{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/v07/MSV000094695/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Benjamin A. Garcia"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=ad61e18698b94367bf28d260abd69cc2"],"submitter_email":["bagarcia@wustl.edu"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["29"],"ptm_modification":["UNIMOD:21 - \"Phosphorylation.\"","UNIMOD:37 - \"Tri-Methylation.\"","UNIMOD:34 - \"Methylation.\"","UNIMOD:36 - \"Di-Methylation.\"","UNIMOD:1 - \"Acetylation.\""],"data_protocol":[""],"omics_type":["Proteomics"],"instrument_platform":["Orbitrap Exploris 240"],"species":["Homo Sapiens (ncbitaxon:9606)"],"submitter_affiliation":["Washington University School of Medicine in St. Louis"],"pubmed_abstract":["Histone post-translational modifications (PTMs) regulate gene expression patterns through epigenetic mechanisms. The five histone proteins (H1, H2A, H2B, H3, and H4) are extensively modified, with over 75 distinct modification types spanning more than 200 sites. Despite strong advances in mass spectrometry (MS)-based approaches, identification and quantification of modified histone peptides remains challenging because of factors, such as isobaric peptides, pseudo-isobaric PTMs, and low stoichiometry of certain marks. Here, we describe the development of a new high-throughput method to identify and quantify over 150 modified histone peptides by LC-MS. Fast gradient microflow liquid chromatography and variable window sequential windows acquisition of all theoretical spectra data-independent acquisition on a new quadrupole time-of-flight platform is compared to a previous method using nanoflow LC-MS on an Orbitrap hybrid. Histones extracted from cells treated with either a histone deacetylase inhibitor or transforming growth factor-beta 1 were analyzed by data-independent acquisition on two mass spectrometers: an Orbitrap Exploris 240 with a 55-min nanoflow LC gradient and the SCIEX ZenoTOF 7600 with a 10-min microflow gradient. To demonstrate the reproducibility and speed advantage of the method, 100 consecutive injections of one sample were performed in less than 2 days on the quadrupole time-of-flight platform. The result is the comprehensive characterization of histone PTMs achieved in less than 20 min of total run time using only 200 ng of sample. Results for drug-treated histone samples are comparable to those produced by the previous method and can be achieved using less than one-third of the instrument time.","Cocaine addiction is a chronic disorder in which the person loses control over drug use. The past memories of the stimuli associated with the drug are a relevant clinical problem, since they trigger compulsive drug-seeking and drug-taking habits. Furthermore, these persistent drug-related memories seemingly coexist with cognitive decline that predicts worse therapeutic output. Here, we use a new animal model of cocaine-altered cognition that allowed to observe these events in the same individual and study their relationship. Mice were chronically administered cocaine in a conditioned place preference (CPP) apparatus for 14 days, and control mice received saline. After 28 days of cocaine withdrawal, animals were tested for retrieval of remote drug-associated memory as well as for cognitive performance in a battery of tests, including novel object and place recognition and spatial memory. The cocaine-withdrawn mice showed persistent CPP memory while impaired in the cognitive tasks, displaying deficits in reference memory acquisition and working memory. However, the CPP expression was not associated with the defective cognitive performance, indicating that they were concomitant but independent occurrences. After completion of the experiment, adult hippocampal neurogenesis (AHN) was studied as a relevant neurobiological correlate due to its potential role in both learning and drug addiction. Results suggested a preserved basal AHN in the cocaine-withdrawn mice but an aberrant learning-induced regulation of these neurons. This paradigm may be useful to investigate maladaptive cognition in drug addiction as well as related therapies."],"pubmed_title":["Development of a High-Throughput Platform for Quantitation of Histone Modifications on a New QTOF Instrument.","Remote memory of drug experiences coexists with cognitive decline and abnormal adult neurogenesis in an animal model of cocaine-altered cognition."],"pubmed_authors":["Zahn Emily E, Xie Yixuan Y, Liu Xingyu X, Karki Rashmi R, Searfoss Richard M RM, de Luna Vitorino Francisca N FN, Lempiäinen Joanna K JK, Gongora Joanna J, Lin Zongtao Z, Zhao Chenfeng C, Yuan Zuo-Fei ZF, Garcia Benjamin A BA","Mañas-Padilla M Carmen MC, Gil-Rodríguez Sara S, Sampedro-Piquero Patricia P, Ávila-Gámiz Fabiola F, Rodríguez de Fonseca Fernando F, Santín Luis J LJ, Castilla-Ortega Estela E"],"pubmed_title_synonyms":["development, hardware., Histone Marks, Mark, instrument, Histone Modifications, Marks, Code, postnatal development, Modifications, instrument configuration, postnatal growth, HardwareType, growth and development, growth, Histone, Histone Mark"],"description_synonyms":["Post Translational Amino Acid Modification, Rps17, CDF, Meth, Product, HDAC Inhibitor, postnatal development, leg, Liquid Chromatography Mass Spectrometry, instrument configuration, RPS17, High Performance Liquid Chromatography Mass Spectrometry, growth and development, Ultra Performance Liquid Chromatography-Mass Spectrometry, Protein Processing, Long Term, High Performance Liquid Chromatography-Mass Spectrometry, l(1)AA33, M(3)67, Histone H2b, Polypeptides, Histone H2a, H2A|O, Techniques, M(3L)i, HPLC-MS, POF, peptido, Liquid Chromatography-Mass, Method, Pharmaceutical Product, 1, 2, Inhibitors, AGAMOUS-like 61, CG5499, Software Engineering, Analysis, h2afx, Injectables, Effect, WMS, Computer Program, HIS2AV, DiA, HDAC, Mass Spectrum Analysis, Post-Translational Protein, H2A|q, Ultra Performance Liquid Chromatography Mass Spectrometry, me75, Gene Expressions, l(2)k07135, peptides, Analyses, Post-Translational, M, l(3)67BDo, Open, min, Computer Programs and Programming, h2AvD, HIS2AVD, HardwareType, H2B.1, DIASP, Posttranslational Protein Processing, D17Mit170, T1, Fast, DIA, Dia, Epigenomic, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, l(3)05146, Methodological Studies, l(1)B2/13.1, Ice, RUN, Run, medicine, Liquid Chromatography-Mass Spectrometries, Pharmaceutical, sample, 38E.16, Histone H5, Histone H4, Deacetylase Inhibitors, Histone H7, D9, 2610009E16Rik, GPHYSD2, M(3)RpS17, Long-Term Effects, Histone H1, FAST, Histone H3, SGS, DmelCG5499, H2AX, H2AZ, Post-Translational Modification, l(1)LB9, HIST2H2AA, Modifications, Liquid Chromatography, M(3)67C, Longterm Effect, H2A.2, H2A, FASTK, H2BQ, H2B, Procedure, Tl3, Tl2, Spectrum Analysis, Source Softwares, H2Av, AA33, Software Tools, ACMICD, Programs, Spectroscopy, Program, Computer Applications, ms(2)04138, Desmoplastic infantile astrocytoma, Post Translational Modifications, M(3)i(55), Computer Applications Software, Computer Applications Softwares, H2A-GL101, Pharmaceutic, H2a, Softwares, H2b, H2AV, H2av, Crystal, l(3)810, ParaT, rpS17, Software Applications, instrument, Epigenetic, High Pressure Liquid Chromatography Mass Spectrometry, H2A.Z, Source Software, POF2, Processing, H2A.X, F27C12_24, Rp S17, H2a.V, F27C12.24, Spectrometry, h2a, Methodological, MASS, H2A/O, Methodological Study, Speed, sample., Applications, Amino Acid Modification, DIANA, Liquid, Posttranslational Modifications, Polypeptide, H2A/q, Epigenetics, GL105, Inhibitor, Posttranslational Modification, HISTONE 2B, Computer Software Applications, Hybrids, HISTONE H2B, CG1849, Post-Translational Protein Modifications, Procedures, Effects, STK10, Hist2av, FBN, Gene, gamma-His2Av, Spectrum Analyses, Computer, Chalk, hardware, Posttranslational, His2, method, M(3)S33, M(3)i, TOF, ECTOL1, Injection, method used in an experiment, DmelCG1768, Tina, Post Translational Modification, Gene Products, Mass, Studies, HILDA, Post-Translational Modifications, Low, Technique, Histone H3.3, Post Translational, Mass Spectroscopy, Application, Drugs, Modification, UPLC-MS, Open Source Softwares, Ultra-Performance Liquid Chromatography-Mass Spectrometry, H2A.F/Z, H2AV_DROM, gamma-HIS2AV, Glass, Longterm, Software Application, Runt, MRN17_11, HisH2Av, Open Source Software, Minute, Spectrometries, Long-Term, l(3)dtOA4, Expressions, Chimeras, Deacetylase Inhibitor, Computer Software Application, Protein Modifications, Hist, MRN17.11, OCTD, Post-Translational Amino Acid Modification, Study, Injectable, drugs, DmelCG3922, Tools, Posttranslational Amino Acid Modification, ATP:Fas-activated serine/threonine protein phosphotransferase activity, H2AvD, H2BFQ, M(3)i[55], Posttranslational Protein, HIS, His, peptidos, Long-Term Effect, Expression, DIA2, Preparation, Chromatography-Mass Spectrometries, LB5, Pharmaceuticals, Applications Software, Products, Open Source, cou, Computer Software, l(3)97Dd, H2avD, Desmoplastic astrocytoma of infancy, Proteins, DmelCG1849, Post-Translational Protein Modification, his, High Pressure Liquid Chromatography-Mass Spectrometry, CG1768, Rnt, Medications, DRF2, Histone, Peptide, Cell, Histone Deacetylase Inhibitor, Tool, lLB5, development, Software Tool, gamma-H2Av, MS, Lr, Hybrid, H2AFQ, Protein, H2AFO, H2BGL105, MLPLI, Long Term Effects, MFS1, BcDNA:RE44119, Dias, Protein Modification, Software, H2a-615, gammaH2Av, Mass Spectrum Analyses, WMS2, Mass Spectrum, l(3)L1602, Pharmaceutic Preparations, histone B2, Post Translational Protein Processing, Histone Deacetylase, M(3)q, postnatal growth, Engineering, His2AvD, l(1)19Ea, Histone H1(s), anon-EST:Posey48, sample population, Longterm Effects, CG3922, Protein Gene Products, plan specification, Drug, Computer Programs, P235, Gene Proteins, Preparations, Post Translational Protein Modification, 5499, Applications Softwares, His2AV, Chromatography-Mass Spectrometry, SSKS, Post-Translational Protein Processing, Bra, M(3L)i[55], LC-MS, Peptid, HDAC Inhibitors, Pharmaceutical Products, growth, Pharmaceutical Preparation"],"pubmed_abstract_synonyms":["Post Translational Amino Acid Modification, Meth, Product, HDAC Inhibitor, postnatal development, leg, Liquid Chromatography Mass Spectrometry, instrument configuration, Longterm., High Performance Liquid Chromatography Mass Spectrometry, DELTA AND GAMMA, growth and development, Ultra Performance Liquid Chromatography-Mass Spectrometry, betaTub1, Protein Processing, Long Term, High Performance Liquid Chromatography-Mass Spectrometry, A10, l(1)AA33, Histone H2b, Polypeptides, Histone H2a, H2A|O, Techniques, B1t, HPLC-MS, peptido, Liquid Chromatography-Mass, Method, Pharmaceutical Product, 1, 2, Inhibitors, Min, CG5499, Transforming, Analysis, 6-piperidinedione, h2afx, Injectables, Effect, WMS, HIS2AV, DmelCG42273, HDAC, Mass Spectrum Analysis, A 10, Post-Translational Protein, H2A|q, Ultra Performance Liquid Chromatography Mass Spectrometry, me75, Gene Expressions, kus, peptides, beta1tub, Analyses, CG9277, Post-Translational, min, h2AvD, HIS2AVD, T, beta-particle, HardwareType, H2B.1, mAPC, Posttranslational Protein Processing, D17Mit170, T1, Fast, DIA, antineoplaston-A10, 3-((phenylacetyl)amino)-2, Epigenomic, AI047805, l(3)05146, 1t, e, Methodological Studies, e-, beta1Tub, l(1)B2/13.1, Ice, RUN, Run, medicine, Liquid Chromatography-Mass Spectrometries, Pharmaceutical, sample, Histone H5, Histone H4, Deacetylase Inhibitors, Histone H7, 2610009E16Rik, GPHYSD2, Long-Term Effects, Histone H1, FAST, Histone H3, SGS, DmelCG5499, H2AX, H2AZ, Post-Translational Modification, BETA 56D, l(1)LB9, HIST2H2AA, Modifications, Liquid Chromatography, Dmel_CG7826, Longterm Effect, H2A.2, H2A, FASTK, H2BQ, H2B, Procedure, Tl3, Tl2, Spectrum Analysis, H2Av, AA33, Transforming Growth, ACMICD, Spectroscopy, 6-dioxo-3-piperidinyl)benzeneacetamide, Post Translational Modifications, l(1)G0108, Dm1, H2A-GL101, FLOWERING TIME CONTROL PROTEIN FCA ALPHA, Pharmaceutic, H2a, H2b, Dmel_CG7835, H2AV, H2av, Crystal, l(3)810, Mnb, MNB, ParaT, beta-tub, Factors, Beta <eudicots>, instrument, Epigenetic, High Pressure Liquid Chromatography Mass Spectrometry, H2A.Z, N-(2, Processing, H2A.X, H2a.V, Spectrometry, FCAALL.331, h2a, Methodological, MASS, beta56D, H2A/O, DmelCG9277, AW124434, Methodological Study, beta1-tub, beta(-), DTB2, Speed, beta-Tub, Amino Acid Modification, i6, DL4180C, transforming growth factors, Liquid, Posttranslational Modifications, Polypeptide, 3-(N-phenylacetylamino)-2, H2A/q, Epigenetics, beta-Tub56D, GL105, Inhibitor, Posttranslational Modification, betaTub, Specbeta, HISTONE 2B, beta1-Tubulin, Hybrids, Transforming Growth Factor, HISTONE H2B, CG1849, Post-Translational Protein Modifications, Procedures, Effects, STK10, e(-), Hist2av, FBN, Gene, gamma-His2Av, Spectrum Analyses, electron, Chalk, CG7826, hardware, Posttranslational, His2, method, Growth Factors, B-spec, TOF, ECTOL1, Injection, betaspec, method used in an experiment, Tina, Post Translational Modification, Gene Products, Mass, Studies, CG7835, CG42273, Post-Translational Modifications, Growth Factor, Low, A-10, Technique, Histone H3.3, Post Translational, Mass Spectroscopy, Drugs, Modification, UPLC-MS, Ultra-Performance Liquid Chromatography-Mass Spectrometry, H2A.F/Z, H2AV_DROM, gamma-HIS2AV, betatub(56D), Glass, Longterm, Runt, Elektron, MRN17_11, beta[[1]] tubulin, HisH2Av, beta1t, Spectrometries, Long-Term, Expressions, Chimeras, Deacetylase Inhibitor, Protein Modifications, Hist, MRN17.11, anon-EST:fe1B3, OCTD, Post-Translational Amino Acid Modification, Study, Injectable, drugs, Posttranslational Amino Acid Modification, ATP:Fas-activated serine/threonine protein phosphotransferase activity, SPEC8, H2AvD, H2BFQ, Posttranslational Protein, HIS, His, peptidos, Long-Term Effect, Expression, CG5870, Preparation, Chromatography-Mass Spectrometries, LB5, Pharmaceuticals, beta-tubulin56D, Spec-beta, Products, Dmbeta1, DYRK1, cou, l(3)97Dd, H2avD, drug, Proteins, DmelCG1849, Post-Translational Protein Modification, his, Tubulin, High Pressure Liquid Chromatography-Mass Spectrometry, Factor, Rnt, i168, Histone, Peptide, Cell, Histone Deacetylase Inhibitor, Animal growth regulators, lLB5, development, gamma-H2Av, MS, Lr, Hybrid, H2AFQ, Protein, H2AFO, H2BGL105, Long Term Effects, betaSpec, MFS1, Dyrk1, Protein Modification, b-Spec, H2a-615, gammaH2Av, Mass Spectrum Analyses, WMS2, AU020952, Mass Spectrum, DmelCG5870, l(1)G0074, l(1)G0198, l(3)L1602, negatron, Pharmaceutic Preparations, histone B2, beta[[1]]-tubulin, Post Translational Protein Processing, Histone Deacetylase, CC1, postnatal growth, b spectrin, beta1, His2AvD, l(1)19Ea, Histone H1(s), sample population, beta, Longterm Effects, ME-IV, Protein Gene Products, plan specification, Tub, Drug, P235, Gene Proteins, Preparations, Post Translational Protein Modification, 5499, beta-spec, His2AV, Chromatography-Mass Spectrometry, SSKS, Post-Translational Protein Processing, BETA, Bra, LC-MS, Peptid, HDAC Inhibitors, Pharmaceutical Products, growth, Spec, Pharmaceutical Preparation"],"name_synonyms":["rpS17, hardware., Rps17, Mark, instrument, Marks, M, postnatal development, l(3)67BDo, M(3)q, Rp S17, Modifications, instrument configuration, postnatal growth, M(3)67C, RPS17, min, Minute, HardwareType, growth and development, l(3)dtOA4, anon-EST:Posey48, Histone, CG3922, development, M(3)67, M(3L)i, M(3)S33, M(3)i, DmelCG3922, Histone Marks, M(3)i(55), Histone Modifications, Code, M(3)i[55], M(3L)i[55], BcDNA:RE44119, D9, growth, M(3)RpS17, Histone Mark"],"additional_accession":["PXD052028"]},"is_claimable":false,"name":"Development of a high-throughput (10 minute microflow gradient) platform for quantitation of histone modifications on a new QTOF instrument ","description":"Histone post-translational modifications (PTMs) regulate gene expression patterns through epigenetic mechanisms. The 5 histone proteins (H1, H2A, H2B, H3, and H4) are extensively modified, with over 75 distinct modification types spanning more than 200 sites. Despite strong advances in mass spectrometry based approaches, identification and quantification of modified histone peptides remains challenging due to factors such as isobaric peptides, pseudo-isobaric PTMs, and low stoichiometry of certain marks. Here we describe the development of a new high-throughput method to identify and quantitate over 150 modified histone peptides by liquid chromatography-mass spectrometry (LC-MS). Fast gradient microflow liquid chromatography and variable window SWATH data-independent acquisition on a new quadrupole time-of-flight platform is compared to a previous method using nanoflow LC-MS on an Orbitrap hybrid instrument. Histones extracted from cells treated with either a histone deacetylase inhibitor (HDACi) or TGF-beta 1 were analyzed by data-independent acquisition (DIA) on two mass spectrometers: an Orbitrap Exploris 240 with a 55 minute nanoflow LC gradient, and the SCIEX ZenoTOF 7600 with 5 and 10 minute microflow gradients, with data analyzed using newly developed in-house software. To demonstrate the reproducibility and speed advantage of the method, 100 consecutive injections of one sample were performed in less than 2 days on the QTOF platform. The result is the comprehensive characterization of histone PTMs achieved in less than 20 minutes of total run time using only 200 ng of sample. Results for histone PTMs extracted from cells treated with epigenetic drugs or undergoing cellular transformation are comparable to those produced by the previous method, but can be achieved using less than one-third of the instrument time and one-fifth of the sample amount.","dates":{"publication":"Mon May 06 14:26:00 BST 2024"},"accession":"MSV000094695","cross_references":{"pubmed":["39708910"]}}