{"database":"panorama","file_versions":[],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Deanna Plubell"],"technology_type":["SRM/MRM"],"species":["Homo Sapiens"],"full_dataset_link":["https://panoramaweb.org/DIAtoSRM.url"],"submitter_email":["plubell@uw.edu"],"submitter_affiliation":["University of Washington"],"sample_protocol":[""],"repository":["PanoramaPublic"],"data_protocol":[""],"pubmed_abstract":["Mass spectrometry based targeted proteomics methods provide a sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semistochastic sampling, or empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of the peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific information on peptide detectability and quantification by mass spectrometry. To demonstrate the suitability of DIA data for selecting peptide targets, we reimplement a portion of an existing assay to measure 98 Alzheimer's disease proteins in cerebrospinal fluid (CSF). Peptides were selected from GPF-DIA based on signal intensity and reproducibility. The resulting SRM assay exhibits a quantitative precision similar to that of published data, despite the inclusion of different peptides between the assays. This workflow enables development of new assays without additional upfront data acquisition, demonstrated here through generation of a separate assay for an unrelated set of proteins in CSF from the same data set."],"pubmed_title":["Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer."],"pubmed_authors":["Plubell Deanna L DL, Huang Eric E, Spencer Sandra E SE, Poston Kathleen L KL, Montine Thomas J TJ, MacCoss Michael J MJ"],"pubmed_title_synonyms":["Peptidomics., postnatal growth, development, growth and development, single-organism developmental process, growth, postnatal development"],"name_synonyms":["measuring, CDF, l(2)k07135, postnatal development., single-organism developmental process, determination, POF2, F27C12_24, Desmoplastic astrocytoma of infancy, F27C12.24, postnatal growth, growth and development, CG1768, DIASP, DRF2, DIA, Dia, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, development, ms(2)04138, Desmoplastic infantile astrocytoma, POF, scientific observation, DmelCG1768, MLPLI, chemical analysis, DIANA, 38E.16, HILDA, AGAMOUS-like 61, assay, DIA2, Dias, growth, DiA"],"pubmed_abstract_synonyms":["Primary senile degenerative dementia, Presenile Alzheimer Dementia, CDF, IPP2A2, Product, single-organism developmental process, determination, Early Onset, selection process, postnatal development, growth and development, protein, Measure, Early Onset Alzheimer Disease, acquired immune deficiency syndrome, Alzheimer's disease, 5730420M11Rik, peptide, Primary Senile Degenerative, Polypeptides, AD, Techniques, B2T, GAS-6, POF, sampling, cerebral spinal fluid, peptido, Method, Biological, liquor cerebrospinalis, AGAMOUS-like 61, germacrene A synthase activity, Analysis, Biological Product, protein aggregate, Work Flow, DiA, Mass Spectrum Analysis, SET, Familial Alzheimer Disease (FAD), Biologic Drugs, l(2)k07135, Acquired Immunodeficiency Syndromes, Alzheimer Diseases, peptides, Analyses, Alzheimer syndrome, TAF-I, Natural, Acquired Immune Deficiency Syndrome, Weights, procedures, Biological Drugs, DIASP, Focal Onset Alzheimer's Disease, Late Onset Alzheimer Disease, DIA, Dia, DmelCG4299, allergic reaction, PA1, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, SDAT, IGAAD, set, Biological Medicine, Methodological Studies, DmelCG10574, scientific observation, Alzheimer Type Dementia, C16orf53, 38E.16, Medicine, Medicines, Presenile, Biologic Drug, GPF, Data Set., (+)-germacrene A synthase activity, phapii, Cerebro Spinal Fluid, Senile, Acquired Immuno-Deficiency Syndrome, Alzheimer disease, Immunodeficiency Syndrome, Biologic Products, Acute Confusional Senile Dementia, StF-IT-1, Acquired Immunodeficiency Syndrome, Procedure, SPDSY, Spectrum Analysis, Immuno-Deficiency Syndromes, Patient Agent, Multiple Reaction Monitoring, Spectroscopy, Alzheimer Type, Cerebro Spinal Fluids, ms(2)04138, Desmoplastic infantile astrocytoma, Workflows, AIDS, Biopharmaceuticals, Alzheimer sclerosis, Biologic Product, GAS, 6-trans-farnesyl-diphosphate diphosphate-lyase (germacrene-A-forming) activity, Dementia, LAMB2T, Acquired, HLA-DR-associated protein II, DI-2, Biological Medicines, Alzheimer, Biological Drug, POF2, I-2Dm, F27C12_24, F27C12.24, Spectrometry, Biologics, Methodological, CG4299, Alzheimer-Type (ATD), Colony-stimulating factor, Csfgm, Cerebro, Methodological Study, I-2PP1, TAF-IBETA, Agents, Syndromes, Senile Dementia, Patient, Acute Confusional, DIANA, Alzheimer-Type Dementia (ATD), Measures and Weights, TAF-Ibeta, Polypeptide, Alzheimer's Disease, Growth-potentiating factor, i2pp2a, Work Flows, Alzheimer Type Dementia (ATD), Procedures, Alzheimers Diseases, Biologic Pharmaceuticals, Peptidomics, SRML1, Sclerosis, number, Gene, 2-trans, GM-CSF, Spectrum Analyses, protein-containing complex, Focal Onset, presence, PHAPII, Cerebrospinal, Agent, method, sensitive, method used in an experiment, DmelCG1768, acquired immunodeficiency syndrome, Mass, Studies, Gene Products, HILDA, Immuno-Deficiency Syndrome, Cerebro Spinal, Technique, sensitivity, GMCSF, Mass Spectroscopy, Biologicals, Drugs, AXL receptor tyrosine kinase ligand, Acquired immunodeficiency syndrome, MRM, BM600, ipp2a2, Natural Product, Measures, 2pp2a, EBR2, CG10574, Acquired Immuno Deficiency Syndrome, Presenile Dementia, Study, Molgramostin, 2PP2A, taf-ibeta, Acquired Immuno-Deficiency, Alzheimer Disease, Syndrome, Cerebral Spinal Fluid, dSET, dSet, peptidos, DIA2, DAT, Biologic, SPS1, Pharmaceuticals, Alzheimers dementia, measuring, Products, protein complex, Biologic Medicines, Alzheimer Syndrome, 6-trans-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-A-forming] activity, Desmoplastic astrocytoma of infancy, Alzheimer-type dementia (ATD), EBR2A, Proteins, PAPT, igaad, Fluids, Cerebrospinal Fluids, spinal fluid, CG1768, Acquired Immunodeficiency, DRF2, (+)-(10R)-germacrene A synthase activity, Peptide, Spinal Fluid, Primary Senile Degenerative Dementia, group, polypeptide, development, Alzheimer Dementias, Proxies, Spinal Fluids, count in organism, MS, Fluid, native protein, I-2PP2A, Sargramostim, Alzheimer's Diseases, chemical analysis, Protein, MLPLI, Dm I-2, Biopharmaceutical, I2PP2A, techniques, Dias, Immunologic Deficiency Syndrome, Mass Spectrum Analyses, Mass Spectrum, Scales, ensemble, postnatal growth, Alzheimer Type Senile Dementia, CSF, Alzheimer Dementia, Alzheimer Sclerosis, Protein Gene Products, Drug, plan specification, Gene Proteins, dSET/TAF-Ibeta, Immunodeficiency Syndromes, sample collection, 2610030F17Rik, Acquired Immuno-Deficiency Syndromes, Late Onset, Familial (FAD), LAMNB2, Natural Products, Peptid, assay, AA407739, growth, Familial Alzheimer Diseases (FAD), methodology"],"description_synonyms":["DUbc9, CDF, IPP2A2, Product, single-organism developmental process, determination, selection process, postnatal development, growth and development, protein, Measure, acquired immune deficiency syndrome, 5730420M11Rik, peptide, Polypeptides, Techniques, B2T, GAS-6, Lwr, POF, sampling, cerebral spinal fluid, peptido, diseases, Method, Biological, liquor cerebrospinalis, diseases and disorders, AGAMOUS-like 61, germacrene A synthase activity, Analysis, Biological Product, protein aggregate, Work Flow, DiA, Mass Spectrum Analysis, SET, human disease, Biologic Drugs, l(2)k07135, Acquired Immunodeficiency Syndromes, peptides, Analyses, TAF-I, Natural, Acquired Immune Deficiency Syndrome, Weights, procedures, Biological Drugs, DIASP, DIA, Dia, DmelCG4299, allergic reaction, PA1, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, IGAAD, set, Biological Medicine, Methodological Studies, DmelCG10574, scientific observation, C16orf53, 38E.16, Medicine, Homo sapiens disease, Medicines, Biologic Drug, GPF, (+)-germacrene A synthase activity, phapii, Cerebro Spinal Fluid, Acquired Immuno-Deficiency Syndrome, Immunodeficiency Syndrome, Biologic Products, StF-IT-1, Acquired Immunodeficiency Syndrome, Procedure, SPDSY, Spectrum Analysis, Immuno-Deficiency Syndromes, Patient Agent, Multiple Reaction Monitoring, Spectroscopy, Cerebro Spinal Fluids, ms(2)04138, Desmoplastic infantile astrocytoma, Workflows, AIDS, Biopharmaceuticals, Diseases, Biologic Product, hbl, GAS, 6-trans-farnesyl-diphosphate diphosphate-lyase (germacrene-A-forming) activity, l(2)02858, l(2)05487, l(2)05486, LAMB2T, Acquired, HLA-DR-associated protein II, DI-2, i56, Biological Medicines, Biological Drug, POF2, I-2Dm, F27C12_24, F27C12.24, Spectrometry, Biologics, Methodological, CG4299, Colony-stimulating factor, Csfgm, Cerebro, Methodological Study, i105, I-2PP1, disease, TAF-IBETA, Agents, Syndromes, Patient, DIANA, Measures and Weights, TAF-Ibeta, Polypeptide, Growth-potentiating factor, i2pp2a, Work Flows, other disease, Procedures, Biologic Pharmaceuticals, Peptidomics, SRML1, Gene, 2-trans, GM-CSF, Spectrum Analyses, protein-containing complex, PHAPII, Cerebrospinal, Agent, method, dip4, sensitive, method used in an experiment, DmelCG1768, acquired immunodeficiency syndrome, Mass, Studies, Gene Products, HILDA, Immuno-Deficiency Syndrome, disease or disorder, Cerebro Spinal, Ubc 9, Technique, sensitivity, GMCSF, Mass Spectroscopy, Biologicals, Drugs, AXL receptor tyrosine kinase ligand, Acquired immunodeficiency syndrome, MRM, DmelCG3018, BM600, ipp2a2, Natural Product, Measures, 2pp2a, Ubc-9, semi, EBR2, CG10574, l(2)01519, Acquired Immuno Deficiency Syndrome, non-neoplastic, Study, Molgramostin, 2PP2A, taf-ibeta, Acquired Immuno-Deficiency, Syndrome, Cerebral Spinal Fluid, dSET, dSet, disorder, peptidos, DIA2, Biologic, SPS1, Pharmaceuticals, measuring, Products, UBC9, Ubc9, protein complex, Biologic Medicines, 6-trans-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-A-forming] activity, Desmoplastic astrocytoma of infancy, EBR2A, Proteins, PAPT, disorders, igaad, Fluids, Cerebrospinal Fluids, medical condition, spinal fluid, CG1768, Acquired 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To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semi-stochastic sampling, or by empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific information on peptide detectability and quantification by mass spectrometry. To demonstrate the suitability of DIA data for selecting peptide targets, we reimplement a portion of an existing assay to measure 100 Alzheimer’s disease proteins in cerebrospinal fluid (CSF).(Spellman). Peptides were selected from GPF-DIA based on signal intensity and reproducibility. The resulting SRM assay exhibits similar quantitative precision to published data, despite the inclusion of different peptides between the assays. This workflow enables development of new assays without additional up-front data acquisition, as demonstrated through a separate assay generated for an unrelated set of proteins in CSF.","dates":{"publication":"Wed Jun 11 00:00:00 GMT+01:00 2025"},"accession":"PXD059611","cross_references":{"TAXONOMY":["9606"],"pubmed":["40328514"]}}