{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/x01/MSV000081828/"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":1,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Lukas Reiter"],"instrument_platform":["Q Exactive"],"species":["Homo Sapiens (ncbitaxon:9606)"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=1fe231ef000c4fa9b6f964e0186aecd7"],"submitter_email":["reiter@biognosys.ch"],"submitter_affiliation":["Research and Development"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["163"],"ptm_modification":["UNIMOD:4 - \"Iodoacetamide derivative.\"","UNIMOD:1 - \"Acetylation.\"","UNIMOD:35 - \"Oxidation or Hydroxylation.\""],"data_protocol":[""],"pubmed_abstract":["The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with the reproducibility and precision of selected reaction monitoring. Here, we evaluate, whether SWATH-MS type DIA effectively translates into a better protein profiling as compared with the established shotgun proteomics. We implemented a novel DIA method on the widely used Orbitrap platform and used retention-time-normalized (iRT) spectral libraries for targeted data extraction using Spectronaut. We call this combination hyper reaction monitoring (HRM). Using a controlled sample set, we show that HRM outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins. The reproducibility of HRM in peptide detection was above 98%, resulting in quasi complete data sets compared with 49% of shotgun proteomics. Utilizing HRM, we profiled acetaminophen (APAP)(1)-treated three-dimensional human liver microtissues. An early onset of relevant proteome changes was revealed at subtoxic doses of APAP. Further, we detected and quantified for the first time human NAPQI-protein adducts that might be relevant for the toxicity of APAP. The adducts were identified on four mitochondrial oxidative stress related proteins (GATM, PARK7, PRDX6, and VDAC2) and two other proteins (ANXA2 and FTCD). Our findings imply that DIA should be the preferred method for quantitative protein profiling."],"pubmed_title":["Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues."],"pubmed_authors":["Bruderer Roland R, Bernhardt Oliver M OM, Gandhi Tejas T, Miladinović Saša M SM, Cheng Lin-Yang LY, Messner Simon S, Ehrenberger Tobias T, Zanotelli Vito V, Butscheid Yulia Y, Escher Claudia C, Vitek Olga O, Rinner Oliver O, Reiter Lukas L"],"name_synonyms":["APAP, Acamol, Acenol, acetaminophene, p-acetaminophenol, Panadol, Tylenol, 4'-hydroxyacetanilide, Acetamidophenol, 4-(Acetylamino)phenol, number, Paracetamol, Acetaminofen, total expressed protein, N-acetyl-p-aminophenol, Acetaco, p-hydroxyacetanilide, paracetamol, presence, p-Acetylaminophenol, jecur, iecur., Livers, Anacin 3, count in organism, p-Hydroxyacetanilide, Acetominophen, p-acetamidophenol, acetaminofen, N-(4-hydroxyphenyl)-, p-Acetamidophenol, Datril, Hydroxyacetanilide, Acetamide, Acephen, N-(4-Hydroxyphenyl)acetanilide, Anacin3, 4-acetamidophenol, p-hydroxyphenolacetamide, Acetaminophen, Proteomes, Algotropyl, paracetamolum, N-Acetyl-p-aminophenol, Anacin-3"],"description_synonyms":["MGC130048, CDF, human being, SGCG_HUMAN, Data Set, 35 kDa dystrophin-associated glycoprotein, Peptidomics, Desmoplastic astrocytoma of infancy, Modern, SG-gamma, A4, CG1768, DRF2, TYPE, SGCG, LGMD2C, Human, jecur, DAGA4, ms(2)04138, Desmoplastic infantile astrocytoma, POF, Homo sapiens, DmelCG1768, MLPLI, 35DAG, HILDA, sarcoglycan, AGAMOUS-like 61, Dias, MAM, gamma-SG, SCG3, Man, DiA, gamma sarcoglycan, l(2)k07135, Man (Taxonomy), DMDA1, POF2, F27C12_24, F27C12.24, DIASP, gamma (35kDa dystrophin-associated glycoprotein), DIA, Dia, human, iecur., 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, Livers, DMDA, 35kD dystrophin-associated glycoprotein, Modern Man, SCARMD2, DIANA, 38E.16, gamma-sarcoglycan, DIA2, humans"],"pubmed_title_synonyms":["APAP, Acamol, Acenol, acetaminophene, p-acetaminophenol, Panadol, Tylenol, 4'-hydroxyacetanilide, Acetamidophenol, 4-(Acetylamino)phenol, Paracetamol, Acetaminofen, total expressed protein, N-acetyl-p-aminophenol, Acetaco, p-hydroxyacetanilide, paracetamol, DIA, p-Acetylaminophenol, jecur, iecur., Livers, Anacin 3, p-Hydroxyacetanilide, Acetominophen, p-acetamidophenol, acetaminofen, N-(4-hydroxyphenyl)-, p-Acetamidophenol, Datril, Hydroxyacetanilide, Acetamide, Acephen, N-(4-Hydroxyphenyl)acetanilide, Anacin3, 4-acetamidophenol, p-hydroxyphenolacetamide, Acetaminophen, Proteomes, Algotropyl, paracetamolum, N-Acetyl-p-aminophenol, Anacin-3"],"pubmed_abstract_synonyms":["DNA Oxidative, MGC130048, CDF, IPP2A2, acetaminophene, p-acetaminophenol, N-acetyl-4-benzoquinoneimine, A4, Nitrative Stress, SBBI10, protein, Brp-12, Damage, Long Term, 5730420M11Rik, peptide, Formiminotransferase-cyclodeaminase, Polypeptides, Prdx5, Techniques, protein polypeptide chains, p-acetamidophenol, POF, peptido, Hydroxyacetanilide, Oxidative DNA, Oxidative, Method, Vdac6, Nitro-Oxidative Stress, N-(4-Hydroxyphenyl)acetanilide, symptoms, ANX2L4, POR, p-hydroxyphenolacetamide, 3, AT, AGAMOUS-like 61, pulmonary alveolar lipoproteinosis acquired, Nitro-Oxidative Stresses, protein aggregate, Oxidative Injury, Fs(3)Hor, 1-Cys Prx, Effect, DNA Damage, WMS, LIP2, DiA, gamma sarcoglycan, SET, Oxidative Injuries, DmelCG2684, mVDAC6, aiPLA2, l(2)k07135, Man (Taxonomy), reference sample, peptides, mVDAC2, Dj1, TAF-I, 4'-hydroxyacetanilide, oncogene DJ1, HEL-S-67p, Acetamidophenol, Oxidative Cleavage, Paracetamol, Acetaminofen, N-acetyl-p-aminophenol, iecur, Age of onset, proteins, DIASP, NTef2, Oxidative DNA Damages, Prdx6, DIA, Dia, Anti-oxidative, retention, DmelCG4299, Ltw4, 9430088D19Rik, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, reaction, IGAAD, set, Oxidative Stress Injuries, mKIAA0106, Oxidative Stresses, Methodological Studies, DmelCG10574, DJ1, sample, PRDX6, 38E.16, HEL-S-128m, Glutamate formyltransferase, gamma-sarcoglycan, pulmonary alveolar lipoproteinosis, Lvtw-4, ORF06, GPHYSD2, Long-Term Effects, pulmonary alveolar proteinosis acquired, SGS, Pap, PAP, APAP, phapii, screening, Panadol, DJ-1, AOP2, Modern, Aop2, SG-gamma, Longterm Effect, StF-IT-1, PRX, Procedure, Formiminotetrahydrofolate cyclodeaminase, acquired, Fs(3)Sz11, ACMICD, Multiple Reaction Monitoring, CAP1, prx-V, Aop2-rs3, ms(2)04138, autoimmune, Desmoplastic infantile astrocytoma, PRXV, PrxV, AOEB166, ATP synthase D chain, Oxidative and Nitrosative Stress, Acephen, GPx, margin of safety, AOPP, P36, sarcoglycan, DNA Oxidative Damages, p29, NSGPx, CC26, Acamol, Mitochondrial, HLA-DR-associated protein II, DI-2, CP-3, POF2, I-2Dm, F27C12_24, F27C12.24, signs, MASS, Methodological, CG4299, gamma (35kDa dystrophin-associated glycoprotein), Methodological Study, paracetamol, human, early, park7a, I-2PP1, Nitro-Oxidative, DMDA, TAF-IBETA, Glutamate formiminotransferase, Prdx6-rs3, 35kD dystrophin-associated glycoprotein, Acetamide, Horka, DIANA, CG2684, LPC2, Fs(3)Horka, Oxidative Stress Injury, AW215814, TAF-Ibeta, acquired pulmonary alveolar proteinosis, Polypeptide, DNA, Glutamate formimidoyltransferase, i2pp2a, Proteomes, humans, Oxidative Damage, Oxidative Stress, Acenol, human being, PAP-IV, SGCG_HUMAN, Procedures, HEL-S-270, Tylenol, Peptidomics, Effects, PARK7, Antioxidative, thioredoxin reductase, pulmonary alveolar proteinosis autoimmune, FBN, Antioxidative Stress, Gene, protein-containing complex, mitochondrial, TYPE, PHAPII, Human, jecur, Stresses, DAGA4, method, PAP acquired, Oxidative Nitrative, polypeptide chain, Homo sapiens, Stress Injury, ECTOL1, DmelCG1768, method used in an experiment, 35DAG, HILDA, Studies, Gene Products, Oxidative Cleavages, B166, Acetaminophen, DmF2, MAM, gamma-SG, SCG3, Technique, Algotropyl, Man, Oxidative Damages, lod, Injury, MRM, parkinson disease protein 7 homolog, NSGP, Longterm, AA690119, 4-(Acetylamino)phenol, ipp2a2, 2pp2a, Acetaco, Long-Term, Cal1h, N-acetyl-p-benzoquinoneimine, CG10574, p-Acetylaminophenol, OCTD, protein DJ-1, Study, p-Hydroxyacetanilide, 4.3.1.4, acetaminofen, NABQ, 2PP2A, Anti oxidative Stress, taf-ibeta, Oxidative DNA Damage, Antioxidative Stresses, pulmonary alveolar proteinosis, dSET, dSet, peptidos, Long-Term Effect, toxic potential, DIA2, SP22, Controlled, Anacin-3, Gene., Controlling, LPC2D, findings, 35 kDa dystrophin-associated glycoprotein, 5-(14)C-labeled cpd, protein complex, FTCD, Desmoplastic astrocytoma of infancy, Proteins, igaad, total expressed protein, CG1768, p-hydroxyacetanilide, Anti-oxidative Stresses, DRF2, Peptide, SGCG, LGMD2C, group, polypeptide, Oxidative Nitrative Stress, native protein, N-(4-hydroxyphenyl)-, p-Acetamidophenol, Datril, natural protein, I-2PP2A, CAL1H, Oxidative Nitrative Stresses, MLPLI, Protein, Long Term Effects, Dm I-2, I2PP2A, Anacin3, 4-acetamidophenol, N-acetyl-4-benzoquinone imine, MFS1, 1-cysPrx, Dias, Library, NAPQI, WMS2, N-Acetyl-p-aminophenol, 2.1.2.5, protein/nucleic acid deglycase DJ-1, 1-Cys, Anti-oxidative Stress, DMDA1, ensemble, DNA Oxidative Damage, storage, HEL-S-55, Formimidoyltetrahydrofolate cyclodeaminase, maillard deglycase, parkinsonism-associated deglycase, Ltw-4, PLP, Age symptoms begin, Cleavage, ANX2, Lds, sample population, Longterm Effects, ACR1, plan specification, Protein Gene Products, Gene Proteins, Livers, dSET/TAF-Ibeta, Anacin 3, 2610030F17Rik, Acetominophen, Pmp20, Modern Man, SSKS, SCARMD2, Stress, AI314789, 1810003P21Rik, KIAA0106, Peptid, sequestering, AA407739, Nitro Oxidative Stress, PMP20, paracetamolum"],"citation_count":["1"],"additional_accession":[]},"is_claimable":true,"name":"PASS00589 - Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues","description":"The data set repersents a fair comparison of shotgun proteomics with HRM (swath type DIA). Additionally, a human liver microtissue was profiled with HRM.","dates":{"publication":"Tue Dec 19 10:10:00 GMT 2017"},"accession":"MSV000081828","cross_references":{"pubmed":["25724911"]}}