panoramaProteomicsJohn KoomenHomo Sapienshttps://panoramaweb.org/Moffitt-LSCC_MRM.urljohn.koomen@moffitt.orgMoffitt Cancer CenterPanoramaPublicLiquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM) has widespread clinical use for detection of inborn errors of metabolism, therapeutic drug monitoring, and numerous other applications. This technique detects proteolytic peptides as surrogates for protein biomarker expression, mutation, and post-translational modification in individual clinical assays and in cancer research with highly multiplexed quantitation across biological pathways. LC-MRM for protein biomarkers must be translated from multiplexed research-grade panels to clinical use. LC-MRM panels provide the capability to quantify clinical biomarkers and emerging protein markers to establish the context of tumor phenotypes that provide highly relevant supporting information. An application to visualize and communicate targeted proteomics data will empower translational researchers to move protein biomarker panels from discovery to clinical use. Therefore, we have developed a web-based tool for targeted proteomics that provides pathway-level evaluations of key biological drivers (<i>e.g.</i>, EGFR signaling), signature scores (representing phenotypes) (<i>e.g.,</i> EMT), and the ability to quantify specific drug targets across a sample cohort. This tool represents a framework for integrating summary information, decision algorithms, and risk scores to support Physician-Interpretable Phenotypic Evaluation in R (PIPER) that can be reused or repurposed by other labs to communicate and interpret their own biomarker panels.Deciphering Phenotypes from Protein Biomarkers for Translational Research with PIPER.Putty Reddy Sudhir S, Alontaga Aileen Y AY, Welsh Eric A EA, Haura Eric B EB, Boyle Theresa A TA, Eschrich Steven A SA, Koomen John M JMBiological Markers, Viral Marker, Pepper, Viral, Surrogate Endpoints, Surrogate Endpoint, Activity, Long Pepper, Clinical Markers, Laboratory, Jaborandi Pepper., protein complex, Clinical Marker, Proteins, Serum Markers, Biochemical, End Point, Gene, Endpoint, Research Priorities, Biochemical Markers, protein, Serum, protein-containing complex, Jaborandi, Biologic Marker, Immune Marker, Surrogate End Points, Ashanti, Surrogate Markers, Long Peppers, Laboratory Markers, Priority, native protein, Marker, Biological, Surrogate End Point, Protein, Research Activities, Gene Products, Research Activity, protein aggregate, Long, Laboratory Research, Biologic Markers, Research and Development, Priorities, Biomarker, Serum Marker, Ashanti Peppers, Clinical, End Points, Piper longum, Research, Cubeb, Surrogate, Biological Marker, Endpoints, Ashanti Pepper, Jaborandi Peppers, Immunologic, Laboratory Marker, Peppers, Surrogate Marker, Protein Gene Products, Activities, Phenotypes, Gene Proteins, Immunologic Markers, Immune, Markers, Biochemical Marker, Viral Markers, Pipers, Development and Research, Research Priority, Cubeb Pepper, Immunologic Marker, Cubeb Peppers, Biologic, Piper guineense, Piper cubeba, Immune MarkersTransitional Epithelial Cell, Transitional, Adenomatous Epithelial Cell, Squamous Cells, Adenomatous Epithelial Cells, Squamous Cell, pulmo, Epithelial Cell, Peptidomics, Glandular Epithelial Cell., lung parenchyma, Glandular Epithelial Cells, Adenomatous, Adenomatous 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complex, EK2-6, Inborn Metabolism Error, Malignant, dIKK-gamma, Errors Metabolisms, Surrogate End Points, Posttranslational, Surrogate Markers, Long Peppers, method, method used in an experiment, DmIKK-gamma, c-erbB, EGFr, Egfr, Mass, Studies, Gene Products, Post Translational Modification, torpedo/Egfr, EGF receptor activity, Therapeutic Drug, Post-Translational Modifications, TOP, Egf-r, dmIKKgamma, IKK[[gamma]], Technique, Therapeutic Drug Monitoring, EMTH, Mass Spectroscopy, Post Translational, Drugs, Errors Metabolism, Metabolism Errors, Modification, Biomarker, EGF-R, Clinical, MRM, Malignancy, Piper longum, Research, Cubeb, Biological Marker, Ashanti Pepper, top, LPFS1, Torpedo/DER, posttranslational protein modification, epithelial-mesenchymal transition, Monitoring, top/flb, Protein Modifications, Study, Post-Translational Amino Acid Modification, Neoplasias, Immunologic Markers, drugs, IKK, Posttranslational Amino Acid Modification, l(2)57EFa, Inborn Metabolism, synopsis, 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top/DER, Pharmaceutic Preparations, Surrogate, Dmikkgamma, Post Translational Protein Processing, Endpoints, Risks, "Metabolic hereditary disorder" EXACT [SNOMEDCT_2005_07_31:363205007], ERBB1, Cancers, wa-2, CG16910, malignant tumor, Surrogate Marker, sample population, post-translational amino acid modification, Drug, plan specification, Protein Gene Products, Gene Proteins, Preparations, Post Translational Protein Modification, Egf, EFG-R, signalling process, Error, Therapeutic, Errp, Erbb, Post-Translational Protein Processing, Der, DER, rare inherited metabolic disorder, Peptid, "inborn metabolism disorder" EXACT [CSP2005:1849-0057], transforming growth factor-alpha receptor activity, Pharmaceutical Products, Cubeb Peppers, Drug Monitoring, Neoplasia, DER/torpedo, HER1, Pharmaceutical Preparation, Immune MarkersDER/faint little ball, Biological Markers, Viral Marker, Surrogate Endpoints, Epithelial Cell, Product, Laboratory, Glandular Epithelial Cell., Organic cation transporter 3, Addresses, Elp-B1, der, Biochemical, Elp-1, Endpoint, Errb1, protein, Tumor, Serum, Glandular, PIG61, Laboratory Markers, Biological, parenchyma of lung, epidermal growth factor-activated receptor activity, AI552599, Pharmaceutical Product, Analysis, protein aggregate, d-egf-r, IKKg, KEY, Key, Mass Spectrum Analysis, Analyses, Adenomatous Epithelial, flb, LYK, Immune, Markers, malignant neoplasm, medicine, Pharmaceutical, Viral Markers, sample, 9030024J15Rik, D-EGFR, Malignancies, Electronic Supplementary Material, NISBD2, single organism signaling, Tumors, DER1, Transitional Epithelial Cell, Viral, anatomical protrusion, Elp, pulmo, Surrogate Endpoint, Wa5, l(2)09261, DEgfr, Liquid Chromatography, lung parenchyma, Adenomatous, Biochemical Markers, Squamous, Biologic Marker, Transitional Epithelial, Spectrum Analysis, CG10079, Multiple Reaction Monitoring, Spectroscopy, DmIKKgamma, torpedo/egfr, Benign, wa2, Marker, dIKK, EMT, Emt, Kenny, Pharmaceutic, Supplementary Information, neoplasms, egfr, Adenomatous Epithelial Cell, Adenomatous Epithelial Cells, Supplementary Material, Squamous Cell, HD-33, El, End Points, DER/EGFR, EGFR, EGfr, EgfR, PSCTK2, dEgfr, IKK-gamma, Spectrometry, Benign Neoplasms, DER flb, Immunologic, Laboratory Marker, Torpedo/Egfr, Malignant Neoplasms, Degfr, Phenotypes, DmelCG16910, pulmonary, Biochemical Marker, spine, DEGFR, l(2)57DEFa, l(2)05351, Cells, dEGFR, Extraneuronal monoamine transporter, DmHD-33, other neoplasm, Tcsk, D-Egf, Clinical Markers, Peptidomics, Clinical Marker, C-erb, Neoplasms, Benign Neoplasm, mor1, Gene, OCT3, Glandular Epithelial, Spectrum Analyses, mENA, protein-containing complex, EK2-6, Malignant, dIKK-gamma, Surrogate End Points, protrusion, Surrogate Markers, Squamous Epithelial Cells, DmIKK-gamma, c-erbB, EGFr, Egfr, Mass, Gene Products, lung, torpedo/Egfr, EGF receptor activity, TOP, Egf-r, dmIKKgamma, IKK[[gamma]], neoplasm, Squamous Epithelial, EMTH, Mass Spectroscopy, Epithelial, Drugs, Biomarker, EGF-R, Clinical, MRM, Malignancy, Biological Marker, top, LPFS1, Torpedo/DER, epithelial-mesenchymal transition, top/flb, Neoplasias, Immunologic Markers, drugs, IKK, l(2)57EFa, Epithelial Cells, Transitional Epithelial Cells, mesenchymal cell differentiation from epithelial cell, l(2)57Ea, Preparation, Squamous Epithelial Cell, Immunologic Marker, Biologic, Cancer, Pharmaceuticals, Elp-B1RB1, Transitional, Products, Squamous Cells, Malignant Neoplasm, protein complex, TGF-alpha receptor activity, ERBB, dEGFR1, drug, Serum Markers, Proteins, End Point, Cell, Immune Marker, IKKgamma, MS, MT, native protein, epidermal growth factor receptor activity, Cuboidal Glandular Epithelial Cells, DmelCG10079, Surrogate End Point, Supporting Information, Tsk, Protein, Neoplasm, Columnar Glandular Epithelial Cells, DER/top, Mass Spectrum Analyses, Biologic Markers, Mass Spectrum, primary cancer, Serum Marker, top/DER, Pharmaceutic Preparations, Surrogate, Dmikkgamma, Endpoints, Glandular Epithelial Cells, ERBB1, Cancers, wa-2, CG16910, malignant tumor, Surrogate Marker, sample population, Protein Gene Products, Drug, Gene Proteins, Preparations, Egf, EFG-R, signalling process, Errp, Erbb, Der, DER, Lungs, transforming growth factor-alpha receptor activity, Pharmaceutical Products, Neoplasia, DER/torpedo, HER1, Pharmaceutical Preparation, Immune MarkersfalseTargeted Proteomics of Lung Squamous Cell CarcinomasTo address the complexity of cancer, liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM) panels provide the capability to quantify clinical biomarkers and emerging protein markers to establish the context of tumor phenotypes that provide highly relevant supporting information. The resulting targeted proteomics data will empower translational researchers to move protein biomarker panels through the process from discovery to clinical use. Here, targeted proteomics panel measurements provide pathway-level evaluations of key biological drivers (e.g., EGFR signaling), phenotypes (e.g., EMT) and the ability to quantify specific drug targets within the context of a sample cohort of lung squamous cell carcinomas.Sun Jul 09 00:00:00 GMT+01:00 2023PXD040680960637171072