{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/v01/MSV000078831/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Thomas Neubert"],"instrument_platform":["Q Exactive"],"species":["Homo Sapiens (ncbitaxon:9606)"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=f80fc3ba51f54b0e815ac085eb50ce0c"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["166"],"data_protocol":[""],"pubmed_abstract":["Measuring the synthesis of new proteins in the context of a much greater number of pre-existing proteins can be difficult. To overcome this obstacle, bioorthogonal noncanonical amino acid tagging (BONCAT) can be combined with stable isotope labeling by amino acid in cell culture (SILAC) for comparative proteomic analysis of de novo protein synthesis (BONLAC). In the present study, we show that alkyne resin-based isolation of l-azidohomoalanine (AHA)-labeled proteins using azide/alkyne cycloaddition minimizes contamination from pre-existing proteins. Using this approach, we isolated and identified 7414 BONCAT-labeled proteins. The nascent proteome isolated by BONCAT was very similar to the steady-state proteome, although transcription factors were highly enriched by BONCAT. About 30% of the methionine residues were replaced by AHA in our BONCAT samples, which allowed for identification of methionine-containing peptides. There was no bias against low-methionine proteins by BONCAT at the proteome level. When we applied the BONLAC approach to screen for brain-derived neurotrophic factor (BDNF)-induced protein synthesis, 53 proteins were found to be significantly changed 2 h after BDNF stimulation. Our study demonstrated that the newly synthesized proteome, even after a short period of stimulation, can be efficiently isolated by BONCAT and analyzed to a depth that is similar to that of the steady-state proteome."],"pubmed_title":["In-depth quantitative proteomic analysis of de novo protein synthesis induced by brain-derived neurotrophic factor."],"pubmed_authors":["Zhang Guoan G, Bowling Heather H, Hom Nancy N, Kirshenbaum Kent K, Klann Eric E, Chao Moses V MV, Neubert Thomas A TA"],"description_synonyms":["protein translation, Brain Derived Neurotrophic Factor, count in organism, protein anabolism, abrineurin, Brain-Derived, protein biosynthetic process, protein synthesis, Brain-Derived Neurotrophic, proteomic analysis, protein formation, number, protein biosynthesis, BDNF., Factor, presence, Neurotrophic Factor"],"pubmed_title_synonyms":["protein translation, Brain Derived Neurotrophic Factor, count in organism, protein anabolism, abrineurin, Brain-Derived, protein biosynthetic process, protein synthesis, Brain-Derived Neurotrophic, proteomic analysis, protein formation, number, protein biosynthesis, BDNF., Factor, presence, Neurotrophic Factor"],"name_synonyms":["Eph-like tyrosine kinase 1, Brain Derived Neurotrophic Factor, EK4, bdnf, ETK1, hEK4, Factor, proBDNF, brain-derived neurotrophic factor, ANON2, abrineurin, BDNF, Brain-Derived, 2.7.10.1, HEK4, Brain-Derived Neurotrophic, HEK, EPH-like kinase 4, Cell., BULN2, Abrineurin, Human embryo kinase, Tyrosine-protein kinase receptor ETK1, TYRO4, Neurotrophic Factor, ETK, Tyrosine-protein kinase TYRO4"],"pubmed_abstract_synonyms":["protein translation, Scientific Bias, PhrB photolyase activity, Aminosaeure, Amino acid, pigmented epithelium, Polypeptides, L-Isomer Methionine, Methionine, peptido, Epidemiologic Biase, 3, Ecological, NUP96, epithelium, Neurotrophic Factor, Isotopically-Coded Affinity Tagging, multicellular organismal biosynthetic process, Ecological Biases, single-organism biosynthetic process, me75, amino acids, peptides, anabolism, M, pigmented retina, purification, D17Mit170, DNA cyclobutane dipyrimidine photolyase activity, T1, SUPPRESSOR OF AUXIN RESISTANCE 3, isolation and purification, Statistical Biases, scientific observation, Ecological Bias, BULN2, Systematic, Tagging, Epidemiologic Biases, Racemethionine, Stable Isotope Labeling, Azide, PRE, Brain Derived Neurotrophic Factor, protein anabolism, protein biosynthetic process, Scientific, Aminokarbonsaeure, Epidemiologic, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, 2-Amino-4-(methylthio)butyric acid, Ecological Fallacies, Tl3, Tl2, alpha-amino carboxylic acids, Outcome Measurement Errors, shortened, Menstruation, Experimental, retinal pigment, anemia, Proteomes., protein formation, dipyrimidine photolyase (photosensitive), Methionin, autoimmune hemolytic, Hmet, Truncation Bias, retinal pigment layer, Culture Technique, Amino Acid, Acid, Bias, Factors, Amino acids, idiopathic autoimmune hemolytic anaemia, Outcome Measurement, proBDNF, Experimental Bias, Outcome Measurement Error, phr A photolyase activity, abrineurin, DNA-photoreactivating enzyme, anaemia hemolytic autoimmune, protein synthesis, Cell Cultures, Acids, Polypeptide, immuno-hemolytic anaemia, short, Liquimeth, Proteomes, 2-amino-4-(methylsulfanyl)butanoic acid, anemia hemolytic autoimmune, Ecological Fallacy, Truncation, number, Aminocarbonsaeure, L Isomer, Gene, Systematic Bias, biosynthesis, alpha-amino acid, photoreactivating enzyme activity, Isotope-Coded Affinity, Transcription Factor, brain-derived neurotrophic factor, isolation, idiopathic autoimmune hemolytic anemia, Brain-Derived Neurotrophic, familial auto-immune hemolytic anemia (subtype), Gene Products, L-Methionine, stratum pigmentosa retinae, Low, Isotopically-Coded Affinity, Cell Culture, Pedameth, Fallacies, study, Transcription, MOS3, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, PRECOCIOUS, formation, Aggregation, F23A5.3, stubby, bdnf, acquired autoimmune hemolytic anemia, Cell Culture Technique, ANON2, synthesis, azido homoalanine, BDNF, 2-amino-4-(methylthio)butanoic acid, Stable, immuno-hemolytic anemia, Isotope-Coded Affinity Tagging, peptidos, metionina, F23A5_3, Alkyne, Biase, measuring, Fallacy, Culture Techniques, cou, DL-Methionine, synthesize, Proteins, total expressed protein, Truncation Biases, alpha-amino acids, Factor, L-Isomer, Labeling, Cell, Peptide, Isotope, MODIFIER OF SNC1, Lr, Brain-Derived, Period, Stable Isotope, Protein, deoxyribonucleic photolyase activity, proteomic analysis, Errors, protein biosynthesis, familial auto-immune hemolytic anaemia (subtype), Acetylenes, Isotope Coded Affinity Tagging, Acetylenic Compounds, Met, RPE, photolyase activity, acquired autoimmune hemolytic anaemia, Biases, Isotope Labeling, Amino, Affinity Tagging, Isotopically-Coded, p. pigmentosa retinae, Protein Gene Products, Gene Proteins, Error, Aggregation Bias, cardinality, Statistical Bias, alpha-amino-gamma-methylmercaptobutyric acid, Bra, Isotope-Coded, Peptid, deoxyribonucleate pyrimidine dimer lyase (photosensitive), Abrineurin, Statistical"],"citation_count":["0"],"additional_accession":[]},"is_claimable":true,"name":"BDNF BONLAC in HEK cells","description":"In-depth Quantitative Proteomic Analysis of De Novo Protein Synthesis Induced by Brain-derived Neurotrophic Factor","dates":{"publication":"Tue Aug 26 09:33:00 BST 2014"},"accession":"MSV000078831","cross_references":{"pubmed":["25271054"]}}