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1. Full Text Proteogenomics connects somatic mutations to signalling in breast cancer
by Mertins, Philipp and Mani, D.R and Ruggles, Kelly V and Gillette, Michael A and Clauser, Karl R and Wang, Pei and Wang, Xianlong and Qiao, Jana W and Cao, Song and Petralia, Francesca and Kawaler, Emily and Mundt, Filip and Krug, Karsten and Tu, Zhidong and Lei, Jonathan T and Gatza, Michael L and Wilkerson, Matthew and Perou, Charles M and Yellapantula, Venkata and Huang, Kuan-Lin and Lin, Chenwei and McLellan, Michael D and Yan, Ping and Davies, Sherri R and Townsend, R. Reid and Skates, Steven J and Wang, Jing and Zhang, Bing and Kinsinger, Christopher R and Mesri, Mehdi and Rodriguez, Henry and Ding, Li and Paulovich, Amanda G and Fenyö, David and Ellis, Matthew J and Carr, Steven A and NCI CPTAC
Nature (London), ISSN 0028-0836, 05/2016, Volume 534, Issue 7605, pp. 55 - 62
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Protein Kinases - metabolism | Focal Adhesion Kinase 1 - genetics | Receptor, Epidermal Growth Factor - genetics | Protein Kinases - genetics | Cyclin-Dependent Kinases - metabolism | Receptor, ErbB-2 - genetics | Receptors, G-Protein-Coupled - metabolism | Genomics | Humans | Gene Expression Regulation, Neoplastic | Receptor, ErbB-2 - metabolism | Phosphoproteins - metabolism | Receptor-Interacting Protein Serine-Threonine Kinase 2 - genetics | Tumor Suppressor Protein p53 - genetics | Breast Neoplasms - metabolism | Receptor-Interacting Protein Serine-Threonine Kinase 2 - metabolism | Breast Neoplasms - enzymology | Receptor, Epidermal Growth Factor - metabolism | Phosphoproteins - analysis | Mass Spectrometry | src-Family Kinases - metabolism | Female | Cyclin-Dependent Kinases - genetics | Focal Adhesion Kinase 1 - metabolism | Chromosomes, Human, Pair 5 - genetics | Breast Neoplasms - classification | Chromosome Deletion | p21-Activated Kinases - genetics | Signal Transduction | Molecular Sequence Annotation | Calcium-Binding Proteins - deficiency | Phosphoproteins - genetics | Mutation - genetics | S-Phase Kinase-Associated Proteins - metabolism | p21-Activated Kinases - metabolism | Phosphatidylinositol 3-Kinases - genetics | Breast Neoplasms - genetics | Class I Phosphatidylinositol 3-Kinases | Proteomics | S-Phase Kinase-Associated Proteins - genetics | Receptors, G-Protein-Coupled - genetics | src-Family Kinases - genetics | Calcium-Binding Proteins - genetics | Breast cancer | Genetic aspects | Research | Oncology, Experimental | Cancer | Physiological aspects | Methods | Mutation (Biology) | Proteins | Gene amplification | Peptides | Protein expression | Genomes | Mutation | Kinases | Deoxyribonucleic acid--DNA | Tumors | Index Medicus | Medicin och hälsovetenskap
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2. Full Text Proteogenomic characterization of human colon and rectal cancer
by Zhang, Bing and Zhang, Bing and Wang, Jing and Wang, Jing and Wang, Xiaojing and Wang, Xiaojing and Zhu, Jing and Zhu, Jing and Liu, Q and Liu, Qi and Shi, Zhiao and Shi, Zhiao and Chambers, Matthew C and Chambers, Matthew C and Zimmerman, Lisa J and Zimmerman, Lisa J and Shaddox, Kent F and Shaddox, Kent F and Kim, Sangtae and Kim, Sangtae and Davies, Sherri R and Davies, Sherri R and Wang, Sean and Wang, Sean and Wang, Pei and Wang, Pei and Kinsinger, Christopher R and Kinsinger, Christopher R and Rivers, Robert C and Rivers, Robert C and Rodriguez, Henry and Rodriguez, Henry and Townsend, R. Reid and Townsend, R Reid and Ellis, Matthew J. C and Ellis, Matthew J C and Carr, Steven A and Carr, Steven A and Tabb, David L and Tabb, David L and Coffey, Robert J and Coffey, Robert J and Slebos, Robbert J C and Slebos, Robbert J. C and Liebler, Daniel C and Liebler, Daniel C and NCI CPTAC, CPTAC and Gillette, Michael A and Klauser, Karl R and Kuhn, Eric and Mani, D.R and Mertins, Philipp and Ketchum, Karen A and Paulovich, Amanda G and Whiteaker, Jeffrey R and Edwards, Nathan J and McGarvey, Peter B and Madhavan, Subha and Chan, Daniel and Pandey, Akhilesh and Shih, Ie-Ming and Zhang, Hui and Zhang, Zhen and Zhu, Heng and Whiteley, Gordon A and Skates, Steven J and White, Forest M and Levine, Douglas A and Boja, Emily S and Hiltke, Tara and Mesri, Mehdi and Shaw, Kenna M and Stein, Stephen E and Fenyo, David and Liu, Tao and McDermott, Jason E and Payne, Samuel H and Rodland, Karin D and Smith, Richard D and Rudnick, Paul and Snyder, Michael and Zhao, Yingming and Chen, Xian and Ransohoff, David F and Hoofnagle, Andrew N and Sanders, Melinda E and Wang, Yue and Ding, Li and NCI CPTAC and the NCI CPTAC
Nature (London), ISSN 0028-0836, 2014, Volume 513, Issue 7518, pp. 382 - 387
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Colonic Neoplasms - genetics | Proteome - genetics | Genomics | Humans | RNA, Messenger - analysis | Neoplasm Proteins - metabolism | RNA, Messenger - metabolism | RNA, Neoplasm - metabolism | Colonic Neoplasms - metabolism | Mutation, Missense - genetics | Mitochondrial Membrane Transport Proteins - genetics | Point Mutation - genetics | DNA Methylation | RNA, Neoplasm - analysis | Rectal Neoplasms - genetics | Neoplasm Proteins - genetics | RNA, Messenger - genetics | DNA Copy Number Variations - genetics | Hepatocyte Nuclear Factor 4 - genetics | Transcriptome - genetics | Proteome - analysis | Microsatellite Repeats - genetics | Proto-Oncogene Proteins pp60(c-src) - genetics | Proteomics | CpG Islands - genetics | RNA, Neoplasm - genetics | Neoplasm Proteins - analysis | Rectal Neoplasms - metabolism | Proteome - metabolism | Chromosomes, Human, Pair 20 - genetics | Care and treatment | Colon cancer | RNA | Analysis | Colorectal cancer | Genetic aspects | Methylation | Proteins | Peptides | Genes | Colon | Mass spectrometry | Tumors | Cancer | Index Medicus
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3. Full Text The R882H DNMT3A Mutation Associated with AML Dominantly Inhibits Wild-Type DNMT3A by Blocking Its Ability to Form Active Tetramers
by Russler-Germain, David A and Spencer, David H and Young, Margaret A and Lamprecht, Tamara L and Miller, Christopher A and Fulton, Robert and Meyer, Matthew R and Erdmann-Gilmore, Petra and Townsend, R. Reid and Wilson, Richard K and Ley, Timothy J
Cancer cell, ISSN 1535-6108, 04/2014, Volume 25, Issue 4, pp. 442 - 454
Oncology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Amino Acid Sequence | Prognosis | Humans | Models, Molecular | Molecular Sequence Data | DNA (Cytosine-5-)-Methyltransferases - chemistry | DNA (Cytosine-5-)-Methyltransferases - genetics | DNA Methylation | Leukemia, Myeloid, Acute - enzymology | Alleles | Protein Conformation | Mutation | Leukemia, Myeloid, Acute - genetics | Physiological aspects | Genetic aspects | Methyltransferases | Genomics | Leukemia | Stem cells | Chromosomes | Index Medicus
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4. Full Text Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry
by Mertins, Philipp and Tang, Lauren C and Krug, Karsten and Clark, David J and Gritsenko, Marina A and Chen, Lijun and Clauser, Karl R and Clauss, Therese R and Shah, Punit and Gillette, Michael A and Petyuk, Vladislav A and Thomas, Stefani N and Mani, D.R and Mundt, Filip and Moore, Ronald J and Hu, Yingwei and Zhao, Rui and Schnaubelt, Michael and Keshishian, Hasmik and Monroe, Matthew E and Zhang, Zhen and Udeshi, Namrata D and Davies, Sherri R and Townsend, R. Reid and Chan, Daniel W and Smith, Richard D and Zhang, Hui and Liu, Tao and Carr, Steven A and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Nature protocols, ISSN 1754-2189, 07/2018, Volume 13, Issue 7, pp. 1632 - 1661
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Neoplasm Transplantation | Humans | Benchmarking | Workflow | Proteome - analysis | Animals | Heterografts | Phosphoproteins - analysis | Breast Neoplasms - pathology | Female | Mice | Proteomics - methods | Chromatography, Liquid - methods | Mass Spectrometry - methods | Disease Models, Animal | High-Throughput Screening Assays - methods | Liquid chromatography | Diagnosis | Mass spectrometry | Methods | Proteomics | Tumors | Multiplexing | Animal models | Laboratories | Xenotransplantation | Tissue analysis | Tissues | Proteins | Data integration | Xenografts | Tags | Spectroscopy | Tumor cells | Stroma | Data processing | Mass spectroscopy | Breast cancer | Reproducibility | Scientific imaging | Deviation | Cancer | Index Medicus | Medicin och hälsovetenskap
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5. Full Text Targeted peptide measurements in biology and medicine: Best practices for mass spectrometry-based assay development using a fit-for-purpose approach
by Carr, Steven A and Abbatiello, Susan E and Ackermann, Bradley L and Borchers, Christoph and Domon, Bruno and Deutsch, Eric W and Grant, Russell P and Hoofnagle, Andrew N and Hüttenhain, Ruth and Koomen, John M and Liebler, Daniel C and Liu, Tao and MacLean, Brendan and Mani, D.R and Mansfield, Elizabeth and Neubert, Hendrik and Paulovich, Amanda G and Reiter, Lukas and Vitek, Olga and Aebersold, Ruedi and Anderson, Leigh and Bethem, Robert and Blonder, Josip and Boja, Emily and Botelho, Julianne and Boyne, Michael and Bradshaw, Ralph A and Burlingame, Alma L and Chan, Daniel and Keshishian, Hasmik and Kuhn, Eric and Kinsinger, Christopher and Lee, Jerry S.H and Lee, Sang-Won and Moritz, Robert and Oses-Prieto, Juan and Rifai, Nader and Ritchie, James and Rodriguez, Henry and Srinivas, Pothur R and Townsend, R. Reid and Van Eyk, Jennifer and Whiteley, Gordon and Wiita, Arun and Weintraub, Susan
Molecular & cellular proteomics, ISSN 1535-9476, 2014, Volume 13, Issue 3, pp. 907 - 917
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Medicine | Guidelines as Topic | Reference Standards | Animals | Peptides - metabolism | Proteomics - standards | Humans | Isotope Labeling | Biological Assay - methods | Biology | Software | Mass Spectrometry - methods | Index Medicus | Technological Innovation and Resources
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6. Full Text Mass spectrometry–based proteomics reveals potential roles of NEK9 and MAP2K4 in resistance to PI3K inhibition in triple-negative breast cancers
by Mundt, Filip and Rajput, Sandeep and Li, Shunqiang and Ruggles, Kelly V and Mooradian, Arshag D and Mertins, Philipp and Gillette, Michael A and Krug, Karsten and Guo, Zhanfang and Hoog, Jeremy and Erdmann-Gilmore, Petra and Primeau, Tina and Huang, Shixia and Edwards, Dean P and Wang, Xiaowei and Wang, Xuya and Kawaler, Emily and Mani, D.R and Clauser, Karl R and Gao, Feng and Luo, Jingqin and Davies, Sherri R and Johnson, Gary L and Huang, Kuan-lin and Yoon, Christopher J and Ding, Li and Fenyo, David and Ellis, Matthew J and Reid Townsend, R and Held, Jason M and Carr, Steven A and Ma, Cynthia X
Cancer research (Chicago, Ill.), ISSN 0008-5472, 05/2018, Volume 78, Issue 10, pp. 2732 - 2746
Life Sciences & Biomedicine | Oncology | Science & Technology | Xenotransplantation | MAP kinase | Mass spectroscopy | Lethality | Breast cancer | 1-Phosphatidylinositol 3-kinase | Signaling | Proteomics | Xenografts | Inhibition | Mass spectrometry | Tumors | Cancer | Index Medicus | Medicin och hälsovetenskap
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7. Full Text DNMT3A Mutations in Acute Myeloid Leukemia
by Ley, Timothy J and Ding, Li and Walter, Matthew J and McLellan, Michael D and Lamprecht, Tamara and Larson, David E and Kandoth, Cyriac and Payton, Jacqueline E and Baty, Jack and Welch, John and Harris, Christopher C and Lichti, Cheryl F and Townsend, R. Reid and Fulton, Lucinda A and Fulton, Robert S and Dooling, David J and Koboldt, Daniel C and Schmidt, Heather and Zhang, Qunyuan and Osborne, John R and Lin, Ling and O'Laughlin, Michelle and McMichael, Joshua F and Delehaunty, Kim D and McGrath, Sean D and Magrini, Vincent J and Vickery, Tammi L and Hundal, Jasreet and Cook, Lisa L and Conyers, Joshua J and Swift, Gary W and Reed, Jerry P and Alldredge, Patricia A and Wylie, Todd and Walker, Jason and Kalicki, Joelle and Watson, Mark A and Heath, Sharon and Shannon, William D and Varghese, Nobish and Nagarajan, Rakesh and Westervelt, Peter and Tomasson, Michael H and Link, Daniel C and Graubert, Timothy A and DiPersio, John F and Mardis, Elaine R and Wilson, Richard K
The New England journal of medicine, ISSN 0028-4793, 12/2010, Volume 363, Issue 25, pp. 2424 - 2433
Medicine, General & Internal | Life Sciences & Biomedicine | General & Internal Medicine | Science & Technology | Hematologic and hematopoietic diseases | Leukemias. Malignant lymphomas. Malignant reticulosis. Myelofibrosis | Biological and medical sciences | General aspects | Medical sciences | Gene Expression | Frameshift Mutation | Prognosis | Humans | Middle Aged | Proportional Hazards Models | Male | DNA Mutational Analysis - methods | Nucleic Acid Amplification Techniques | Leukemia, Myeloid, Acute - mortality | DNA (Cytosine-5-)-Methyltransferases - genetics | DNA Methylation | Karyotyping | Survival Analysis | Adult | Female | Mutation | Leukemia, Myeloid, Acute - genetics | Amino acids | Usage | Chemical properties | Nucleotide sequencing | Health aspects | DNA methylation | Genes | Deoxyribonucleic acid--DNA | Cancer | Index Medicus | Abridged Index Medicus
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8. Full Text Proteogenomic integration reveals therapeutic targets in breast cancer xenografts
by Huang, Kuan-Lin and Li, Shunqiang and Mertins, Philipp and Cao, Song and Gunawardena, Harsha P and Ruggles, Kelly V and Mani, D.R and Clauser, Karl R and Tanioka, Maki and Usary, Jerry and Kavuri, Shyam M and Xie, Ling and Yoon, Christopher and Qiao, Jana W and Wrobel, John and Wyczalkowski, Matthew A and Erdmann-Gilmore, Petra and Snider, Jacqueline E and Hoog, Jeremy and Singh, Purba and Niu, Beifung and Guo, Zhanfang and Sun, Sam Qiancheng and Sanati, Souzan and Kawaler, Emily and Wang, Xuya and Scott, Adam and Ye, Kai and McLellan, Michael D and Wendl, Michael C and Malovannaya, Anna and Held, Jason M and Gillette, Michael A and Fenyö, David and Kinsinger, Christopher R and Mesri, Mehdi and Rodriguez, Henry and Davies, Sherri R and Perou, Charles M and Ma, Cynthia and Reid Townsend, R and Chen, Xian and Carr, Steven A and Ellis, Matthew J and Ding, Li
Nature communications, ISSN 2041-1723, 03/2017, Volume 8, Issue 1, pp. 14864 - 14864
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Breast Neoplasms - therapy | Xenograft Model Antitumor Assays | Phosphorylation | Animals | Breast Neoplasms - genetics | Proteogenomics | Signal Transduction | Humans | Female | Mice | Transcriptome - genetics | Molecular Targeted Therapy | Index Medicus
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