{"database":"panorama","file_versions":[],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["David Kotol"],"species":["Homo Sapiens"],"full_dataset_link":["https://panoramaweb.org/QKcywA.url"],"submitter_email":["david.kotol@scilifelab.se"],"submitter_affiliation":["KTH Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, Stockholm, Sweden"],"sample_protocol":[""],"repository":["PanoramaPublic"],"data_protocol":[""],"pubmed_abstract":["Mass spectrometry based on data-independent acquisition (DIA) has developed into a powerful quantitative tool with a variety of implications, including precision medicine. Combined with stable isotope recombinant protein standards, this strategy provides confident protein identification and precise quantification on an absolute scale. Here, we describe a comprehensive targeted proteomics approach to profile a pan-cancer cohort consisting of 1800 blood plasma samples representing 15 different cancer types. We successfully performed an absolute quantification of 253 proteins in multiplex. The assay had low intra-assay variability with a coefficient of variation below 20% (CV = 17.2%) for a total of 1013 peptides quantified across almost two thousand injections. This study identified a potential biomarker panel of seven protein targets for the diagnosis of multiple myeloma patients using differential expression analysis and machine learning. The combination of markers, including the complement C1 complex, JCHAIN, and CD5L, resulted in a prediction model with an AUC of 0.96 for the identification of multiple myeloma patients across various cancer patients. All these proteins are known to interact with immunoglobulins."],"pubmed_title":["Absolute Quantification of Pan-Cancer Plasma Proteomes Reveals Unique Signature in Multiple Myeloma."],"pubmed_authors":["Kotol David D, Woessmann Jakob J, Hober Andreas A, Álvez María Bueno MB, Tran Minh Khue Hua KH, Pontén Fredrik F, Fagerberg Linn L, Uhlén Mathias M, Edfors Fredrik F"],"pubmed_title_synonyms":["Fresh, CG34403, l(4)13, Polyarteritis Nodosa, Fresh Frozen Plasma, Multiple myeloma (disorder), Periarteritis Nodosa, Neoplasms, Blood, Kahler's disease, LEF/TCF-1, Cell Myelomas, Benign Neoplasm, DmelCG34403, Tumor, Malignant, Myeloma-Multiples, IA5, Myeloma-Multiple, LEF-1, Dmel_CG32005, Multiple Myelomas, [M]Plasma cell myeloma, LEF1/TCF, Myelomatoses, Classic Polyarteritis Nodosa, Plasmacytic myeloma, systemic, Fresh Frozen Plasmas, Fresh Frozen, amyloidosis, TCF/LEF, Blood Plasma, Multiple myeloma, Malignancy, Plasma Cell Myelomas, myeloma, Tcf-1, d-TCF, cTCF, Neoplasias, Cell Myeloma, malignant neoplasm, TCF/LEF1, Blood Plasmas, chimpanzees, Malignancies, Plasma Cell, polyarteritis, Pan, PAN, plasma, myeloma - multiple, Cancer, Tumors, Plasma-Cell Myelomas, Plasma-cell myeloma, Disease, Frozen Plasma, Malignant Neoplasm, Myelomas, Myeloma, Dmel_CG17964, Myeloma Multiple, Plasmas, LEF/TCF, Dm Pan, Multiple Myeloma, MM, Al amyloidosis, Frozen Plasmas, multiple myeloma, Kahler, MT, Benign, pan.dTCF, PERIANTHIA, Neoplasm, NOS, Myelomatosis, Tcf, TCF, Tcf/LEF, MULT MYELM W/O REMISSION, morphology (morphologic abnormality), Plasma-Cell, Plasma-Cell Myeloma, Lef1, periarteritis, Plasma, no ICD-O subtype (morphologic abnormality)., primary cancer, LEF1, F24J5.12, Classical Polyarteritis Nodosa, Panarteritis Nodosa, DTCF, DTcf, Benign Neoplasms, portion of plasma, Kahler Disease, tcf, Cancers, CG17964, l(4)102ABb, malignant tumor, CG32005, F24J5_12, Malignant Neoplasms, Multiple myeloma without mention of remission, Multiple, no ICD-O subtype, multiple, Plasma Cell Myeloma, Lef, lef1, Multiple myeloma (clinical), Proteomes, Neoplasia, dTCF, dTcf"],"name_synonyms":["Fresh, CG34403, IBGC5, l(4)13, Polyarteritis Nodosa, Fresh Frozen Plasma, Immunoglobulin, Multiple myeloma (disorder), Periarteritis Nodosa, Neoplasms, Blood, Globulin, Kahler's disease, LEF/TCF-1, Cell Myelomas, Benign Neoplasm, Immune Globulin, Gene, DmelCG34403, protein, Tumor, protein-containing complex, Malignant, Myeloma-Multiples, IA5, Myeloma-Multiple, LEF-1, Dmel_CG32005, Multiple Myelomas, [M]Plasma cell myeloma, LEF1/TCF, Gene Products, Myelomatoses, Classic Polyarteritis Nodosa, PDGF2, protein aggregate, Plasmacytic myeloma, systemic, Fresh Frozen Plasmas, Fresh Frozen, amyloidosis, TCF/LEF, Blood Plasma, Multiple myeloma, Malignancy, Plasma Cell Myelomas, myeloma, Tcf-1, d-TCF, cTCF, Neoplasias, Immune, Cell Myeloma, malignant neoplasm, TCF/LEF1, Blood Plasmas, chimpanzees, Malignancies, Plasma Cell, polyarteritis, Pan, PAN, plasma, myeloma - multiple, Cancer, Tumors, Plasma-Cell Myelomas, Plasma-cell myeloma, Disease, Frozen Plasma, Malignant Neoplasm, Myelomas, protein complex, Myeloma, Dmel_CG17964, Proteins, total expressed protein, Myeloma Multiple, Plasmas, LEF/TCF, Immune Globulins, Dm Pan, Multiple Myeloma, MM, Al amyloidosis, Frozen Plasmas, multiple myeloma, Kahler, MT, Benign, pan.dTCF, native protein, PDGF-B, PERIANTHIA, Protein, Neoplasm, NOS, Myelomatosis, Tcf, TCF, Tcf/LEF, MULT MYELM W/O REMISSION, SIS, Sis, morphology (morphologic abnormality), Plasma-Cell, Plasma-Cell Myeloma, Lef1, periarteritis, Plasma, no ICD-O subtype (morphologic abnormality)., primary cancer, LEF1, F24J5.12, Classical Polyarteritis Nodosa, Panarteritis Nodosa, DTCF, DTcf, Benign Neoplasms, portion of plasma, Kahler Disease, tcf, Cancers, CG17964, PDGF-2, l(4)102ABb, malignant tumor, sis, CG32005, F24J5_12, Malignant Neoplasms, Multiple myeloma without mention of remission, Protein Gene Products, Gene Proteins, Multiple, pdgf2, no ICD-O subtype, multiple, Plasma Cell Myeloma, Lef, Globulins, lef1, Multiple myeloma (clinical), SSV, c-sis, Proteomes, Neoplasia, dTCF, dTcf"],"pubmed_abstract_synonyms":["CDF, scale tissue, l(4)13, Biological Markers, Viral Marker, Antemortem Diagnosis, Polyarteritis Nodosa, Surrogate Endpoints, determination, Laboratory, Individualized Medicine, Blood, Globulin, Cell Myelomas, Immune Globulin, Biochemical, Endpoint, DmelCG34403, protein, Tumor, Serum, Diagnosis, Myeloma-Multiples, IA5, Myeloma-Multiple, LEF-1, Polypeptides, Dmel_CG32005, Laboratory Markers, POF, peptido, Biological, LEF1/TCF, symptoms, AGAMOUS-like 61, Analysis, protein aggregate, Transfer, Injectables, DiA, Mass Spectrum Analysis, systemic, Fresh Frozen Plasmas, Fresh Frozen, amyloidosis, TCF/LEF, me75, l(2)k07135, peptides, Analyses, plant peltate hair, Machine, C1, myeloma, Complement Component 1, Immune Globulins., DIASP, cTCF, D17Mit170, DIA, Dia, T1, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, Immune, Markers, Cell Myeloma, malignant neoplasm, no ICD-O subtype (morphologic abnormality), scientific observation, Viral Markers, 38E.16, Medicine, Malignancies, Plasma Cell, Reference Standard, polyarteritis, Pan, PAN, plasma, Diagnose, Tumors, Plasma-Cell Myelomas, screening, Standard Preparation, Standard Preparations, Frozen Plasma, Standardization, Viral, Myelomas, Surrogate Endpoint, Myeloma, Learning, Biochemical Markers, Tl3, Plasmas, Tl2, Biologic Marker, Spectrum Analysis, LEF/TCF, Dm Pan, Diagnoses, Multiple Myeloma, Spectroscopy, ms(2)04138, Kahler, Desmoplastic infantile astrocytoma, Benign, Postmortem, Screenings, Personalized Medicine, Marker, PERIANTHIA, Examinations and Diagnoses, NOS, Postmortem Diagnosis, morphology (morphologic abnormality), Plasma-Cell Myeloma, Diagnoses and Examination, portion of blood plasma, Postmortem Diagnoses, End Points, Standard, Complement, F24J5.12, POF2, F27C12_24, Classical Polyarteritis Nodosa, F27C12.24, Panarteritis Nodosa, Spectrometry, DTCF, DTcf, signs, Benign Neoplasms, Immunologic, CG17964, Laboratory Marker, F24J5_12, Malignant Neoplasms, Multiple, blood plasm, multiple, Patient, Biochemical Marker, Theranostics, DIANA, Globulins, Polypeptide, Multiple myeloma (clinical), dTCF, dTcf, Fresh, CG34403, criteria, Fresh Frozen Plasma, Immunoglobulin, Peptidomics, Clinical Markers, Component 1, Clinical Marker, Multiple myeloma (disorder), Periarteritis Nodosa, Neoplasms, Kahler's disease, peltate hair, LEF/TCF-1, number, Benign Neoplasm, Gene, Spectrum Analyses, guidelines, protein-containing complex, Malignant, presence, Surrogate End Points, Surrogate Markers, Multiple Myelomas, Injection, DmelCG1768, [M]Plasma cell myeloma, Mass, HILDA, Gene Products, Myelomatoses, Screening, Classic Polyarteritis Nodosa, Precision, Low, C1 Complement, Antemortem, Mass Spectroscopy, Plasmacytic myeloma, study, Biomarker, Transfer Learning, Blood Plasma, Multiple myeloma, Individualized, Clinical, Malignancy, Biological Marker, Plasma Cell Myelomas, Tcf-1, d-TCF, Diagnoses and Examinations, Neoplasias, Injectable, Immunologic Markers, Reference, Clients, TCF/LEF1, Blood Plasmas, chimpanzees, peptidos, DIA2, Preparation, Predictive, Immunologic Marker, Biologic, myeloma - multiple, Cancer, Plasma-cell myeloma, measuring, Antemortem Diagnoses, Disease, findings, Malignant Neoplasm, cou, Predictive Medicine, protein complex, Desmoplastic astrocytoma of infancy, Proteins, Dmel_CG17964, Serum Markers, End Point, Myeloma Multiple, CG1768, Personalized, DRF2, Client, Peptide, Examination and Diagnoses, Immune Marker, MM, Al amyloidosis, Frozen Plasmas, multiple myeloma, Complement 1, Isotope, count in organism, MS, Lr, MT, native protein, pan.dTCF, Surrogate End Point, Mass Screenings, MLPLI, Protein, chemical analysis, Neoplasm, Myelomatosis, Tcf, TCF, Dias, scales, Tcf/LEF, MULT MYELM W/O REMISSION, Mass Spectrum Analyses, Plasma-Cell, Biologic Markers, Lef1, periarteritis, Plasma, Mass Spectrum, primary cancer, Serum Marker, LEF1, scale, Surrogate, Endpoints, portion of plasma, Kahler Disease, Theranostic, tcf, Cancers, l(4)102ABb, malignant tumor, CG32005, Surrogate Marker, Multiple myeloma without mention of remission, Protein Gene Products, Gene Proteins, Preparations, no ICD-O subtype, P-Health, Plasma Cell Myeloma, Lef, Standards, Bra, P Health, Peptid, assay, lef1, Neoplasia, Immune Markers"],"description_synonyms":["CDF, scale tissue, l(4)13, Biological Markers, Viral Marker, Antemortem Diagnosis, Polyarteritis Nodosa, Surrogate Endpoints, determination, Laboratory, Individualized Medicine, Blood, Cell Myelomas, Biochemical, Endpoint, DmelCG34403, protein, Tumor, Serum, Diagnosis, Myeloma-Multiples, IA5, Myeloma-Multiple, LEF-1, Liquid Biopsies, Polypeptides, Dmel_CG32005, Techniques, Laboratory Markers, POF, peptido, Method, Biological, LEF1/TCF, symptoms, AGAMOUS-like 61, Analysis, protein aggregate, Transfer, Injectables, DiA, Mass Spectrum Analysis, systemic, Fresh Frozen Plasmas, Fresh Frozen, amyloidosis, TCF/LEF, me75, l(2)k07135, Biopsies, peptides, Analyses, plant peltate hair, Machine, myeloma, DIASP, cTCF, D17Mit170, DIA, Dia, T1, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, Immune, Markers, Cell Myeloma, Methodological Studies, malignant neoplasm, no ICD-O subtype (morphologic abnormality), scientific observation, Viral Markers, 38E.16, Medicine, Malignancies, Biopsy, Plasma Cell, Reference Standard, polyarteritis, Pan, PAN, plasma, Diagnose, Tumors, Plasma-Cell Myelomas, screening, Standard Preparation, Standard Preparations, Frozen Plasma, Standardization, Viral, Myelomas, Surrogate Endpoint, Myeloma, Learning, Biochemical Markers, Procedure, Tl3, Plasmas, Tl2, Biologic Marker, Spectrum Analysis, LEF/TCF, Dm Pan, Diagnoses, Multiple Myeloma, Spectroscopy, ms(2)04138, Kahler, Desmoplastic infantile astrocytoma, Benign, Postmortem, Screenings, Personalized Medicine, Marker, PERIANTHIA, Examinations and Diagnoses, NOS, Postmortem Diagnosis, morphology (morphologic abnormality), Plasma-Cell Myeloma, Diagnoses and Examination, portion of blood plasma, Postmortem Diagnoses, End Points, Standard, Complement, F24J5.12, POF2, F27C12_24, Classical Polyarteritis Nodosa, F27C12.24, Panarteritis Nodosa, Spectrometry, DTCF, DTcf, signs, Benign Neoplasms, Methodological, Immunologic, CG17964, Laboratory Marker, Methodological Study, F24J5_12, Malignant Neoplasms, Multiple, blood plasm, multiple, Patient, Biochemical Marker, Theranostics, DIANA, Liquid, Complement System, Polypeptide, Multiple myeloma (clinical), dTCF, dTcf, Fresh, CG34403, criteria, Fresh Frozen Plasma, Procedures, Peptidomics, Clinical Markers, Clinical Marker, Multiple myeloma (disorder), Periarteritis Nodosa, Neoplasms, Kahler's disease, peltate hair, LEF/TCF-1, Benign Neoplasm, Gene, Spectrum Analyses, guidelines, protein-containing complex, Complement Protein, Malignant, Surrogate End Points, Surrogate Markers, method, Multiple Myelomas, Client., Injection, DmelCG1768, method used in an experiment, [M]Plasma cell myeloma, Mass, HILDA, Gene Products, Studies, Myelomatoses, Screening, Classic Polyarteritis Nodosa, Precision, Low, Antemortem, Technique, Mass Spectroscopy, Plasmacytic myeloma, study, Biomarker, Transfer Learning, Blood Plasma, Multiple myeloma, Individualized, Clinical, Malignancy, Biological Marker, Plasma Cell Myelomas, Tcf-1, d-TCF, Diagnoses and Examinations, Neoplasias, Study, Injectable, Immunologic Markers, Reference, Clients, TCF/LEF1, Blood Plasmas, chimpanzees, peptidos, Hemolytic, DIA2, Preparation, Predictive, Immunologic Marker, Biologic, myeloma - multiple, Cancer, Plasma-cell myeloma, measuring, Antemortem Diagnoses, Disease, findings, Malignant Neoplasm, cou, Predictive Medicine, protein complex, Desmoplastic astrocytoma of infancy, Proteins, Dmel_CG17964, Serum Markers, End Point, Myeloma Multiple, CG1768, Personalized, DRF2, Client, Peptide, Examination and Diagnoses, Immune Marker, MM, Al amyloidosis, Frozen Plasmas, multiple myeloma, Isotope, MS, Lr, MT, native protein, pan.dTCF, Surrogate End Point, Mass Screenings, MLPLI, Protein, chemical analysis, Neoplasm, Myelomatosis, Tcf, TCF, Dias, scales, Hemolytic Complement, Tcf/LEF, MULT MYELM W/O REMISSION, Mass Spectrum Analyses, Plasma-Cell, Biologic Markers, Lef1, periarteritis, Plasma, Mass Spectrum, primary cancer, Serum Marker, LEF1, scale, Surrogate, Endpoints, portion of plasma, Kahler Disease, Theranostic, tcf, Cancers, l(4)102ABb, malignant tumor, CG32005, Surrogate Marker, Multiple myeloma without mention of remission, Protein Gene Products, plan specification, Gene Proteins, Complement Proteins, Preparations, no ICD-O subtype, P-Health, Plasma Cell Myeloma, Lef, Standards, Bra, P Health, Peptid, assay, lef1, Neoplasia, Immune Markers"],"additional_accession":[]},"is_claimable":false,"name":"Pan-cancer plasma proteome profiling using SIS recombinant protein fragments reveals downregulation of proteins interacting with immunoglobulins in multiple myeloma","description":"Mass spectrometry based on Data Independent Acquisition (DIA) strategies has developed into powerful tools suitable for precision medicine applications. Assays performed in this setting provide confident protein identification and precise quantification on an absolute scale when combined with stable isotope recombinant protein standards. Here, we describe a comprehensive targeted proteomics approach to profile a pan-cancer cohort consisting of 1,800 blood plasma samples representing 15 different types of cancer. Using liquid biopsies, 253 proteins were absolutely quantified in multiplex. The targeted method resulted in a low intra-assay variability (CV 17.2%) and a total of 1,013 peptides were quantified across almost two thousand injections. The study identified several protein targets as potential biomarker panel for the diagnosis of multiple myeloma patients using differential expression analysis and machine learning. The combination of multiple markers, including the complement complex C1, JCHAIN and CD5L, resulted in an accurate predictive model with an AUC of 0.96 for the identification of multiple myeloma patients across a cohort of various cancer patients.","dates":{"publication":"Wed Jul 03 00:00:00 GMT+01:00 2024"},"accession":"PXD037946","cross_references":{"TAXONOMY":["9606"],"pubmed":["37835457"]}}