MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/x01/MSV000084878/primaryOK2006000Lukas Reiterhttps://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=a555209360f64458887143db87f85e4alukas.reiter@biognosys.comMassIVE168MOD: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."ProteomicsQ Exactive HF-XHomo Sapiens (ncbitaxon:9606)Biognosys AGComprehensive proteome quantification is crucial for a better understanding of underlying mechanisms of diseases. Liquid chromatography mass spectrometry (LC-MS) has become the method of choice for comprehensive proteome quantification due to its power and versatility. Even though great advances have been made in recent years, full proteome coverage for complex samples remains challenging due to the high dynamic range of protein expression. Additionally, when studying disease regulatory proteins, biomarkers or potential drug targets are often low abundant, such as for instance kinases and transcription factors. Here, we show that with improvements in chromatography and data analysis the single shot proteome coverage can go beyond 10 000 proteins in human tissue. In a testis cancer study, we quantified 11 200 proteins using data independent acquisition (DIA). This depth was achieved with a false discovery rate of 1% which was experimentally validated using a two species test. We introduce the concept of hybrid libraries which combines the strength of direct searching of DIA data as well as the use of large project-specific or published DDA data sets. Remarkably deep proteome coverage is possible using hybrid libraries without the additional burden of creating a project-specific library. Within the testis cancer set, we found a large proportion of proteins in an altered expression (in total: 3351; 1453 increased in cancer). Many of these proteins could be linked to the hallmarks of cancer. For example, the complement system was downregulated which helps to evade the immune response and chromosomal replication was upregulated indicating a dysregulated cell cycle.Surpassing 10 000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy.Muntel Jan J, Gandhi Tejas T, Verbeke Lynn L, Bernhardt Oliver M OM, Treiber Tobias T, Bruderer Roland R, Reiter Lukas Ll(2)k04204, CDF, Biological Markers, Viral Marker, Library., Surrogate Endpoints, Product, Laboratory, Biochemical, Mbp1, Endpoint, Cancer of the Testis, protein, 6330543G17Rik, testis cancer, Serum, Tumor, Rete, Readability, Techniques, Personal, protein polypeptide chains, Laboratory Markers, POF, diseases, Method, Biological, Pharmaceutical Product, diseases and disorders, AGAMOUS-like 61, Analysis, protein aggregate, myd, Testicular, DiA, INSL3R, Mass Spectrum Analysis, Psychological, Testis, human disease, me75, F, Man (Taxonomy), l(2)k07135, Analyses, Tissue, Su(Mir)1, Mbp-1, proteins, DIASP, D17Mit170, T1, DIA, Dia, Social, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, GREAT, Immune, Markers, Methodological Studies, medicine, Pharmaceutical, Viral Markers, 38E.16, Great, Homo sapiens disease, l(2)CA4, Social Power, Testicular Tumor, testicular tumor, Prx3, Power, Tumors, Viral, Surrogate Endpoint, gyltl1b-b, Modern, Liquid Chromatography, Testicular Tumors, Biochemical Markers, Psychological Powers, Procedure, Tl3, Biologic Marker, Tl2, Spectrum Analysis, Testicular Cancers, shortstop/kakapo, Testis Neoplasm, Spectroscopy, ms(2)04138, Desmoplastic infantile astrocytoma, Marker, MDDGA6, DmelCG18076, mKIAA0609, Diseases, Pharmaceutic, simple tissue, KIAA0609, fg, LGR8, Lgr8, Factors, gyltl1b, End Points, Grv, POF2, F27C12_24, F27C12.24, mdc1d, Spectrometry, expanded, Methodological, Immunologic, Laboratory Marker, Methodological Study, SHOT, human, Testis Cancers, disease, data analysis, MDC1D, enr, Cancer of Testis, enlarged, Biochemical Marker, grv, DIANA, Powers, Proteomes, 42/4, humans, big, Psychological Power, other disease, OG12X, human being, Procedures, Tumor of Rete Testis, Professional Power, Clinical Markers, False, Clinical Marker, Neoplasms, Testis Cancer, Gene, Spectrum Analyses, protein-containing complex, Transcription Factor, froggy, Gyltl1a, Surrogate End Points, Human, l(2)k05821, Surrogate Markers, method, large, polypeptide chain, l(2)k15606, Homo sapiens, method used in an experiment, DmelCG1768, Mass, Studies, Gene Products, HILDA, disease or disorder, Low, testis neoplasm, Technique, Man, Mass Spectroscopy, Shot, Drugs, paediatric testicular neoplasm, Biomarker, study, Transcription, Testicular Neoplasm, l(2)k10821, Gpr106, Clinical, neoplasm of testis, MDDGB6, Biological Marker, RXFPR2, LARGE, non-neoplastic, Study, BPFD#36, Immunologic Markers, drugs, data processing, great, disorder, species, Preparation, DIA2, Chromatographies, Immunologic Marker, GPR106, Biologic, Pharmaceuticals, Cancer, Products, cou, protein complex, kop, drug, Desmoplastic astrocytoma of infancy, Proteins, Serum Markers, disorders, CG18076, total expressed protein, End Point, medical condition, Factor, Rete Testis Tumors, CG1768, CG18637, Cancer of the Testes, DRF2, Immune Marker, MS, Lr, Rete Testis Tumor, pediatric testicular neoplasm, childhood neoplasm of the testis, native protein, natural protein, Surrogate End Point, Protein, MLPLI, Neoplasm, condition, Professional, Testis Tumor, Dias, Library, Mass Spectrum Analyses, Biologic Markers, Mass Spectrum, l(2)k05434, Serum Marker, Pharmaceutic Preparations, Testicular Cancer, Surrogate, l(2)k03010, Endpoints, kak, Cancers, Understanding, LGR8.1, Testis Tumors, Surrogate Marker, OG12, plan specification, Protein Gene Products, Drug, Gene Proteins, Personal Power, Preparations, Data, Modern Man, Power (Psychology), Bra, Testis Neoplasms, Og12x, Pharmaceutical Products, Data Analyses, Pharmaceutical Preparation, Immune Markersl(2)k04204, sodium salt, CDF, Surrogate Endpoints, Product, Laboratory, Liquid Chromatography Mass Spectrometry, Ultra Performance Liquid Chromatography-Mass Spectrometry, testis cancer, Tumor, 5730420M11Rik, Rete, Personal, protein polypeptide chains, HPLC-MS, Method, Biological, 10.5, AGAMOUS-like 61, Kinase, Analysis, bis(p-chlorophenyl)acetic acid, myd, 10.9, DiA, INSL3R, Testis, Cell Division Cycles, Ultra Performance Liquid Chromatography Mass Spectrometry, SET, F, Analyses, Tissue, Su(Mir)1, Mbp-1, V, proteins, DIASP, D17Mit170, DIA, Dia, Social, DmelCG4299, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, set, medicine, Homo sapiens disease, Social Power, Testicular Tumor, testicular tumor, ATP Phosphotransferases, Prx3, Power, Tumors, Viral, Procedure, Tl3, Tl2, Testicular Cancers, Testis Neoplasm, Benign, Marker, mKIAA0609, numerical data, simple tissue, fg, LGR8, Lgr8, HLA-DR-associated protein II, End Points, Grv, DI-2, Complement, High Pressure Liquid Chromatography Mass Spectrometry, I-2Dm, F27C12_24, F27C12.24, Spectrometry, expanded, Benign Neoplasms, Methodological, Immunologic, Laboratory Marker, human, Malignant Neoplasms, I-2PP1, Testis Cancers, MDC1D, TAF-IBETA, enr, Cancer of Testis, grv, DIANA, eve2, Complement System, TAF-Ibeta, 42/4, humans, CG2328, big, Psychological Power, Hybrids, OG12X, Tumor of Rete Testis, Clinical Marker, Neoplasms, protein-containing complex, Complement Protein, Transcription Factor, Human, l(2)k05821, large, l(2)k15606, Gene Products, HILDA, disease or disorder, even, Technique, Man, paediatric testicular neoplasm, Cycles, UPLC-MS, Transcription, anatomical systems, Clinical, neoplasm of testis, MDDGB6, Cell Division Cycle, cell-division cycle, 2pp2a, Spectrometries, CG10574, Study, Neoplasias, drugs, 2PP2A, dSET, dSet, species, Chromatographies, GPR106, Biologic, Pharmaceuticals, Cancer, Products, use, cou, Malignant Neoplasm, Proteins, Serum Markers, disorders, CG18076, High Pressure Liquid Chromatography-Mass Spectrometry, Factor, Rete Testis Tumors, Cancer of the Testes, DRF2, Cell, Immune Marker, Lr, childhood neoplasm of the testis, MT, native protein, I-2PP2A, Surrogate End Point, Dm I-2, Neoplasm, condition, Eve, EVE, Hemolytic Complement, Library, Biologic Markers, primary cancer, Pharmaceutic Preparations, Testicular Cancer, ensemble, Surrogate, Endpoints, kak, Cancers, Understanding, Testis Tumors, malignant tumor, OG12, plan specification, Gene Proteins, Complement Proteins, Power (Psychology), Bra, Testis Neoplasms, LC-MS, Og12x, Pharmaceutical Products, Data Analyses, Neoplasia, Immune Markers, IPP2A2, Biological Markers, Viral Marker, Biochemical, Mbp1, High Performance Liquid Chromatography Mass Spectrometry, Endpoint, Cancer of the Testis, protein, 6330543G17Rik, Serum, High Performance Liquid Chromatography-Mass Spectrometry, Readability, Techniques, Laboratory Markers, POF, Liquid Chromatography-Mass, diseases, Pharmaceutical Product, diseases and disorders, protein aggregate, Testicular, Psychological, Immune Processes, human disease, me75, Immune Responses, Man (Taxonomy), l(2)k07135, DmelCG2328, TAF-I, T1, GREAT, IGAAD, Immune, Markers, Methodological Studies, DmelCG10574, malignant neoplasm, Liquid Chromatography-Mass Spectrometries, Pharmaceutical, Viral Markers, 38E.16, Great, l(2)CA4, Malignancies, ATP, phapii, Surrogate Endpoint, Process, gyltl1b-b, statistics and numerical data, Modern, Testicular Tumors, StF-IT-1, Biochemical Markers, Psychological Powers, Biologic Marker, Division Cycles, shortstop/kakapo, ms(2)04138, Desmoplastic infantile astrocytoma, MDDGA6, DmelCG18076, Diseases, VI, Pharmaceutic, KIAA0609, Transphosphorylases, 20.35, Factors, gyltl1b, Division Cycle, POF2, mdc1d, CG4299, Cell Cycles., Methodological Study, SHOT, disease, data analysis, enlarged, Biochemical Marker, Liquid, Powers, i2pp2a, Proteomes, 14.10, other disease, human being, Procedures, Professional Power, Clinical Markers, Benign Neoplasm, Testis Cancer, Gene, Malignant, froggy, PHAPII, Gyltl1a, Surrogate End Points, Surrogate Markers, method, potassium salt, polypeptide chain, Homo sapiens, utilization, 14C-labeled, method used in an experiment, DmelCG1768, Cycle, Studies, Low, testis neoplasm, Phosphotransferase, Shot, Drugs, Biomarker, study, Ultra-Performance Liquid Chromatography-Mass Spectrometry, Testicular Neoplasm, l(2)k10821, Gpr106, Malignancy, Biological Marker, ipp2a2, RXFPR2, LARGE, Cell Division, Transphosphorylase, Chimeras, non-neoplastic, BPFD#36, Immunologic Markers, Immune Response, data processing, taf-ibeta, great, disorder, Hemolytic, Preparation, DIA2, Chromatography-Mass Spectrometries, Immune Process, Immunologic Marker, protein complex, kop, drug, Desmoplastic astrocytoma of infancy, igaad, total expressed protein, End Point, medical condition, CG1768, CG18637, Phosphotransferases, group, Rete Testis Tumor, pediatric testicular neoplasm, Hybrid, natural protein, Protein, MLPLI, I2PP2A, Professional, Testis Tumor, Dias, DDA, l(2)k05434, Serum Marker, Kinases, l(2)k03010, l(2)46Ce, LGR8.1, l(2)46Cg, Surrogate Marker, l(2)46CFj, Protein Gene Products, Drug, l(2)46CFh, dSET/TAF-Ibeta, Personal Power, Preparations, 2610030F17Rik, l(2)46CFp, Data, Modern Man, Chromatography-Mass Spectrometry, Response, E(eve), AA407739, l(2)46CFg, Pharmaceutical PreparationCG1849, apparatus, l(1)LB9, leg, Proteins, Liquid Chromatography Mass Spectrometry, DmelCG1849, High Performance Liquid Chromatography Mass Spectrometry, instruments, Gene, Ultra Performance Liquid Chromatography-Mass Spectrometry, High Pressure Liquid Chromatography-Mass Spectrometry, Rnt, AA33, High Performance Liquid Chromatography-Mass Spectrometry, lLB5, l(1)AA33, devices, HPLC-MS, Liquid Chromatography-Mass, equipment, Protein, Gene Products, 1, 2, Data Analyses., Analysis, UPLC-MS, Ultra Performance Liquid Chromatography Mass Spectrometry, Ultra-Performance Liquid Chromatography-Mass Spectrometry, appliances, Analyses, High Pressure Liquid Chromatography Mass Spectrometry, Runt, Spectrometry, Spectrometries, l(1)19Ea, Protein Gene Products, P235, Gene Proteins, data analysis, data processing, l(1)B2/13.1, RUN, Run, Data, Liquid Chromatography-Mass Spectrometries, Chromatography-Mass Spectrometry, Liquid, LC-MS, Chromatography-Mass Spectrometries, LB5CG1849, apparatus, l(1)LB9, appliances, Analyses, Runt, leg, Proteins, DmelCG1849, instruments, Gene, l(1)19Ea, Rnt, AA33, Protein Gene Products, P235, lLB5, l(1)AA33, Gene Proteins, data analysis, devices, data processing, l(1)B2/13.1, equipment, RUN, Run, Data, Protein, Gene Products, 1, 2, Data Analyses., Analysis, LB56PXD013658falseSurpassing 10,000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategyComprehensive proteome quantification is crucial for a better understanding of underlying mechanisms of diseases. Liquid chromatography mass spectrometry (LC-MS) has become the method of choice for comprehensive proteome quantification due to its power and versatility. Even though great advances have been made in recent years, full proteome coverage for complex samples remains challenging due to the high dynamic range of protein expression. Additionally, when studying diseases regulatory proteins, biomarkers or potential drug targets are often low abundant, such as for instance kinases and transcription factors. Here, we show that with improvements in chromatography and data analysis the single shot proteome coverage can go beyond 10,000 proteins in human tissue. In a testis cancer study, we quantified 11,200 proteins using data independent acquisition (DIA). This depth was achieved with a false discovery rate of 1% which was experimentally validated using a two species test. We introduce the concept of hybrid libraries which combine the strength of direct searching of DIA data as well as the use of large project-specific or published DDA data sets. Remarkably deep proteome coverage is possible using hybrid libraries without the additional burden of creating a project-specific library.Fri Jan 31 17:16:00 GMT 2020MSV00008487831465043