{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/x01/MSV000084859/"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":3,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"submitter":["Lukas Reiter"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=64942c4e1f7b46b695703bc0683a70b7"],"submitter_email":["lukas.reiter@biognosys.com"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["107"],"ptm_modification":["MOD:00397 - \"A protein modification that is produced by reaction with iodoacetamide, usually replacement of a reactive hydrogen with a methylcarboxamido group.\"","MOD:00425 - \"A protein modification that effectively replaces one hydrogen atom with a hydroxyl group.\"","MOD:00394 - \"A protein modification that effectively replaces a hydrogen atom with an acetyl group.\""],"data_protocol":[""],"omics_type":["Proteomics"],"instrument_platform":["Orbitrap Fusion Lumos"],"species":["Mus Musculus (ncbitaxon:10090)"],"submitter_affiliation":["Biognosys AG"],"pubmed_abstract":["Label-free quantification (LFQ) and isobaric labeling quantification (ILQ) are among the most popular protein quantification workflows in discovery proteomics. Here, we compared the TMT SPS/MS3 10-plex workflow to a label free single shot data-independent acquisition (DIA) workflow on a controlled sample set. The sample set consisted of ten samples derived from 10 biological replicates of mouse cerebelli spiked with the UPS2 protein standard in five different concentrations. For a fair comparison, we matched the instrument time for the two workflows. The LC-MS data were acquired at two facilities to assess interlaboratory reproducibility. Both methods resulted in a high proteome coverage (>5000 proteins) with low missing values on protein level (<2%). The TMT workflow led to 15-20% more identified proteins and a slightly better quantitative precision, whereas the quantitative accuracy was better for the DIA method. The quantitative performance was benchmarked by the number of true positives (UPS2 proteins) within the top 100 candidates. TMT and DIA showed a similar performance. The quantitative performance of the DIA data stayed in a similar range when searching the spectra against a fasta database directly, instead of using a project-specific library. Our experiments also demonstrated that both workflows are readily transferrable between facilities."],"pubmed_title":["Comparison of Protein Quantification in a Complex Background by DIA and TMT Workflows with Fixed Instrument Time."],"pubmed_authors":["Muntel Jan J, Kirkpatrick Joanna J, Bruderer Roland R, Huang Ting T, Huang Ting T, Vitek Olga O, Ori Alessandro A, Reiter Lukas L"],"pubmed_abstract_synonyms":["l(2)k04204, CDF, IPP2A2, Product, Laboratory, Mus domesticus, instrument configuration, Liquid Chromatography Mass Spectrometry, High Performance Liquid Chromatography Mass Spectrometry, LFQ, protein, 6330543G17Rik, Ultra Performance Liquid Chromatography-Mass Spectrometry, progressive encephalomyelitis with rigidity, House Mouse, Long Term, High Performance Liquid Chromatography-Mass Spectrometry, ischiocoxopodopatellar syndrome, 5730420M11Rik, Morsch Woltman syndrome, DmelCG11081, protein polypeptide chains, Techniques, POF, HPLC-MS, AW111620, Liquid Chromatography-Mass, Biological, Method, DPlexA, congenital coxa vara, sucrose phosphate synthetase activity, Work Flows., AGAMOUS-like 61, Biological Product, protein aggregate, Work Flow, Effect, tarsal synostosis, DiA, AI505014, SET, Ultra Performance Liquid Chromatography Mass Spectrometry, me75, l(2)k07135, Biologic Drugs, reference sample, TAF-I, Natural, UDP-glucose-fructose-phosphate glucosyltransferase activity, Su(Mir)1, HardwareType, Swiss Mice, proteins, procedures, DIASP, Biological Drugs, CG17245, D17Mit170, DIA, Dia, T1, DmelCG4299, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, IGAAD, set, Biological Medicine, Methodological Studies, DmelCG10574, Liquid Chromatography-Mass Spectrometries, sample, 38E.16, Medicine, l(2)CA4, Medicines, house mouse, Biologic Drug, Prx3, Long-Term Effects, AA589574, 1110046B24Rik, sucrose phosphate-uridine diphosphate glucosyltransferase activity, phapii, Biologic Products, mouse, Longterm Effect, StF-IT-1, Procedure, Tl3, Tl2, not genetically inherited, shortstop/kakapo, TPSG1, ms(2)04138, Workflows, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Desmoplastic infantile astrocytoma, Biopharmaceuticals, DmelCG18076, Biologic Product, PlexA1, uridine diphosphoglucose-fructose phosphate glucosyltransferase activity, BcDNA:GM05237, Mus musculus, HLA-DR-associated protein II, PlexB, Grv, DI-2, instrument, PlexA, Biological Medicines, High Pressure Liquid Chromatography Mass Spectrometry, mice, POF2, I-2Dm, Biological Drug, F27C12_24, F27C12.24, Swiss Mouse, Spectrometry, Biologics, CG4299, Methodological, Plex1, Methodological Study, SHOT, ICPPS, domesticus, MRSR, I-2PP1, TAF-IBETA, grv, label, PRSS31, DIANA, Liquid, TAF-Ibeta, Mouse, MSF1, PLEXB, TMT, i2pp2a, 42/4, Proteomes, Work Flows, OG12X, sucrose 6-phosphate synthase activity, Procedures, Biologic Pharmaceuticals, Peptidomics, Effects, Stiff-trunk syndrome, Gene, MSF1', CG11081, protein-containing complex, PHAPII, GEP1, hardware, l(2)k05821, method, UDPglucose-fructose-phosphate glucosyltransferase activity, polypeptide chain, l(2)k15606, UDP-glucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity, House, DmelCG1768, method used in an experiment, Gene Products, HILDA, Studies, Mus musculus domesticus, Coxo-podo-patellar syndrome, D-Plex A, Low, SMS, Mice, Technique, Shot, Biologicals, Drugs, SPMSY, UPLC-MS, patella aplasia, Ultra-Performance Liquid Chromatography-Mass Spectrometry, l(2)k10821, sucrosephosphate-UDP glucosyltransferase activity, Longterm, MS3, Swiss, plex A, ipp2a2, plex B, Natural Product, 2pp2a, Spectrometries, labeling, Long-Term, CG10574, DmelCG17245, Study, UDPglucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity, 2PP2A, taf-ibeta, SELD, dSET, dSet, Long-Term Effect, DIA2, SpS, Chromatography-Mass Spectrometries, thiol methyltransferase activity, SPS1, Biologic, Controlled, Pharmaceuticals, coxa vara, Stiff person syndrome and related disorders, Products, Controlling, STIFF-PERSON syndrome, cou, protein complex, Biologic Medicines, kop, Desmoplastic astrocytoma of infancy, Proteins, igaad, CG18076, total expressed protein, SPS, High Pressure Liquid Chromatography-Mass Spectrometry, CG1768, CG18637, DRF2, plex, group, Lr, native protein, natural protein, I-2PP2A, Mus, Protein, MLPLI, Dm I-2, Long Term Effects, I2PP2A, Biopharmaceutical, techniques, Dias, Library, Data Base, Stiff-Man syndrome, l(2)k05434, ensemble, l(2)k03010, kak, SRS, House Mice, OG12, sample population, Longterm Effects, Laboratory Mice, Protein Gene Products, Drug, plan specification, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, Chromatography-Mass Spectrometry, Bra, Natural Products, LC-MS, AIM30, patella aplasia and tarsal synostosis, Og12x, AA407739, Laboratory Mouse, methodology"],"name_synonyms":["CDF, l(2)k07135, protein complex, POF2, F27C12_24, Desmoplastic astrocytoma of infancy, Proteins, F27C12.24, introduction., Gene, proteins, protein, CG1768, DIASP, DRF2, protein-containing complex, DIA, Dia, Protein Gene Products, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, Gene Proteins, ms(2)04138, TPSG1, protein polypeptide chains, Desmoplastic infantile astrocytoma, S-adenosyl-L-methionine:thiol S-methyltransferase activity, POF, native protein, natural protein, polypeptide chain, DmelCG1768, MLPLI, PRSS31, Protein, DIANA, 38E.16, HILDA, Gene Products, AGAMOUS-like 61, DIA2, background, Dias, protein aggregate, TMT, DiA, thiol methyltransferase activity"],"pubmed_title_synonyms":["CDF, Effects, protein complex, Desmoplastic astrocytoma of infancy, Proteins, instrument configuration, Longterm., Longterm Effect, Gene, protein, CG1768, protein-containing complex, DRF2, Long Term, hardware, protein polypeptide chains, ms(2)04138, TPSG1, Desmoplastic infantile astrocytoma, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Workflows, POF, native protein, natural protein, polypeptide chain, DmelCG1768, Protein, MLPLI, Long Term Effects, Gene Products, HILDA, AGAMOUS-like 61, Dias, protein aggregate, Work Flow, Effect, DiA, l(2)k07135, instrument, Longterm, POF2, F27C12_24, F27C12.24, HardwareType, proteins, Long-Term, DIASP, DIA, Dia, Longterm Effects, Protein Gene Products, Gene Proteins, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, PRSS31, DIANA, 38E.16, Long-Term Effect, DIA2, TMT, Long-Term Effects, Work Flows, thiol methyltransferase activity"],"description_synonyms":["l(2)k04204, CDF, IPP2A2, OG12X, Procedures, Peptidomics, Laboratory, Effects, Mus domesticus, instrument configuration, number, Gene, MSF1', protein, 6330543G17Rik, protein-containing complex, House Mouse, presence, PHAPII, GEP1, Long Term, hardware, l(2)k05821, 5730420M11Rik, protein polypeptide chains, method, Techniques, POF, polypeptide chain, l(2)k15606, House, Method, DmelCG1768, method used in an experiment, Gene Products, HILDA, Studies, Mus musculus domesticus, AGAMOUS-like 61, Low, protein aggregate, Work Flow, methodology., Mice, Effect, Technique, Shot, DiA, SET, me75, l(2)k10821, l(2)k07135, reference sample, TAF-I, Longterm, Swiss, ipp2a2, Su(Mir)1, 2pp2a, HardwareType, Swiss Mice, labeling, proteins, procedures, Long-Term, DIASP, free, D17Mit170, DIA, Dia, CG10574, T1, DmelCG4299, Study, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, IGAAD, set, 2PP2A, Methodological Studies, DmelCG10574, taf-ibeta, sample, 38E.16, dSET, dSet, l(2)CA4, Long-Term Effect, DIA2, house mouse, Prx3, Long-Term Effects, thiol methyltransferase activity, Controlled, phapii, Controlling, cou, protein complex, kop, Desmoplastic astrocytoma of infancy, Proteins, igaad, mouse, CG18076, Longterm Effect, StF-IT-1, total expressed protein, CG1768, CG18637, Procedure, DRF2, Tl3, Tl2, not genetically inherited, shortstop/kakapo, group, TPSG1, ms(2)04138, count in organism, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Workflows, Desmoplastic infantile astrocytoma, Lr, native protein, natural protein, I-2PP2A, Mus, DmelCG18076, Protein, MLPLI, Dm I-2, Long Term Effects, I2PP2A, laboratory, techniques, Dias, Library, Data Base, Mus musculus, l(2)k05434, HLA-DR-associated protein II, Grv, ensemble, DI-2, instrument, mice, l(2)k03010, POF2, I-2Dm, F27C12_24, F27C12.24, Swiss Mouse, kak, House Mice, Methodological, CG4299, Methodological Study, SHOT, OG12, sample population, Longterm Effects, domesticus, Laboratory Mice, Protein Gene Products, plan specification, I-2PP1, Gene Proteins, dSET/TAF-Ibeta, 2610030F17Rik, TAF-IBETA, grv, label, PRSS31, cardinality, DIANA, Bra, TAF-Ibeta, Mouse, AIM30, MSF1, Og12x, AA407739, TMT, i2pp2a, 42/4, Laboratory Mouse, Proteomes, Work Flows, methodology"],"citation_count":["3"],"additional_accession":["PXD011691"]},"is_claimable":false,"name":"Comparison of DIA and TMT based protein quantification in complex background","description":"Label free quantification (LFQ) and isobaric labelling quantification (ILQ) are among the most popular protein quantification workflows in discovery proteomics. Here, we compared the TMT 10-plex workflow to label free single shot data-independent acquisition (DIA) method on a controlled sample set. The sample set consisted of ten samples derived from 10 different mouse cerebelli spiked with the UPS2 protein standard in five different concentrations. To match instrument time between the methods, the combined TMT sample was fractionated into ten fractions. The LC-MS data were acquired at two facilities to assess inter-laboratory reproducibility.  Both methods resulted in a high proteome coverage (>5,000 proteins) with low missing values on protein level (<2%) The TMT workflow led to 15-20% more identified proteins and a slightly better quantitative precision whereas the quantitative accuracy was better for the DIA method. The quantitative performance was benchmarked by the number of true positives (UPS2 proteins) within the top 100 candidates. TMT and DIA performed similar. The quantitative performance of the DIA data could be even improved by searching them directly against a database instead of using a project specific library. Our experiments also demonstrated that both methods can be easily transferred between facilities.","dates":{"publication":"Wed Jan 29 19:09:00 GMT 2020"},"accession":"MSV000084859","cross_references":{"pubmed":["30726097"]}}