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Currently this classification relies mainly on histological assessment, but gene expression analysis by microarrays has shown great promise. Here we show that high accuracy, quantitative proteomics can robustly segregate cancer subtypes directly at the level of expressed proteins. We investigated two histologically indistinguishable subtypes of diffuse large B-cell lymphoma (DLBCL): activated B-cell-like (ABC) and germinal-center B-cell-like (GCB) subtypes, by first developing a general lymphoma stable isotope labeling with amino acids in cell culture (SILAC) mix from heavy stable isotope-labeled cell lines. This super-SILAC mix was combined with cell lysates from five ABC-DLBCL and five GCB-DLBCL cell lines. Shotgun proteomic analysis on a linear ion trap Orbitrap mass spectrometer with high mass accuracy at the MS and MS/MS levels yielded a proteome of more than 7,500 identified proteins. High accuracy of quantification allowed robust separation of subtypes by principal component analysis. The main contributors to the classification included proteins known to be differentially expressed between the subtypes such as the transcription factors IRF4 and SPI1/PU.1, cell surface markers CD44 and CD27, as well as novel candidates. We extracted a signature of 55 proteins that segregated subtypes and contained proteins connected to functional differences between the ABC and GCB-DLBCL subtypes, including many NF-κB-regulated genes. Shortening the analysis time to single-shot analysis combined with use of the new linear quadrupole Orbitrap analyzer (Q Exactive) also clearly differentiated between the subtypes. These results show that high resolution shotgun proteomics combined with super-SILAC-based quantification is a promising new technology for tumor characterization and classification."],"pubmed_title":["Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles."],"pubmed_authors":["Deeb Sally J SJ,D'Souza Rochelle C J RC,Cox Jürgen J,Schmidt-Supprian Marc M,Mann Matthias M,","Deeb Sally J SJ, D'Souza Rochelle C J RC, Cox Jürgen J, Schmidt-Supprian Marc M, Mann Matthias M"],"name_synonyms":["Histiocytic Lymphoma, DLBCL, Taxonomy, taxonomy, Histiocytic, Large-Cell Lymphomas, Systematics, LYMPHOMA LARGE DIFFUSE, DIFFUSE LARGE LYMPHOMA, LARGE LYMPHOMA DIFFUSE, Diffuse, Diffuse Large-Cell, Classifications, polypeptide, Taxonomies, Large-Cell, Large Cell Lymphoma, Diffuse Histiocytic Lymphomas, proteins., Diffuse Large Cell Lymphoma, hierarchies, hierarchy, Large Lymphoid Lymphoma, Histiocytic Lymphomas, Large B-Cell, systematics, LARGE LYMPHOMA, LYMPHOMA LARGE, Lymphoma, Diffuse Histiocytic Lymphoma, Diffuse Large-Cell Lymphomas, large B-cell lymphoma, Large Cell, Diffuse Large Cell, Lymphomas, LYMPHOMA DIFFUSE LARGE, Diffuse Large-Cell Lymphoma, Large Lymphoid, Diffuse Histiocytic, Large-Cell Lymphoma"],"description_synonyms":["B Cells, GBA1, mol, Bursa-Dependent Lymphocytes, Aminosaeure, Lymphoma (clinical), number, B cell, Aminocarbonsaeure, GLUC, Gene, high weight, DIFFUSE LARGE LYMPHOMA, Germinoblastoma, LARGE LYMPHOMA DIFFUSE, Isotope-Coded Affinity, Malignant, Germinoblastic Sarcoma, presence, DUH3, Malignant Lymphomas, Large Lymphoid Lymphoma, Malignant lymphoma NOS, heavy, Gene Products, Line, Isotopically-Coded Affinity, cell line., Lymphomas, malignant tumour, Isotopically-Coded Affinity Tagging, MIX, Reticulolymphosarcoma, Histiocytic Lymphoma, DLBCL, ABC, Sarcomas, B-cell, amino acids, cell, Lymphoma (Non-Hodgkin), malignant neoplasia, cell line cell, proteins, ABC14, cell line, Diffuse, Large-Cell, Large Cell Lymphoma, Malignant Lymphoma, Diffuse Large Cell Lymphoma, Sarcoma, lymphoma (Hodgkin and Non-Hodgkin), B lymphocyte, Histiocytic Lymphomas, Stable, Isotope-Coded Affinity Tagging, MCOPCB7, Diffuse Large-Cell Lymphomas, LAN, Tagging, LYMPHOMA DIFFUSE LARGE, MTABC3, Stable Isotope Labeling, Cancer, data, Malignant Neoplasm, B Lymphocytes, Aminokarbonsaeure, Large-Cell Lymphomas, PRP, Proteins, Cell Lines, cell_line, Labeling, Cell, lymphoma (Hodgkin's and non-Hodgkin's), polypeptide, Isotope, count in organism, Experiment, Reticulolymphosarcomas, count, Large B-Cell, Stable Isotope, LARGE LYMPHOMA, LYMPHOMA LARGE, Protein, NOS, Germinoblastic Sarcomas, MIXL, large B-cell lymphoma, Germinoblastic, Large Cell, Diffuse Large Cell, Diffuse Large-Cell Lymphoma, Isotope Coded Affinity Tagging, Large-Cell Lymphoma, Lines, MILD1, B-Lymphocytes, Histiocytic, LYMPHOMA LARGE DIFFUSE, Bursa-Equivalent Lymphocyte, Cancers, Isotope Labeling, Germinoblastomas, Amino, Affinity Tagging, malignant tumor, Isotopically-Coded, Protein Gene Products, Diffuse Large-Cell, Gene Proteins, Diffuse Histiocytic Lymphomas, B-Cells, GCB, B-Lymphocyte, Lymphoma, Diffuse Histiocytic Lymphoma, Isotope-Coded, Acids, quantitative, B-lymphocyte, Large Lymphoid, Diffuse Histiocytic, umat, presence or absence in organism"],"pubmed_title_synonyms":["Histiocytic Lymphoma, DLBCL, Taxonomy, taxonomy, Histiocytic, Large-Cell Lymphomas, Systematics, LYMPHOMA LARGE DIFFUSE, DIFFUSE LARGE LYMPHOMA, LARGE LYMPHOMA DIFFUSE, Diffuse, Diffuse Large-Cell, Classifications, polypeptide, Taxonomies, Large-Cell, Large Cell Lymphoma, Diffuse Histiocytic Lymphomas, proteins., Diffuse Large Cell Lymphoma, hierarchies, hierarchy, Large Lymphoid Lymphoma, Histiocytic Lymphomas, Large B-Cell, systematics, LARGE LYMPHOMA, LYMPHOMA LARGE, Lymphoma, Diffuse Histiocytic Lymphoma, Diffuse Large-Cell Lymphomas, large B-cell lymphoma, Large Cell, Diffuse Large Cell, Lymphomas, LYMPHOMA DIFFUSE LARGE, Diffuse Large-Cell Lymphoma, Large Lymphoid, Diffuse Histiocytic, Large-Cell Lymphoma"],"pubmed_abstract_synonyms":["SPI1, Ly-24, B Cells, Antemortem Diagnosis, AU023126, Materials, determination, GBA1, Pgp-1, Epican, Bursa-Dependent Lymphocytes, Aminosaeure, CD44A, B cell, GLUC, PGP-1, hyaluronate receptor, 6330543G17Rik, Germinoblastoma, Principal Component Analyses, Tumor, Diagnosis, Tp55, Long Term, cell associated, Classifications, Malignant Lymphomas, hierarchies, Extracellular matrix receptor III, hierarchy, systematics, Lymphocyte antigen 24, symptoms, Line, Analysis, Lymphomas, Effect, Isotopically-Coded Affinity Tagging, MIX, PGP-I, Pgp1, Reticulolymphosarcoma, treatment, Histiocytic Lymphoma, ABC, Spip, amino acids, Gene Expressions, Analyses, Lymphoma (Non-Hodgkin), cell line cell, proteins, analyzer, ABC14, LHR, heparan sulfate proteoglycan, cell line, Large Cell Lymphoma, Malignant Lymphoma, Sarcoma, B lymphocyte, HERMES, disease management, MDU2, MDU3, MCOPCB7, Tagging, Hyaluronate receptor, CD27, MTABC3, Long-Term Effects, Prx3, Stable Isotope Labeling, S152. LPFS2, Tumors, METAA, screening, SPI-1, systematics., B Lymphocytes, Tnfrsf7, Aminokarbonsaeure, Pu.1, PRP, IRF-4, Arts, Systematics, Longterm Effect, MC56, CD44 antigen, SFPI1, large mass, hermes antigen, results, tumours, Diagnoses, GP90 lymphocyte homing|adhesion receptor, lymphoma (Hodgkin's and non-Hodgkin's), Taxonomies, AW146109, Hermes antigen, Reticulolymphosarcomas, Postmortem, count, ly-24, LARGE LYMPHOMA, LYMPHOMA LARGE, Examinations and Diagnoses, PU.1, Genetic Materials, NOS, Germinoblastic, Postmortem Diagnosis, Diffuse Large Cell, Genetic Material, Large-Cell Lymphoma, CD44, Lines, MILD1, HUTCH-I, Postmortem Diagnoses, Sfpi1, Industrial, CDW44, Factors, B-Lymphocytes, Industrial Arts, MIC4, SHEP8, expanded, signs, Germinoblastomas, SHOT, Diffuse Large-Cell, Principal Component, CDw44, GCB, Patient, enlarged, B-Lymphocyte, Material, Lymphoma, ECMR-III, Cistron, Acids, Spi-1, SPI-A, cell bound, Proteomes, time, Diffuse Histiocytic, umat, AW121933, big, LSIRF, OG12X, MUM1, taxonomy, Effects, RHAMM, Neoplasms, Lymphoma (clinical), number, Aminocarbonsaeure, Gene, high weight, DIFFUSE LARGE LYMPHOMA, TNFRSF7, LARGE LYMPHOMA DIFFUSE, Isotope-Coded Affinity, Malignant, Germinoblastic Sarcoma, Transcription Factor, presence, DUH3, 31 kDa-transforming protein, NEOPL, period, large, Sfpi-1, IN, T-cell activation antigen CD27, Large Lymphoid Lymphoma, Malignant lymphoma NOS, heavy, Gene Products, Tfpu.1, Antemortem, Isotopically-Coded Affinity, malignant tumour, DLBCL, Sarcomas, Transcription, Taxonomy, B-cell, epican, Genetic, Longterm, cell, Tcfpu1, phagocytic glycoprotein I, malignant neoplasia, tumour, Diagnoses and Examinations, Long-Term, Expressions, Diffuse, Large-Cell, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), Diffuse Large Cell Lymphoma, Phagocytic glycoprotein I, CSPG8, lymphoma (Hodgkin and Non-Hodgkin), phagocytic glycoprotein 1, Histiocytic Lymphomas, Stable, Clients, great, Isotope-Coded Affinity Tagging, Diffuse Large-Cell Lymphomas, Long-Term Effect, Expression, T14, LAN, LYMPHOMA DIFFUSE LARGE, Neoplastic Growth, Dis-1, S152, Cancer, Antemortem Diagnoses, use, findings, SFFV proviral integration 1 protein, Malignant Neoplasm, high mass, Phagocytic glycoprotein 1, Large-Cell Lymphomas, Proteins, Cell Lines, cell_line, Factor, Cistrons, Client, Labeling, Cell, Heparan sulfate proteoglycan, polypeptide, Isotope, Dis1, count in organism, AI385587, Large B-Cell, Stable Isotope, chemical analysis, Protein, CD27L receptor, Long Term Effects, proteomic analysis, Germinoblastic Sarcomas, MIXL, large B-cell lymphoma, Large Cell, Diffuse Large-Cell Lymphoma, Isotope Coded Affinity Tagging, HCELL, Tumor necrosis factor receptor superfamily member 7, Histiocytic, extracellular matrix receptor III, LYMPHOMA LARGE DIFFUSE, Bursa-Equivalent Lymphocyte, Cancers, OF, Isotope Labeling, Amino, Affinity Tagging, malignant tumor, Isotopically-Coded, OG12, Longterm Effects, Protein Gene Products, lymphocyte antigen 24, Gene Proteins, Diffuse Histiocytic Lymphomas, B-Cells, Diffuse Histiocytic Lymphoma, Isotope-Coded, NF-EM5, assay, quantitative, Og12x, B-lymphocyte, Large Lymphoid, NEOPLASMS BENIGN, Neoplasia, GP90 lymphocyte homing/adhesion receptor, presence or absence in 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Experiment: TMD8(2), file: folder summary. Published as part of Mol Cell Proteomics. 2012 May;11(5):77-89  . From the Abstract: {{i}} ... Here we show that high accuracy, quantitative proteomics can robustly segregate cancer subtypes directly at the level of expressed proteins. We investigated two histologically indistinguishable subtypes of diffuse large B-cell lymphoma (DLBCL): activated B-cell-like (ABC) and germinal-center B-cell-like (GCB) subtypes, by first developing a general lymphoma stable isotope labeling with amino acids in cell culture (SILAC) mix from heavy stable isotope-labeled cell lines. This super-SILAC mix was combined with cell lysates from five ABC-DLBCL and five GCB-DLBCL cell lines ... {{/i}}","dates":{"submission":"2015-05-07"},"accession":"GPM32310019515","cross_references":{"pubmed":["22442255"],"Pride":["PXD002098"],"pride":[],"Pride Archive":["PXD002098"]}}