (Mtb) biology and complex host-Mtb interactions requires consistent and precise quantitative measurements of Mtb proteins. We describe the generation and validation of a compendium of assays to quantify 97% of the 4,012 annotated Mtb proteins by the targeted mass spectrometric method selected reaction monitoring (SRM). Furthermore, we estimate the absolute abundance for 55% of all Mtb proteins, revealing a dynamic range within the Mtb proteome of over four orders of magnitude, and identify previously unannotated proteins. As an example of the assay library utility, we monitored the entire Mtb dormancy survival regulon (DosR), which is linked to anaerobic survival and Mtb persistence, and show its dynamic protein-level regulation during hypoxia. In conclusion, we present a publicly available research resource that supports the sensitive, precise, and reproducible quantification of virtually any Mtb protein by a robust and widely accessible mass spectrometric method."],"pubmed_title":["The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis."],"pubmed_authors":["Schubert Olga T OT, Mouritsen Jeppe J, Ludwig Christina C, Röst Hannes L HL, Rosenberger George G, Arthur Patrick K PK, Claassen Manfred M, Campbell David S DS, Sun Zhi Z, Farrah Terry T, Gengenbacher Martin M, Maiolica Alessio A, Kaufmann Stefan H E SHE, Moritz Robert L RL, Aebersold Ruedi 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":["LUZP5, Bacillus tuberculosis, T2SS-associated complexes, Mycobacterium tuberculosis H37Rv., Bacterium tuberculosis, Sec-dependent secretion system-associated complex, mCAP-G2, Mycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896 (Approved Lists 1980), CAP-G2, 5830426I05Rik, Mycobacterium tuberculosis var. hominis, general secretion pathway-associated complex, Luzp5, main terminal branch, CAPG2, total expressed protein, MTB, Mtb, hCAP-G2, Proteomes, Library, Mycobacterium tuberculosis typus humanus"],"name_synonyms":["Koch's Disease, Koerper., Koch Disease, organism, multi-cellular organism, whole organism, Infections, Kochs Disease, body, Infection, Tuberculosis, Mycobacterium tuberculosis, whole body, Mycobacterium tuberculosis Infection, Tuberculoses, Mycobacterium tuberculosis Infections, animal, active tuberculosis"],"pubmed_abstract_synonyms":["Regulations, host organism, Activity, Procedures, determination, Laboratory, SRML1, Luzp5, Deficiencies, number, FBN, Gene, dormancy, protein, protein-containing complex, presence, Social Controls, Oxygen Deficiency, Oxygen Deficiencies, Readability, Sec-dependent secretion system-associated complex, method, Techniques, protein polypeptide chains, polypeptide chain, ECTOL1, Method, sensitive, Mycobacterium tuberculosis var. hominis, method used in an experiment, Gene Products, Studies, CAPG2, Research Activity, protein aggregate, Hypoxia, Laboratory Research, Technique, Formal Social Controls, sensitivity, WMS, Priorities, Bacillus tuberculosis, Bacterium tuberculosis, MRM, Research, 5830426I05Rik, proteins, OCTD, Social, Study, allergic reaction, Oxygen, mCAP-G2, Methodological Studies, method used in an experiment., scientific observation, time of survival, main terminal branch, Development and Research, Research Priority, GPHYSD2, MTB, Mtb, SPS1, SGS, measuring, Mycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896 (Approved Lists 1980), Formal Social Control, protein complex, Proteins, PAPT, total expressed protein, Research Priorities, Procedure, SPDSY, ACMICD, Multiple Reaction Monitoring, T2SS-associated complexes, Anoxia, count in organism, Priority, survival, native protein, natural protein, Social Control, Protein, chemical analysis, Research Activities, MFS1, diapause, hCAP-G2, Library, WMS2, Research and Development, LUZP5, death rate, CAP-G2, Mycobacterium tuberculosis H37Rv, general secretion pathway-associated complex, Control, Hypoxemia, Regulons, MASS, Methodological, Understanding, Controls, Methodological Study, Activities, Protein Gene Products, plan specification, Gene Proteins, Deficiency, lethargus, SSKS, regulation, assay, Anoxemia, Regulation, Proteomes, Mycobacterium tuberculosis typus humanus"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"M.tuberculosis - Whole organism, absolute concentration (Schubertetal,cellhostmicrobe2014)","description":"abundance based on absolute concentration, Interaction consistency score: 1.0, Coverage: 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