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2. Targeted mass-spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP kinase, and AKT signaling

Author

Whiteaker, Jeffrey R, Sharma, Kanika, Hoffman, Melissa A, Kuhn, Eric, Zhao, Lei, Cocco, Alexandra R, Schoenherr, Regine M, Kennedy, Jacob J, Voytovich, Ulianna, Lin, Chenwei, Fang, Bin, Bowers, Kiah, Whiteley, Gordon, Colantonio, Simona, Bocik, William, Roberts, Rhonda, Hiltke, Tara, Boja, Emily, Rodriguez, Henry, McCormick, Frank, Holderfield, Matthew, Carr, Steven A, Koomen, John M, and Paulovich, Amanda G

Subjects
Biotechnology, Colo-Rectal Cancer, Bioengineering, Cancer, Digestive Diseases, AKT, Cancer signaling, MAP kinase, RAS, RTK, assay resource, immuno-MRM, pharmacodynamics, quantitative proteomics, targeted therapy
Abstract

SummaryA primary goal of the US National Cancer Institute's Ras initiative at the Frederick National Laboratory for Cancer Research is to develop methods to quantify RAS signaling to facilitate development of novel cancer therapeutics. We use targeted proteomics technologies to develop a community resource consisting of 256 validated multiple reaction monitoring (MRM)-based, multiplexed assays for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. As proof of concept, we quantify the response of melanoma (A375 and SK-MEL-2) and colorectal cancer (HCT-116 and HT-29) cell lines to BRAF inhibition by PLX-4720. These assays replace over 60 Western blots with quantitative mass spectrometry-based assays of high molecular specificity and quantitative precision, showing the value of these methods for pharmacodynamic measurements and mechanism of action studies. Methods, fit-for-purpose validation, and results are publicly available as a resource for the community at assays.cancer.gov.MotivationA lack of quantitative, multiplexable assays for phosphosignaling limits comprehensive investigation of aberrant signaling in cancer and evaluation of novel treatments. To alleviate this limitation, we sought to develop assays using targeted mass spectrometry for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. The resulting assays provide a resource for replacing over 60 Western blots in examining cancer signaling and tumor biology with high molecular specificity and quantitative rigor.

Published
2021

3. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics

Author

Yang, Mi, Petralia, Francesca, Li, Zhi, Li, Hongyang, Ma, Weiping, Song, Xiaoyu, Kim, Sunkyu, Lee, Heewon, Yu, Han, Lee, Bora, Bae, Seohui, Heo, Eunji, Kaczmarczyk, Jan, Stępniak, Piotr, Warchoł, Michał, Yu, Thomas, Calinawan, Anna P, Boutros, Paul C, Payne, Samuel H, Reva, Boris, Consortium, NCI-CPTAC-DREAM, Aderinwale, Tunde, Afyounian, Ebrahim, Agrawal, Piyush, Ali, Mehreen, Amadoz, Alicia, Azuaje, Francisco, Bachman, John, Bhalla, Sherry, Carbonell-Caballero, José, Chakraborty, Priyanka, Chaudhary, Kumardeep, Choi, Yonghwa, Choi, Yoonjung, Çubuk, Cankut, Dhanda, Sandeep Kumar, Dopazo, Joaquín, Elo, Laura L, Fóthi, Ábel, Gevaert, Olivier, Granberg, Kirsi, Greiner, Russell, Hidalgo, Marta R, Jayaswal, Vivek, Jeon, Hwisang, Jeon, Minji, Kalmady, Sunil V, Kambara, Yasuhiro, Kang, Jaewoo, Kang, Keunsoo, Kaoma, Tony, Kaur, Harpreet, Kazan, Hilal, Kesar, Devishi, Kesseli, Juha, Kim, Daehan, Kim, Keonwoo, Kim, Sang-Yoon, Kumar, Sajal, Liu, Yunpeng, Luethy, Roland, Mahajan, Swapnil, Mahmoudian, Mehrad, Muller, Arnaud, Nazarov, Petr V, Nguyen, Hien, Nykter, Matti, Okuda, Shujiro, Park, Sungsoo, Raghava, Gajendra Pal Singh, Rajapakse, Jagath C, Rantapero, Tommi, Ryu, Hobin, Salavert, Francisco, Saraei, Sohrab, Sharma, Ruby, Siitonen, Ari, Sokolov, Artem, Subramanian, Kartik, Suni, Veronika, Suomi, Tomi, Tranchevent, Léon-Charles, Usmani, Salman Sadullah, Välikangas, Tommi, Vega, Roberto, Zhong, Hua, Boja, Emily, Rodriguez, Henry, Stolovitzky, Gustavo, Guan, Yuanfang, Wang, Pei, Fenyö, David, and Saez-Rodriguez, Julio

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biotechnology, Cancer, Genetics, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Crowdsourcing, Female, Genomics, Humans, Machine Learning, Male, Neoplasms, Phosphoproteins, Proteins, Proteomics, Transcriptome, NCI-CPTAC-DREAM Consortium, cancer, crowdsourcing, genomics, machine learning, protein regulation, proteogenomics, proteomics, Biochemistry and Cell Biology, Biochemistry and cell biology
Abstract

Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer protein levels from other omics measurements, we leveraged crowdsourcing via the NCI-CPTAC DREAM proteogenomic challenge. We asked for methods to predict protein and phosphorylation levels from genomic and transcriptomic data in cancer patients. The best performance was achieved by an ensemble of models, including as predictors transcript level of the corresponding genes, interaction between genes, conservation across tumor types, and phosphosite proximity for phosphorylation prediction. Proteins from metabolic pathways and complexes were the best and worst predicted, respectively. The performance of even the best-performing model was modest, suggesting that many proteins are strongly regulated through translational control and degradation. Our results set a reference for the limitations of computational inference in proteogenomics. A record of this paper's transparent peer review process is included in the Supplemental Information.

Published
2020

5. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

Author

Olson, Nathan D., Wagner, Justin, McDaniel, Jennifer, Stephens, Sarah H., Westreich, Samuel T., Prasanna, Anish G., Johanson, Elaine, Boja, Emily, Maier, Ezekiel J., Serang, Omar, Jáspez, David, Lorenzo-Salazar, José M., Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A., Flores, Carlos, Kyriakidis, Konstantinos, Malousi, Andigoni, Shafin, Kishwar, Pesout, Trevor, Jain, Miten, Paten, Benedict, Chang, Pi-Chuan, Kolesnikov, Alexey, Nattestad, Maria, Baid, Gunjan, Goel, Sidharth, Yang, Howard, Carroll, Andrew, Eveleigh, Robert, Bourgey, Mathieu, Bourque, Guillaume, Li, Gen, Ma, ChouXian, Tang, LinQi, Du, YuanPing, Zhang, ShaoWei, Morata, Jordi, Tonda, Raúl, Parra, Genís, Trotta, Jean-Rémi, Brueffer, Christian, Demirkaya-Budak, Sinem, Kabakci-Zorlu, Duygu, Turgut, Deniz, Kalay, Özem, Budak, Gungor, Narcı, Kübra, Arslan, Elif, Brown, Richard, Johnson, Ivan J., Dolgoborodov, Alexey, Semenyuk, Vladimir, Jain, Amit, Tetikol, H. Serhat, Jain, Varun, Ruehle, Mike, Lajoie, Bryan, Roddey, Cooper, Catreux, Severine, Mehio, Rami, Ahsan, Mian Umair, Liu, Qian, Wang, Kai, Ebrahim Sahraeian, Sayed Mohammad, Fang, Li Tai, Mohiyuddin, Marghoob, Hung, Calvin, Jain, Chirag, Feng, Hanying, Li, Zhipan, Chen, Luoqi, Sedlazeck, Fritz J., and Zook, Justin M.

Published
2022
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6. Proteogenomic characterization of pancreatic ductal adenocarcinoma

Author

Amin, Mitual, An, Eunkyung, Ayad, Christina, Bauer, Thomas, Birger, Chet, Birrer, Michael J., Boca, Simina M., Bocik, William, Borucki, Melissa, Cai, Shuang, Carr, Steven A., Cerda, Sandra, Chen, Huan, Chen, Steven, Chesla, David, Chinnaiyan, Arul M., Colaprico, Antonio, Cottingham, Sandra, Derejska, Magdalena, Dhanasekaran, Saravana M., Domagalski, Marcin J., Druker, Brian J., Duffy, Elizabeth, Dyer, Maureen A., Edwards, Nathan J., Ellis, Matthew J., Eschbacher, Jennifer, Francis, Alicia, Francis, Jesse, Gabriel, Stacey, Gabrovski, Nikolay, Gardner, Johanna, Getz, Gad, Gillette, Michael A., Goldthwaite, Charles A., Jr., Grady, Pamela, Guo, Shuai, Hariharan, Pushpa, Hiltke, Tara, Hindenach, Barbara, Hoadley, Katherine A., Huang, Jasmine, Jones, Corbin D., Ketchum, Karen A., Kinsinger, Christopher R., Koziak, Jennifer M., Kusnierz, Katarzyna, Liu, Tao, Long, Jiang, Mallery, David, Mareedu, Sailaja, Matteotti, Ronald, Maunganidze, Nicollette, McGarvey, Peter B., Minoo, Parham, Paklina, Oxana V., Paulovich, Amanda G., Payne, Samuel H., Potapova, Olga, Pruetz, Barbara, Qi, Liqun, Roche, Nancy, Rodland, Karin D., Rohrer, Daniel C., Schadt, Eric E., Shabunin, Alexey V., Shelton, Troy, Shutack, Yvonne, Singh, Shilpi, Smith, Michael, Smith, Richard D., Sokoll, Lori J., Suh, James, Thangudu, Ratna R., Tsang, Shirley X., Um, Ki Sung, Valley, Dana R., Vatanian, Negin, Wang, Wenyi, Wilson, George D., Wiznerowicz, Maciej, Zhang, Zhen, Zhao, Grace, Cao, Liwei, Huang, Chen, Cui Zhou, Daniel, Hu, Yingwei, Lih, T. Mamie, Savage, Sara R., Krug, Karsten, Clark, David J., Schnaubelt, Michael, Chen, Lijun, da Veiga Leprevost, Felipe, Eguez, Rodrigo Vargas, Yang, Weiming, Pan, Jianbo, Wen, Bo, Dou, Yongchao, Jiang, Wen, Liao, Yuxing, Shi, Zhiao, Terekhanova, Nadezhda V., Cao, Song, Lu, Rita Jui-Hsien, Li, Yize, Liu, Ruiyang, Zhu, Houxiang, Ronning, Peter, Wu, Yige, Wyczalkowski, Matthew A., Easwaran, Hariharan, Danilova, Ludmila, Mer, Arvind Singh, Yoo, Seungyeul, Wang, Joshua M., Liu, Wenke, Haibe-Kains, Benjamin, Thiagarajan, Mathangi, Jewell, Scott D., Hostetter, Galen, Newton, Chelsea J., Li, Qing Kay, Roehrl, Michael H., Fenyö, David, Wang, Pei, Nesvizhskii, Alexey I., Mani, D.R., Omenn, Gilbert S., Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Bathe, Oliver F., Chan, Daniel W., Hruban, Ralph H., Ding, Li, Zhang, Bing, and Zhang, Hui

Published
2021
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7. How many human proteoforms are there?

Author

Aebersold, Ruedi, Agar, Jeffrey N, Amster, I Jonathan, Baker, Mark S, Bertozzi, Carolyn R, Boja, Emily S, Costello, Catherine E, Cravatt, Benjamin F, Fenselau, Catherine, Garcia, Benjamin A, Ge, Ying, Gunawardena, Jeremy, Hendrickson, Ronald C, Hergenrother, Paul J, Huber, Christian G, Ivanov, Alexander R, Jensen, Ole N, Jewett, Michael C, Kelleher, Neil L, Kiessling, Laura L, Krogan, Nevan J, Larsen, Martin R, Loo, Joseph A, Ogorzalek Loo, Rachel R, Lundberg, Emma, MacCoss, Michael J, Mallick, Parag, Mootha, Vamsi K, Mrksich, Milan, Muir, Tom W, Patrie, Steven M, Pesavento, James J, Pitteri, Sharon J, Rodriguez, Henry, Saghatelian, Alan, Sandoval, Wendy, Schlüter, Hartmut, Sechi, Salvatore, Slavoff, Sarah A, Smith, Lloyd M, Snyder, Michael P, Thomas, Paul M, Uhlén, Mathias, Van Eyk, Jennifer E, Vidal, Marc, Walt, David R, White, Forest M, Williams, Evan R, Wohlschlager, Therese, Wysocki, Vicki H, Yates, Nathan A, Young, Nicolas L, and Zhang, Bing

Subjects
Humans, Proteins, Protein Isoforms, Proteome, Ubiquitin, Proteomics, Protein Biosynthesis, Protein Processing, Post-Translational, Phenotype, Genome, Human, Databases, Protein, Mass Spectrometry, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Medicinal and Biomolecular Chemistry, Biochemistry and Cell Biology, Biochemistry & Molecular Biology
Abstract

Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype.

Published
2018

9. Proteogenomic and metabolomic characterization of human glioblastoma

Author

Agarwal, Anupriya, Amin, Mitual, An, Eunkyung, Anderson, Matthew L., Andrews, David W., Bauer, Thomas, Birger, Chet, Birrer, Michael J., Blumenberg, Lili, Bocik, William E., Borate, Uma, Borucki, Melissa, Burke, Meghan C., Cai, Shuang, Calinawan, Anna P., Carr, Steven A., Cerda, Sandra, Chan, Daniel W., Charamut, Alyssa, Chen, Lin S., Chesla, David, Chinnaiyan, Arul M., Chowdhury, Shrabanti, Cieślik, Marcin P., Clark, David J., Culpepper, Houston, Czernicki, Tomasz, D'Angelo, Fulvio, Day, Jacob, De Young, Stephanie, Demir, Emek, Dhanasekaran, Saravana Mohan, Dhir, Rajiv, Domagalski, Marcin J., Druker, Brian, Duffy, Elizabeth, Dyer, Maureen, Edwards, Nathan J., Edwards, Robert, Elburn, Kimberly, Ellis, Matthew J., Eschbacher, Jennifer, Francis, Alicia, Gabriel, Stacey, Gabrovski, Nikolay, Garofano, Luciano, Getz, Gad, Gillette, Michael A., Godwin, Andrew K., Golbin, Denis, Hanhan, Ziad, Hannick, Linda I., Hariharan, Pushpa, Hindenach, Barbara, Hoadley, Katherine A., Hostetter, Galen, Huang, Chen, Jaehnig, Eric, Jewell, Scott D., Ji, Nan, Jones, Corbin D., Karz, Alcida, Kaspera, Wojciech, Kim, Lyndon, Kothadia, Ramani B., Kumar-Sinha, Chandan, Lei, Jonathan, Leprevost, Felipe D., Li, Kai, Liao, Yuxing, Lilly, Jena, Liu, Hongwei, Lubínski, Jan, Madan, Rashna, Maggio, William, Malc, Ewa, Malovannaya, Anna, Mareedu, Sailaja, Markey, Sanford P., Marrero-Oliveras, Annette, Martinez, Nina, Maunganidze, Nicollette, McDermott, Jason E., McGarvey, Peter B., McGee, John, Mieczkowski, Piotr, Migliozzi, Simona, Modugno, Francesmary, Montgomery, Rebecca, Newton, Chelsea J., Omenn, Gilbert S., Ozbek, Umut, Paklina, Oxana V., Paulovich, Amanda G., Perou, Amy M., Pico, Alexander R., Piehowski, Paul D., Placantonakis, Dimitris G., Polonskaya, Larisa, Potapova, Olga, Pruetz, Barbara, Qi, Liqun, Ramkissoon, Shakti, Resnick, Adam, Richey, Shannon, Riggins, Gregory, Robinson, Karna, Roche, Nancy, Rohrer, Daniel C., Rood, Brian R., Rossell, Larissa, Savage, Sara R., Schadt, Eric E., Shi, Yan, Shi, Zhiao, Shutack, Yvonne, Singh, Shilpi, Skelly, Tara, Sokoll, Lori J., Stawicki, Jakub, Stein, Stephen E., Suh, James, Szopa, Wojciech, Tabor, Dave, Tan, Donghui, Tansil, Darlene, Thangudu, Ratna R., Tognon, Cristina, Traer, Elie, Tsang, Shirley, Tyner, Jeffrey, Um, Ki Sung, Valley, Dana R., Vasaikar, Suhas, Vatanian, Negin, Velvulou, Uma, Vernon, Michael, Wan, Weiqing, Wang, Junmei, Webster, Alex, Wen, Bo, Whiteaker, Jeffrey R., Wilson, George D., Zakhartsev, Yuriy, Zelt, Robert, Zhang, Hui, Zhang, Liwei, Zhang, Zhen, Zhao, Grace, Zhu, Jun, Wang, Liang-Bo, Karpova, Alla, Gritsenko, Marina A., Kyle, Jennifer E., Cao, Song, Li, Yize, Rykunov, Dmitry, Colaprico, Antonio, Rothstein, Joseph H., Hong, Runyu, Stathias, Vasileios, Cornwell, MacIntosh, Petralia, Francesca, Wu, Yige, Reva, Boris, Krug, Karsten, Pugliese, Pietro, Kawaler, Emily, Olsen, Lindsey K., Liang, Wen-Wei, Song, Xiaoyu, Dou, Yongchao, Wendl, Michael C., Caravan, Wagma, Liu, Wenke, Cui Zhou, Daniel, Ji, Jiayi, Tsai, Chia-Feng, Petyuk, Vladislav A., Moon, Jamie, Ma, Weiping, Chu, Rosalie K., Weitz, Karl K., Moore, Ronald J., Monroe, Matthew E., Zhao, Rui, Yang, Xiaolu, Yoo, Seungyeul, Krek, Azra, Demopoulos, Alexis, Zhu, Houxiang, Wyczalkowski, Matthew A., McMichael, Joshua F., Henderson, Brittany L., Lindgren, Caleb M., Boekweg, Hannah, Lu, Shuangjia, Baral, Jessika, Yao, Lijun, Stratton, Kelly G., Bramer, Lisa M., Zink, Erika, Couvillion, Sneha P., Bloodsworth, Kent J., Satpathy, Shankha, Sieh, Weiva, Boca, Simina M., Schürer, Stephan, Chen, Feng, Wiznerowicz, Maciej, Ketchum, Karen A., Boja, Emily S., Kinsinger, Christopher R., Robles, Ana I., Hiltke, Tara, Thiagarajan, Mathangi, Nesvizhskii, Alexey I., Zhang, Bing, Mani, D.R., Ceccarelli, Michele, Chen, Xi S., Cottingham, Sandra L., Li, Qing Kay, Kim, Albert H., Fenyö, David, Ruggles, Kelly V., Rodriguez, Henry, Mesri, Mehdi, Payne, Samuel H., Resnick, Adam C., Wang, Pei, Smith, Richard D., Iavarone, Antonio, Chheda, Milan G., Barnholtz-Sloan, Jill S., Rodland, Karin D., Liu, Tao, and Ding, Li

Published
2021
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10. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma

Author

Agarwal, Anupriya, Anderson, Matthew L., Avanessian, Shayan C., Avtonomov, Dmitry, Bathe, Oliver F., Birger, Chet, Birrer, Michael J., Blumenberg, Lili, Bocik, William E., Borate, Uma, Borucki, Melissa, Burke, Meghan C., Cai, Shuang, Calinawan, Anna Pamela, Cerda, Sandra, Charamut, Alyssa, Chen, Lin S., Chowdhury, Shrabanti, Clauser, Karl R., Culpepper, Houston, Czernicki, Tomasz, D'Angelo, Fulvio, Day, Jacob, De Young, Stephanie, Demir, Emek, Ding, Fei, Domagalski, Marcin J., Dort, Joseph C., Druker, Brian, Duffy, Elizabeth, Dyer, Maureen, Edwards, Nathan J., Elburn, Kimberly, Ermakova, Tatiana S., Fenyo, David, Ferrarotto, Renata, Francis, Alicia, Gabriel, Stacey, Garofano, Luciano, Geffen, Yifat, Getz, Gad, Goldthwaite, Charles A., Hannick, Linda I., Hariharan, Pushpa, Hayes, David N., Heiman, David, Hindenach, Barbara, Hoadley, Katherine A., Hostetter, Galen, Hyrcza, Martin, Jewell, Scott D., Jones, Corbin D., Kane, M. Harry, Karz, Alicia, Kothadia, Ramani B., Krek, Azra, Kumar-Sinha, Chandan, Liu, Tao, Liu, Hongwei, Ma, Weiping, Malc, Ewa, Malovannaya, Anna, Mareedu, Sailaja, Markey, Sanford P., Marrero-Oliveras, Annette, Maunganidze, Nicollette, McDermott, Jason E., McGarvey, Peter B., McGee, John, Mieczkowski, Piotr, Migliozzi, Simona, Montgomery, Rebecca, Newton, Chelsea J., Ozbek, Umut, Paulovich, Amanda G., Payne, Samuel H., Pazardzhikliev, Dimitar Dimitrov, Perou, Amy M., Petralia, Francesca, Petrenko, Lyudmila, Piehowski, Paul D., Placantonakis, Dmitris, Polonskaya, Larisa, Ponomareva, Elena V., Potapova, Olga, Qi, Liqun, Qu, Ning, Ramkissoon, Shakti, Reva, Boris, Richey, Shannon, Robinson, Karna, Roche, Nancy, Rodland, Karin, Rohrer, Daniel C., Rykunov, Dmitry, Schadt, Eric E., Shi, Yan, Shutack, Yvonne, Singh, Shilpi, Skelly, Tara, Smith, Richard, Sokoll, Lori J., Stawicki, Jakub, Stein, Stephen E., Suh, James, Szopa, Wojciech, Tabor, Dave, Tan, Donghui, Tansil, Darlene, Teo, Guo Ci, Thangudu, Ratna R., Tognon, Cristina, Traer, Elie, Tsang, Shirley, Tyner, Jeffrey, Um, Ki Sung, Valley, Dana R., Vasilev, Lyubomir Valkov, Vatanian, Negin, Velvulou, Uma, Vernon, Michael, Westbrook, Thomas F., Whiteaker, Jeffrey R., Wu, Yige, Xu, Midie, Yao, Lijun, Yi, Xinpei, Yu, Fengchao, Zaalishvili, Kakhaber, Zakhartsev, Yuriy, Zelt, Robert, Zhao, Grace, Zhu, Jun, Huang, Chen, Chen, Lijun, Savage, Sara R., Eguez, Rodrigo Vargas, Dou, Yongchao, Li, Yize, da Veiga Leprevost, Felipe, Jaehnig, Eric J., Lei, Jonathan T., Wen, Bo, Schnaubelt, Michael, Krug, Karsten, Song, Xiaoyu, Cieślik, Marcin, Chang, Hui-Yin, Wyczalkowski, Matthew A., Li, Kai, Colaprico, Antonio, Li, Qing Kay, Clark, David J., Hu, Yingwei, Cao, Liwei, Pan, Jianbo, Wang, Yuefan, Cho, Kyung-Cho, Shi, Zhiao, Liao, Yuxing, Jiang, Wen, Anurag, Meenakshi, Ji, Jiayi, Yoo, Seungyeul, Zhou, Daniel Cui, Liang, Wen-Wei, Wendl, Michael, Vats, Pankaj, Carr, Steven A., Mani, D.R., Zhang, Zhen, Qian, Jiang, Chen, Xi S., Pico, Alexander R., Wang, Pei, Chinnaiyan, Arul M., Ketchum, Karen A., Kinsinger, Christopher R., Robles, Ana I., An, Eunkyung, Hiltke, Tara, Mesri, Mehdi, Thiagarajan, Mathangi, Weaver, Alissa M., Sikora, Andrew G., Lubiński, Jan, Wierzbicka, Małgorzata, Wiznerowicz, Maciej, Satpathy, Shankha, Gillette, Michael A., Miles, George, Ellis, Matthew J., Omenn, Gilbert S., Rodriguez, Henry, Boja, Emily S., Dhanasekaran, Saravana M., Ding, Li, Nesvizhskii, Alexey I., El-Naggar, Adel K., Chan, Daniel W., Zhang, Hui, and Zhang, Bing

Published
2021
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11. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Author

Francis, Alicia, Morgan, Allison M., Waanders, Angela J., Viaene, Angela N., Buccoliero, Anna Maria, Chinnaiyan, Arul M., Leonard, Carina A., Kline, Cassie N., Caporalini, Chiara, Kinsinger, Christopher R., Li, Chunde, Kram, David E., Hanson, Derek, Appert, Elizabeth, Kawaler, Emily A., Raabe, Eric H., Jackson, Eric M., Greenfield, Jeffrey P., Stone, Gabrielle S., Getz, Gad, Grant, Gerald, Teo, Guo Ci, Pollack, Ian F., Cain, Jason E., Foster, Jessica B., Phillips, Joanna J., Palma, July E., Ketchum, Karen A., Ruggles, Kelly V., Blumenberg, Lili, Cornwell, Macintosh, Sarmady, Mahdi, Domagalski, Marcin J., Cieślik, Marcin P., Santi, Mariarita, Li, Marilyn M., Ellis, Matthew J., Wyczalkowski, Matthew A., Connors, Meghan, Scagnet, Mirko, Gupta, Nalin, Edwards, Nathan J., Vitanza, Nicholas A., Vaske, Olena M., Becher, Oren, McGarvey, Peter B., Firestein, Ron, Mueller, Sabine, Winebrake, Samuel G., Dhanasekaran, Saravana Mohan, Cai, Shuang, Partap, Sonia, Patton, Tatiana, Le, Toan, Lorentzen, Travis D., Liu, Wenke, Bocik, William E., Petralia, Francesca, Tignor, Nicole, Reva, Boris, Koptyra, Mateusz, Chowdhury, Shrabanti, Rykunov, Dmitry, Krek, Azra, Ma, Weiping, Zhu, Yuankun, Ji, Jiayi, Calinawan, Anna, Whiteaker, Jeffrey R., Colaprico, Antonio, Stathias, Vasileios, Omelchenko, Tatiana, Song, Xiaoyu, Raman, Pichai, Guo, Yiran, Brown, Miguel A., Ivey, Richard G., Szpyt, John, Guha Thakurta, Sanjukta, Gritsenko, Marina A., Weitz, Karl K., Lopez, Gonzalo, Kalayci, Selim, Gümüş, Zeynep H., Yoo, Seungyeul, da Veiga Leprevost, Felipe, Chang, Hui-Yin, Krug, Karsten, Katsnelson, Lizabeth, Wang, Ying, Kennedy, Jacob J., Voytovich, Uliana J., Zhao, Lei, Gaonkar, Krutika S., Ennis, Brian M., Zhang, Bo, Baubet, Valerie, Tauhid, Lamiya, Lilly, Jena V., Mason, Jennifer L., Farrow, Bailey, Young, Nathan, Leary, Sarah, Moon, Jamie, Petyuk, Vladislav A., Nazarian, Javad, Adappa, Nithin D., Palmer, James N., Lober, Robert M., Rivero-Hinojosa, Samuel, Wang, Liang-Bo, Wang, Joshua M., Broberg, Matilda, Chu, Rosalie K., Moore, Ronald J., Monroe, Matthew E., Zhao, Rui, Smith, Richard D., Zhu, Jun, Robles, Ana I., Mesri, Mehdi, Boja, Emily, Hiltke, Tara, Rodriguez, Henry, Zhang, Bing, Schadt, Eric E., Mani, D.R., Ding, Li, Iavarone, Antonio, Wiznerowicz, Maciej, Schürer, Stephan, Chen, Xi S., Heath, Allison P., Rokita, Jo Lynne, Nesvizhskii, Alexey I., Fenyö, David, Rodland, Karin D., Liu, Tao, Gygi, Steven P., Paulovich, Amanda G., Resnick, Adam C., Storm, Phillip B., Rood, Brian R., and Wang, Pei

Published
2020
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12. Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy

Author

Avanessian, Shayan C., Cai, Shuang, Chan, Daniel, Chen, Xian, Edwards, Nathan J., Hoofnagle, Andrew N., Kane, M. Harry, Ketchum, Karen A., Kuhn, Eric, Levine, Douglas A., Li, Shunqiang, Liebler, Daniel C., Liu, Tao, Luo, Jingqin, Madhavan, Subha, Maher, Chris, McDermott, Jason E., McGarvey, Peter B., Oberti, Mauricio, Pandey, Akhilesh, Payne, Samuel H., Ransohoff, David F., Rivers, Robert C., Rodland, Karin D., Rudnick, Paul, Sanders, Melinda E., Shaw, Kenna M., Shih, Ie-Ming, Slebos, Robbert J.C., Smith, Richard D., Snyder, Michael, Stein, Stephen E., Tabb, David L., Thangudu, Ratna R., Thomas, Stefani, Wang, Yue, White, Forest M., Whiteaker, Jeffrey R., Whiteley, Gordon A., Zhang, Hui, Zhang, Zhen, Zhao, Yingming, Zhu, Heng, Zimmerman, Lisa J., Krug, Karsten, Jaehnig, Eric J., Satpathy, Shankha, Blumenberg, Lili, Karpova, Alla, Anurag, Meenakshi, Miles, George, Mertins, Philipp, Geffen, Yifat, Tang, Lauren C., Heiman, David I., Cao, Song, Maruvka, Yosef E., Lei, Jonathan T., Huang, Chen, Kothadia, Ramani B., Colaprico, Antonio, Birger, Chet, Wang, Jarey, Dou, Yongchao, Wen, Bo, Shi, Zhiao, Liao, Yuxing, Wiznerowicz, Maciej, Wyczalkowski, Matthew A., Chen, Xi Steven, Kennedy, Jacob J., Paulovich, Amanda G., Thiagarajan, Mathangi, Kinsinger, Christopher R., Hiltke, Tara, Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Westbrook, Thomas F., Ding, Li, Getz, Gad, Clauser, Karl R., Fenyö, David, Ruggles, Kelly V., Zhang, Bing, Mani, D.R., Carr, Steven A., Ellis, Matthew J., and Gillette, Michael A.

Published
2020
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13. Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma

Author

Pandey, Akhilesh, Paulovich, Amanda, Hoofnagle, Andrew, Zhang, Bing, Mani, D.R., Liebler, Daniel C., Ransohoff, David F., Fenyo, David, Tabb, David L., Levine, Douglas A., Kuhn, Eric, White, Forest M., Whiteley, Gordon A., Zhu, Heng, Shih, Ie-Ming, Bavarva, Jasmin, McDermott, Jason E., Whiteaker, Jeffrey, Ketchum, Karen A., Clauser, Karl R., Ruggles, Kelly, Elburn, Kimberly, Ding, Li, Hannick, Linda, Zimmerman, Lisa J., Watson, Mark, Thiagarajan, Mathangi, Ellis, Matthew J.C., Oberti, Mauricio, Mesri, Mehdi, Sanders, Melinda E., Borucki, Melissa, Gillette, Michael A., Snyder, Michael, Edwards, Nathan J., Vatanian, Negin, Rudnick, Paul A., McGarvey, Peter B., Mertins, Philip, Townsend, R. Reid, Thangudu, Ratna R., Smith, Richard D., Rivers, Robert C., Slebos, Robert J.C., Payne, Samuel H., Davies, Sherri R., Cai, Shuang, Stein, Stephen E., Carr, Steven A., Skates, Steven J., Madhavan, Subha, Liu, Tao, Chen, Xian, Zhao, Yingming, Wang, Yue, Shi, Zhiao, Hu, Yingwei, Pan, Jianbo, Shah, Punit, Ao, Minghui, Thomas, Stefani N., Liu, Yang, Chen, Lijun, Schnaubelt, Michael, Clark, David J., Rodriguez, Henry, Boja, Emily S., Hiltke, Tara, Kinsinger, Christopher R., Rodland, Karin D., Li, Qing Kay, Qian, Jiang, Zhang, Zhen, Chan, Daniel W., and Zhang, Hui

Published
2020
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14. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

Author

Webster, Alex, Francis, Alicia, Charamut, Alyssa, Paulovich, Amanda G., Perou, Amy M., Godwin, Andrew K., Karnuta, Andrii, Marrero-Oliveras, Annette, Hindenach, Barbara, Pruetz, Barbara, Kubisa, Bartosz, Druker, Brian J., Birger, Chet, Jones, Corbin D., Valley, Dana R., Rohrer, Daniel C., Zhou, Daniel Cui, Chan, Daniel W., Chesla, David, Clark, David J., Rykunov, Dmitry, Tan, Donghui, Ponomareva, Elena V., Duffy, Elizabeth, Burks, Eric J., Schadt, Eric E., Bergstrom, Erik J., Fedorov, Eugene S., Malc, Ewa, Wilson, George D., Chen, Hai-Quan, Krzystek, Halina M., Liu, Hongwei, Culpepper, Houston, Sun, Hua, Zhang, Hui, Day, Jacob, Suh, James, Whiteaker, Jeffrey R., Eschbacher, Jennifer, McGee, John, Ketchum, Karen A., Rodland, Karin D., Robinson, Karna, Hoadley, Katherine A., Suzuki, Kei, Um, Ki Sung, Elburn, Kim, Wang, Liang-Bo, Chen, Lijun, Hannick, Linda, Qi, Liqun, Sokoll, Lori J., Wojtyś, Małgorzata, Domagalski, Marcin J., Gritsenko, Marina A., Beasley, Mary B., Monroe, Matthew E., Ellis, Matthew J., Dyer, Maureen, Burke, Meghan C., Borucki, Melissa, Sun, Meng-Hong, Roehrl, Michael H., Birrer, Michael J., Noble, Michael, Schnaubelt, Michael, Vernon, Michael, Chaikin, Michelle, Krotevich, Mikhail, Khan, Munziba, Selvan, Myvizhi Esai, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Potapova, Olga, Grady, Pamela, McGarvey, Peter B., Mieczkowski, Piotr, Hariharan, Pushpa, Madan, Rashna, Thangudu, Ratna R., Smith, Richard D., Welsh, Robert J., Zelt, Robert, Mehra, Rohit, Matteotti, Ronald, Mareedu, Sailaja, Payne, Samuel H., Cottingham, Sandra, Markey, Sanford P., Chugh, Seema, Smith, Shaleigh, Tsang, Shirley, Cai, Shuang, Boca, Simina M., Carter, Sonya, Gabriel, Stacey, De Young, Stephanie, Stein, Stephen E., Shankar, Sunita, Krubit, Tanya, Liu, Tao, Skelly, Tara, Bauer, Thomas, Velvulou, Uma, Ozbek, Umut, Petyuk, Vladislav A., Sovenko, Volodymyr, Bocik, William E., Maggio, William W., Chen, Xi, Shi, Yan, Wu, Yige, Hu, Yingwei, Liao, Yuxing, Zhang, Zhen, Shi, Zhiao, Gillette, Michael A., Satpathy, Shankha, Cao, Song, Dhanasekaran, Saravana M., Vasaikar, Suhas V., Krug, Karsten, Petralia, Francesca, Li, Yize, Liang, Wen-Wei, Reva, Boris, Krek, Azra, Ji, Jiayi, Song, Xiaoyu, Liu, Wenke, Hong, Runyu, Yao, Lijun, Blumenberg, Lili, Savage, Sara R., Wendl, Michael C., Wen, Bo, Li, Kai, Tang, Lauren C., MacMullan, Melanie A., Avanessian, Shayan C., Kane, M. Harry, Newton, Chelsea J., Cornwell, MacIntosh, Kothadia, Ramani B., Ma, Weiping, Yoo, Seungyeul, Mannan, Rahul, Vats, Pankaj, Kumar-Sinha, Chandan, Kawaler, Emily A., Omelchenko, Tatiana, Colaprico, Antonio, Geffen, Yifat, Maruvka, Yosef E., da Veiga Leprevost, Felipe, Wiznerowicz, Maciej, Gümüş, Zeynep H., Veluswamy, Rajwanth R., Hostetter, Galen, Heiman, David I., Wyczalkowski, Matthew A., Hiltke, Tara, Mesri, Mehdi, Kinsinger, Christopher R., Boja, Emily S., Omenn, Gilbert S., Chinnaiyan, Arul M., Rodriguez, Henry, Li, Qing Kay, Jewell, Scott D., Thiagarajan, Mathangi, Getz, Gad, Zhang, Bing, Fenyö, David, Ruggles, Kelly V., Cieslik, Marcin P., Robles, Ana I., Clauser, Karl R., Govindan, Ramaswamy, Wang, Pei, Nesvizhskii, Alexey I., Ding, Li, Mani, D.R., and Carr, Steven A.

Published
2020
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15. Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability

Author

McDermott, Jason E., Arshad, Osama A., Petyuk, Vladislav A., Fu, Yi, Gritsenko, Marina A., Clauss, Therese R., Moore, Ronald J., Schepmoes, Athena A., Zhao, Rui, Monroe, Matthew E., Schnaubelt, Michael, Tsai, Chia-Feng, Payne, Samuel H., Huang, Chen, Wang, Liang-Bo, Foltz, Steven, Wyczalkowski, Matthew, Wu, Yige, Song, Ehwang, Brewer, Molly A., Thiagarajan, Mathangi, Kinsinger, Christopher R., Robles, Ana I., Boja, Emily S., Rodriguez, Henry, Chan, Daniel W., Zhang, Bing, Zhang, Zhen, Ding, Li, Smith, Richard D., Liu, Tao, and Rodland, Karin D.

Published
2020
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16. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

Author

Zhang, Hui, Liu, Tao, Zhang, Zhen, Payne, Samuel H, Zhang, Bai, McDermott, Jason E, Zhou, Jian-Ying, Petyuk, Vladislav A, Chen, Li, Ray, Debjit, Sun, Shisheng, Yang, Feng, Chen, Lijun, Wang, Jing, Shah, Punit, Cha, Seong Won, Aiyetan, Paul, Woo, Sunghee, Tian, Yuan, Gritsenko, Marina A, Clauss, Therese R, Choi, Caitlin, Monroe, Matthew E, Thomas, Stefani, Nie, Song, Wu, Chaochao, Moore, Ronald J, Yu, Kun-Hsing, Tabb, David L, Fenyö, David, Bafna, Vineet, Wang, Yue, Rodriguez, Henry, Boja, Emily S, Hiltke, Tara, Rivers, Robert C, Sokoll, Lori, Zhu, Heng, Shih, Ie-Ming, Cope, Leslie, Pandey, Akhilesh, Zhang, Bing, Snyder, Michael P, Levine, Douglas A, Smith, Richard D, Chan, Daniel W, Rodland, Karin D, Investigators, the CPTAC, Carr, Steven A, Gillette, Michael A, Klauser, Karl R, Kuhn, Eric, Mani, DR, Mertins, Philipp, Ketchum, Karen A, Thangudu, Ratna, Cai, Shuang, Oberti, Mauricio, Paulovich, Amanda G, Whiteaker, Jeffrey R, Edwards, Nathan J, McGarvey, Peter B, Madhavan, Subha, Wang, Pei, Whiteley, Gordon A, Skates, Steven J, White, Forest M, Kinsinger, Christopher R, Mesri, Mehdi, Shaw, Kenna M, Stein, Stephen E, Fenyo, David, Rudnick, Paul, Snyder, Michael, Zhao, Yingming, Chen, Xian, Ransohoff, David F, Hoofnagle, Andrew N, Liebler, Daniel C, Sanders, Melinda E, Shi, Zhiao, and Slebos, Robbert JC

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Human Genome, Genetics, Biotechnology, Ovarian Cancer, Rare Diseases, Cancer, Acetylation, Chromosomal Instability, DNA Repair, DNA, Neoplasm, Female, Gene Dosage, Humans, Mass Spectrometry, Neoplasm Proteins, Neoplasms, Cystic, Mucinous, and Serous, Ovarian Neoplasms, Phosphoproteins, Protein Processing, Post-Translational, Proteome, Survival Analysis, CPTAC Investigators, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, and the ones most associated with short overall survival. Specific protein acetylations associated with homologous recombination deficiency suggest a potential means for stratifying patients for therapy. In addition to providing a valuable resource, these findings provide a view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC. VIDEO ABSTRACT.

Published
2016

17. Proteogenomic Characterization of Endometrial Carcinoma

Author

Agarwal, Anupriya, Anurag, Meenakshi, Avtonomov, Dmitry, Birger, Chet, Birrer, Michael J., Boca, Simina M., Bocik, William E., Borate, Uma, Borucki, Melissa, Burke, Meghan C., Cai, Shuang, Calinawan, Anna, Carr, Steven A., Carter, Sonya, Castro, Patricia, Cerda, Sandra, Chaikin, Michelle, Chan, Daniel W., Chan, Doug, Charamut, Alyssa, Chen, Feng, Chen, Jin, Chen, Lijun, Chen, Lin S., Chesla, David, Chheda, Milan G., Chinnaiyan, Arul M., Chowdhury, Shrabanti, Cieslik, Marcin P., Clark, David J., Cottingham, Sandra, Culpepper, Houston, Day, Jacob, De Young, Stephanie, Demir, Emek, Dhanasekaran, Saravana Mohan, Dhir, Rajiv, Domagalski, Marcin J., Dottino, Peter, Druker, Brian, Duffy, Elizabeth, Dyer, Maureen, Edwards, Nathan J., Edwards, Robert, Elburn, Kim, Field, Jayson B., Francis, Alicia, Gabriel, Stacey, Geffen, Yifat, Geiszler, Daniel, Gillette, Michael A., Godwin, Andrew K., Grady, Pamela, Hannick, Linda, Hariharan, Pushpa, Hilsenbeck, Sue, Hindenach, Barbara, Hoadley, Katherine A., Hong, Runyu, Hostetter, Galen, Hsieh, James J., Hu, Yingwei, Ittmann, Michael M., Jaehnig, Eric, Jewell, Scott D., Ji, Jiayi, Jones, Corbin D., Karabon, Renee, Ketchum, Karen A., Khan, Munziba, Kim, Beom-Jun, Krek, Azra, Krubit, Tanya, Kumar-Sinha, Chandan, Leprevost, Felipe D., Lewis, Michael, Li, Qing Kay, Li, Yize, Liu, Hongwei, Lubinski, Jan, Ma, Weiping, Madan, Rashna, Malc, Ewa, Malovannaya, Anna, Mareedu, Sailaja, Markey, Sanford P., Marrero-Oliveras, Annette, Martignetti, John, McDermott, Jason, McGarvey, Peter B., McGee, John, Mieczkowski, Piotr, Modugno, Francesmary, Montgomery, Rebecca, Newton, Chelsea J., Omenn, Gilbert S., Paulovich, Amanda G., Perou, Amy M., Petralia, Francesca, Piehowski, Paul, Polonskaya, Larisa, Qi, Liqun, Richey, Shannon, Robinson, Karna, Roche, Nancy, Rohrer, Daniel C., Schadt, Eric E., Schnaubelt, Michael, Shi, Yan, Skelly, Tara, Sokoll, Lori J., Song, Xiaoyu, Stein, Stephen E., Suh, James, Tan, Donghui, Tansil, Darlene, Teo, Guo Ci, Thangudu, Ratna R., Tognon, Cristina, Traer, Elie, Tyner, Jeffrey, Um, Ki Sung, Valley, Dana R., Vatanian, Negin, Vats, Pankaj, Velvulou, Uma, Vernon, Michael, Wang, Liang-Bo, Wang, Ying, Webster, Alex, Westbrook, Thomas, Wheeler, David, Whiteaker, Jeffrey R., Wilson, George D., Zakhartsev, Yuriy, Zelt, Robert, Zhang, Hui, Zhang, Yuping, Zhang, Zhen, Zhao, Grace, Dou, Yongchao, Kawaler, Emily A., Cui Zhou, Daniel, Gritsenko, Marina A., Huang, Chen, Blumenberg, Lili, Karpova, Alla, Petyuk, Vladislav A., Savage, Sara R., Satpathy, Shankha, Liu, Wenke, Wu, Yige, Tsai, Chia-Feng, Wen, Bo, Li, Zhi, Cao, Song, Moon, Jamie, Shi, Zhiao, Cornwell, MacIntosh, Wyczalkowski, Matthew A., Chu, Rosalie K., Vasaikar, Suhas, Zhou, Hua, Gao, Qingsong, Moore, Ronald J., Li, Kai, Sethuraman, Sunantha, Monroe, Matthew E., Zhao, Rui, Heiman, David, Krug, Karsten, Clauser, Karl, Kothadia, Ramani, Maruvka, Yosef, Pico, Alexander R., Oliphant, Amanda E., Hoskins, Emily L., Pugh, Samuel L., Beecroft, Sean J.I., Adams, David W., Jarman, Jonathan C., Kong, Andy, Chang, Hui-Yin, Reva, Boris, Liao, Yuxing, Rykunov, Dmitry, Colaprico, Antonio, Chen, Xi Steven, Czekański, Andrzej, Jędryka, Marcin, Matkowski, Rafał, Wiznerowicz, Maciej, Hiltke, Tara, Boja, Emily, Kinsinger, Christopher R., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Mutch, David, Fuh, Katherine, Ellis, Matthew J., DeLair, Deborah, Thiagarajan, Mathangi, Mani, D.R., Getz, Gad, Noble, Michael, Nesvizhskii, Alexey I., Wang, Pei, Anderson, Matthew L., Levine, Douglas A., Smith, Richard D., Payne, Samuel H., Ruggles, Kelly V., Rodland, Karin D., Ding, Li, Zhang, Bing, Liu, Tao, and Fenyö, David

Published
2020
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18. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Author

Hashimi, Abdul Samad, Pico, Alexander R., Karpova, Alla, Charamut, Alyssa, Paulovich, Amanda G., Perou, Amy M., Malovannaya, Anna, Marrero-Oliveras, Annette, Agarwal, Anupriya, Hindenach, Barbara, Pruetz, Barbara, Kim, Beom-Jun, Druker, Brian J., Newton, Chelsea J., Birger, Chet, Jones, Corbin D., Tognon, Cristina, Mani, D.R., Valley, Dana R., Rohrer, Daniel C., Zhou, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Wheeler, David, Tan, Donghui, Chan, Doug, Demir, Emek, Malc, Ewa, Modugno, Francesmary, Getz, Gaddy, Hostetter, Galen, Wilson, George D., Hart, Gerald W., Zhu, Heng, Liu, Hongwei, Culpepper, Houston, Sun, Hua, Zhou, Hua, Day, Jacob, Suh, James, Huang, Jasmine, McDermott, Jason, Whiteaker, Jeffrey R., Tyner, Jeffrey W., Eschbacher, Jennifer, Chen, Jin, McGee, John, Zhu, Jun, Ketchum, Karen A., Rodland, Karin D., Clauser, Karl, Robinson, Karna, Krug, Karsten, Hoadley, Katherine A., Um, Ki Sung, Elburn, Kim, Holloway, Kimberly, Wang, Liang-Bo, Blumenberg, Lili, Hannick, Linda, Qi, Liqun, Sokoll, Lori J., Cornwell, MacIntosh, Loriaux, Marc, Domagalski, Marcin J., Gritsenko, Marina A., Anderson, Matthew, Monroe, Matthew E., Ellis, Matthew J., Dyer, Maureen, Anurag, Meenakshi, Burke, Meghan C., Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Lewis, Michael, Ittmann, Michael M., Smith, Michael, Vernon, Michael, Chaikin, Michelle, Chheda, Milan G., Khan, Munziba, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Tignor, Nicole, Beckmann, Noam, Grady, Pamela, Castro, Patricia, Piehowski, Paul, McGarvey, Peter B., Mieczkowski, Piotr, Hariharan, Pushpa, Gao, Qingsong, Dhir, Rajiv, Kothadia, Ramani Bhupendra, Thangudu, Ratna R., Montgomery, Rebecca, Jayasinghe, Reyka G., Smith, Richard D., Edwards, Robert, Zelt, Robert, Bremner, Ross, Liu, Ruiyang, Hong, Runyu, Mareedu, Sailaja, Payne, Samuel H., Cottingham, Sandra, Markey, Sanford P., Jewell, Scott D., Patel, Shalin, Satpathy, Shankha, Richey, Shannon, Davies, Sherri R., Cai, Shuang, Boca, Simina M., Patil, Snehal, Sengupta, Sohini, Carter, Sonya, Gabriel, Stacey, Thomas, Stefani N., De Young, Stephanie, Stein, Stephen E., Carr, Steven A., Foltz, Steven M., Hilsenbeck, Sue, Krubit, Tanya, Liu, Tao, Skelly, Tara, Westbrook, Thomas, Borate, Uma, Velvulou, Uma, Petyuk, Vladislav A., Bocik, William E., Chen, Xi, Shi, Yan, Geffen, Yifat, Lu, Yihao, Wang, Ying, Maruvka, Yosef, Li, Zhi, Shi, Zhiao, Tu, Zhidong, Clark, David J., Dhanasekaran, Saravana M., Petralia, Francesca, Pan, Jianbo, Song, Xiaoyu, Hu, Yingwei, da Veiga Leprevost, Felipe, Reva, Boris, Lih, Tung-Shing M., Chang, Hui-Yin, Ma, Weiping, Huang, Chen, Ricketts, Christopher J., Chen, Lijun, Krek, Azra, Li, Yize, Rykunov, Dmitry, Li, Qing Kay, Chen, Lin S., Ozbek, Umut, Vasaikar, Suhas, Wu, Yige, Yoo, Seungyeul, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Ji, Jiayi, Schnaubelt, Michael, Kong, Andy, Sethuraman, Sunantha, Avtonomov, Dmitry M., Ao, Minghui, Colaprico, Antonio, Cao, Song, Cho, Kyung-Cho, Kalayci, Selim, Ma, Shiyong, Liu, Wenke, Ruggles, Kelly, Calinawan, Anna, Gümüş, Zeynep H., Geiszler, Daniel, Kawaler, Emily, Teo, Guo Ci, Wen, Bo, Zhang, Yuping, Keegan, Sarah, Li, Kai, Chen, Feng, Edwards, Nathan, Pierorazio, Phillip M., Chen, Xi Steven, Pavlovich, Christian P., Hakimi, A. Ari, Brominski, Gabriel, Hsieh, James J., Antczak, Andrzej, Omelchenko, Tatiana, Lubinski, Jan, Wiznerowicz, Maciej, Linehan, W. Marston, Kinsinger, Christopher R., Thiagarajan, Mathangi, Boja, Emily S., Mesri, Mehdi, Hiltke, Tara, Robles, Ana I., Rodriguez, Henry, Qian, Jiang, Fenyö, David, Zhang, Bing, Ding, Li, Schadt, Eric, Chinnaiyan, Arul M., Zhang, Zhen, Omenn, Gilbert S., Cieslik, Marcin, Chan, Daniel W., Nesvizhskii, Alexey I., Wang, Pei, and Zhang, Hui

Published
2019
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19. Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma

Author

Gao, Qiang, Zhu, Hongwen, Dong, Liangqing, Shi, Weiwei, Chen, Ran, Song, Zhijian, Huang, Chen, Li, Junqiang, Dong, Xiaowei, Zhou, Yanting, Liu, Qian, Ma, Lijie, Wang, Xiaoying, Zhou, Jian, Liu, Yansheng, Boja, Emily, Robles, Ana I., Ma, Weiping, Wang, Pei, Li, Yize, Ding, Li, Wen, Bo, Zhang, Bing, Rodriguez, Henry, Gao, Daming, Zhou, Hu, and Fan, Jia

Published
2019
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20. Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

Author

Pandey, Akhilesh, Paulovich, Amanda, Hoofnagle, Andrew, Mani, D.R., Chan, Daniel W., Ransohoff, David F., Fenyo, David, Tabb, David L., Levine, Douglas A., Boja, Emily S., Kuhn, Eric, White, Forest M., Whiteley, Gordon A., Zhu, Heng, Zhang, Hui, Shih, Ie-Ming, Bavarva, Jasmin, Whiteaker, Jeffrey, Ketchum, Karen A., Clauser, Karl R., Ruggles, Kelly, Elburn, Kimberly, Hannick, Linda, Watson, Mark, Oberti, Mauricio, Mesri, Mehdi, Sanders, Melinda E., Borucki, Melissa, Gillette, Michael A., Snyder, Michael, Edwards, Nathan J., Vatanian, Negin, Rudnick, Paul A., McGarvey, Peter B., Mertins, Philip, Townsend, R. Reid, Thangudu, Ratna R., Rivers, Robert C., Payne, Samuel H., Davies, Sherri R., Cai, Shuang, Stein, Stephen E., Carr, Steven A., Skates, Steven J., Madhavan, Subha, Hiltke, Tara, Chen, Xian, Zhao, Yingming, Wang, Yue, Zhang, Zhen, Vasaikar, Suhas, Huang, Chen, Wang, Xiaojing, Petyuk, Vladislav A., Savage, Sara R., Wen, Bo, Dou, Yongchao, Zhang, Yun, Shi, Zhiao, Arshad, Osama A., Gritsenko, Marina A., Zimmerman, Lisa J., McDermott, Jason E., Clauss, Therese R., Moore, Ronald J., Zhao, Rui, Monroe, Matthew E., Wang, Yi-Ting, Chambers, Matthew C., Slebos, Robbert J.C., Lau, Ken S., Mo, Qianxing, Ding, Li, Ellis, Matthew, Thiagarajan, Mathangi, Kinsinger, Christopher R., Rodriguez, Henry, Smith, Richard D., Rodland, Karin D., Liebler, Daniel C., Liu, Tao, and Zhang, Bing

Published
2019
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21. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Author

Carr, Steven A, Abbatiello, Susan E, Ackermann, Bradley L, Borchers, Christoph, Domon, Bruno, Deutsch, Eric W, Grant, Russell P, Hoofnagle, Andrew N, Hüttenhain, Ruth, Koomen, John M, Liebler, Daniel C, Liu, Tao, MacLean, Brendan, Mani, DR, Mansfield, Elizabeth, Neubert, Hendrik, Paulovich, Amanda G, Reiter, Lukas, Vitek, Olga, Aebersold, Ruedi, Anderson, Leigh, Bethem, Robert, Blonder, Josip, Boja, Emily, Botelho, Julianne, Boyne, Michael, Bradshaw, Ralph A, Burlingame, Alma L, Chan, Daniel, Keshishian, Hasmik, Kuhn, Eric, Kinsinger, Christopher, Lee, Jerry SH, Lee, Sang-Won, Moritz, Robert, Oses-Prieto, Juan, Rifai, Nader, Ritchie, James, Rodriguez, Henry, Srinivas, Pothur R, Townsend, R Reid, Van Eyk, Jennifer, Whiteley, Gordon, Wiita, Arun, and Weintraub, Susan

Subjects
Animals, Humans, Peptides, Biological Assay, Isotope Labeling, Proteomics, Biology, Medicine, Reference Standards, Software, Mass Spectrometry, Guidelines as Topic, Biochemistry & Molecular Biology
Abstract

Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this "fit-for-purpose" approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.

Published
2014

23. The Making of a PreCancer Atlas: Promises, Challenges, and Opportunities

Author

Boja, Emily, Chuaqui, Rodrigo, Chavarria-Johnson, Eric, Davidsen, Tanja, Eary, Janet, Haim, Todd, Hanlon, Sean, Hewitt, Stephen, Hughes, Shannon, Jacobs, Paula, Li, Jerry, Lively, Tracy, Lockett, Stephen, Misteli, Tom, Nelson, Stefanie, Odeh, Hana, Ossandon, Miguel, Rosenfield, Sonia, Samimi, Goli, Shern, Jack, Star, Rob, Takebe, Naoko, Tavares, Norbert, Tricoli, James, Trimble, Ted, Umar, Asad, Velazquez, Jose, Wang, Chiayeng, Zenklusen, JC, Oberdoerffer, Philipp, Lee, Jerry, Kenney, Nicholas, Srivastava, Sudhir, Ghosh, Sharmistha, Kagan, Jacob, and Mazurchuk, Richard

Published
2018
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25. Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

Author

Wang, Jing, Ma, Zihao, Carr, Steven A., Mertins, Philipp, Zhang, Hui, Zhang, Zhen, Chan, Daniel W., Ellis, Matthew J.C., Townsend, R. Reid, Smith, Richard D., McDermott, Jason E., Chen, Xian, Paulovich, Amanda G., Boja, Emily S., Mesri, Mehdi, Kinsinger, Christopher R., Rodriguez, Henry, Rodland, Karin D., Liebler, Daniel C., and Zhang, Bing

Published
2017
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26. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

Author

Carr, Steven A., Gillette, Michael A., Klauser, Karl R., Kuhn, Eric, Mani, D.R., Mertins, Philipp, Ketchum, Karen A., Thangudu, Ratna, Cai, Shuang, Oberti, Mauricio, Paulovich, Amanda G., Whiteaker, Jeffrey R., Edwards, Nathan J., McGarvey, Peter B., Madhavan, Subha, Wang, Pei, Chan, Daniel W., Pandey, Akhilesh, Shih, Ie-Ming, Zhang, Hui, Zhang, Zhen, Zhu, Heng, Cope, Leslie, Whiteley, Gordon A., Skates, Steven J., White, Forest M., Levine, Douglas A., Boja, Emily S., Kinsinger, Christopher R., Hiltke, Tara, Mesri, Mehdi, Rivers, Robert C., Rodriguez, Henry, Shaw, Kenna M., Stein, Stephen E., Fenyo, David, Liu, Tao, McDermott, Jason E., Payne, Samuel H., Rodland, Karin D., Smith, Richard D., Rudnick, Paul, Snyder, Michael, Zhao, Yingming, Chen, Xian, Ransohoff, David F., Hoofnagle, Andrew N., Liebler, Daniel C., Sanders, Melinda E., Shi, Zhiao, Slebos, Robbert J.C., Tabb, David L., Zhang, Bing, Zimmerman, Lisa J., Wang, Yue, Davies, Sherri R., Ding, Li, Ellis, Matthew J.C., Townsend, R. Reid, Zhang, Bai, Zhou, Jian-Ying, Petyuk, Vladislav A., Chen, Li, Ray, Debjit, Sun, Shisheng, Yang, Feng, Chen, Lijun, Wang, Jing, Shah, Punit, Cha, Seong Won, Aiyetan, Paul, Woo, Sunghee, Tian, Yuan, Gritsenko, Marina A., Clauss, Therese R., Choi, Caitlin, Monroe, Matthew E., Thomas, Stefani, Nie, Song, Wu, Chaochao, Moore, Ronald J., Yu, Kun-Hsing, Fenyö, David, Bafna, Vineet, Sokoll, Lori, and Snyder, Michael P.

Published
2016
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28. A dataset describing a suite of novel antibody reagents for the RAS signaling network

Author

Schoenherr, Regine M., Huang, Dongqing, Voytovich, Uliana J., Ivey, Richard G., Kennedy, Jacob J., Saul, Richard G., Colantonio, Simona, Roberts, Rhonda R., Knotts, Joseph G., Kaczmarczyk, Jan A., Perry, Candice, Hewitt, Stephen M., Bocik, William, Whiteley, Gordon R., Hiltke, Tara, Boja, Emily S., Rodriguez, Henry, Whiteaker, Jeffrey R., and Paulovich, Amanda G.

Published
2019
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32. Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy

Author

Krug, Karsten, Jaehnig, Eric J., Satpathy, Shankha, Blumenberg, Lili, Karpova, Alla, Anurag, Meenakshi, Miles, George, Mertins, Philipp, Geffen, Yifat, Tang, Lauren C., Heiman, David I., Cao, Song, Maruvka, Yosef E., Lei, Jonathan T., Huang, Chen, Kothadia, Ramani B., Colaprico, Antonio, Birger, Chet, Wang, Jarey, Dou, Yongchao, Wen, Bo, Shi, Zhiao, Liao, Yuxing, Wiznerowicz, Maciej, Wyczalkowski, Matthew A., Chen, Xi Steven, Kennedy, Jacob J., Paulovich, Amanda G., Thiagarajan, Mathangi, Kinsinger, Christopher R., Hiltke, Tara, Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Westbrook, Thomas F., Ding, Li, Getz, Gad, Clauser, Karl R., Fenyö, David, Ruggles, Kelly V., Zhang, Bing, Mani, D.R., Carr, Steven A., Ellis, Matthew J., Gillette, Michael A., Avanessian, Shayan C., Cai, Shuang, Chan, Daniel, Chen, Xian, Edwards, Nathan J., Hoofnagle, Andrew N., Kane, M. Harry, Ketchum, Karen A., Kuhn, Eric, Levine, Douglas A., Li, Shunqiang, Liebler, Daniel C., Liu, Tao, Luo, Jingqin, Madhavan, Subha, Maher, Chris, McDermott, Jason E., McGarvey, Peter B., Oberti, Mauricio, Pandey, Akhilesh, Payne, Samuel H., Ransohoff, David F., Rivers, Robert C., Rodland, Karin D., Rudnick, Paul, Sanders, Melinda E., Shaw, Kenna M., Shih, Ie-Ming, Slebos, Robbert J.C., Smith, Richard D., Snyder, Michael, Stein, Stephen E., Tabb, David L., Thangudu, Ratna R., Thomas, Stefani, Wang, Yue, White, Forest M., Whiteaker, Jeffrey R., Whiteley, Gordon A., Zhang, Hui, Zhang, Zhen, Zhao, Yingming, Zhu, Heng, Zimmerman, Lisa J., Krug, Karsten, Jaehnig, Eric J., Satpathy, Shankha, Blumenberg, Lili, Karpova, Alla, Anurag, Meenakshi, Miles, George, Mertins, Philipp, Geffen, Yifat, Tang, Lauren C., Heiman, David I., Cao, Song, Maruvka, Yosef E., Lei, Jonathan T., Huang, Chen, Kothadia, Ramani B., Colaprico, Antonio, Birger, Chet, Wang, Jarey, Dou, Yongchao, Wen, Bo, Shi, Zhiao, Liao, Yuxing, Wiznerowicz, Maciej, Wyczalkowski, Matthew A., Chen, Xi Steven, Kennedy, Jacob J., Paulovich, Amanda G., Thiagarajan, Mathangi, Kinsinger, Christopher R., Hiltke, Tara, Boja, Emily S., Mesri, Mehdi, Robles, Ana I., Rodriguez, Henry, Westbrook, Thomas F., Ding, Li, Getz, Gad, Clauser, Karl R., Fenyö, David, Ruggles, Kelly V., Zhang, Bing, Mani, D.R., Carr, Steven A., Ellis, Matthew J., Gillette, Michael A., Avanessian, Shayan C., Cai, Shuang, Chan, Daniel, Chen, Xian, Edwards, Nathan J., Hoofnagle, Andrew N., Kane, M. Harry, Ketchum, Karen A., Kuhn, Eric, Levine, Douglas A., Li, Shunqiang, Liebler, Daniel C., Liu, Tao, Luo, Jingqin, Madhavan, Subha, Maher, Chris, McDermott, Jason E., McGarvey, Peter B., Oberti, Mauricio, Pandey, Akhilesh, Payne, Samuel H., Ransohoff, David F., Rivers, Robert C., Rodland, Karin D., Rudnick, Paul, Sanders, Melinda E., Shaw, Kenna M., Shih, Ie-Ming, Slebos, Robbert J.C., Smith, Richard D., Snyder, Michael, Stein, Stephen E., Tabb, David L., Thangudu, Ratna R., Thomas, Stefani, Wang, Yue, White, Forest M., Whiteaker, Jeffrey R., Whiteley, Gordon A., Zhang, Hui, Zhang, Zhen, Zhao, Yingming, Zhu, Heng, and Zimmerman, Lisa J.

Abstract

© 2020 The Authors The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this “proteogenomics” approach was applied to 122 treatment-naive primary breast cancers accrued to preserve post-translational modifications, including protein phosphorylation and acetylation. Proteogenomics challenged standard breast cancer diagnoses, provided detailed analysis of the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint therapy, and allowed more accurate assessment of Rb status for prediction of CDK4/6 inhibitor responsiveness. Phosphoproteomics profiles uncovered novel associations between tumor suppressor loss and targetable kinases. Acetylproteome analysis highlighted acetylation on key nuclear proteins involved in the DNA damage response and revealed cross-talk between cytoplasmic and mitochondrial acetylation and metabolism. Our results underscore the potential of proteogenomics for clinical investigation of breast cancer through more accurate annotation of targetable pathways and biological features of this remarkably heterogeneous malignancy.

Published
2022

34. Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays

Author

Whiteaker, Jeffrey R., primary, Halusa, Goran N., additional, Hoofnagle, Andrew N., additional, Sharma, Vagisha, additional, MacLean, Brendan, additional, Yan, Ping, additional, Wrobel, John A., additional, Kennedy, Jacob, additional, Mani, D. R., additional, Zimmerman, Lisa J., additional, Meyer, Matthew R., additional, Mesri, Mehdi, additional, Boja, Emily, additional, Carr, Steven A., additional, Chan, Daniel W., additional, Chen, Xian, additional, Chen, Jing, additional, Davies, Sherri R., additional, Ellis, Matthew J. C., additional, Fenyö, David, additional, Hiltke, Tara, additional, Ketchum, Karen A., additional, Kinsinger, Chris, additional, Kuhn, Eric, additional, Liebler, Daniel C., additional, Liu, Tao, additional, Loss, Michael, additional, MacCoss, Michael J., additional, Qian, Wei-Jun, additional, Rivers, Robert, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Scott, Mitchell G., additional, Smith, Richard D., additional, Thomas, Stefani, additional, Townsend, R. Reid, additional, Whiteley, Gordon, additional, Wu, Chaochao, additional, Zhang, Hui, additional, Zhang, Zhen, additional, Rodriguez, Henry, additional, and Paulovich, Amanda G., additional

Published
2016
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36. Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens

Author

Whiteaker, Jeffrey R., primary, Lundeen, Rachel A., additional, Zhao, Lei, additional, Schoenherr, Regine M., additional, Burian, Aura, additional, Huang, Dongqing, additional, Voytovich, Ulianna, additional, Wang, Tao, additional, Kennedy, Jacob J., additional, Ivey, Richard G., additional, Lin, Chenwei, additional, Murillo, Oscar D., additional, Lorentzen, Travis D., additional, Thiagarajan, Mathangi, additional, Colantonio, Simona, additional, Caceres, Tessa W., additional, Roberts, Rhonda R., additional, Knotts, Joseph G., additional, Reading, Joshua J., additional, Kaczmarczyk, Jan A., additional, Richardson, Christopher W., additional, Garcia-Buntley, Sandra S., additional, Bocik, William, additional, Hewitt, Stephen M., additional, Murray, Karen E., additional, Do, Nhan, additional, Brophy, Mary, additional, Wilz, Stephen W., additional, Yu, Hongbo, additional, Ajjarapu, Samuel, additional, Boja, Emily, additional, Hiltke, Tara, additional, Rodriguez, Henry, additional, and Paulovich, Amanda G., additional

Published
2021
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37. Proteogenomic characterization of pancreatic ductal adenocarcinoma

Author

Cao, Liwei, primary, Huang, Chen, additional, Cui Zhou, Daniel, additional, Hu, Yingwei, additional, Lih, T. Mamie, additional, Savage, Sara R., additional, Krug, Karsten, additional, Clark, David J., additional, Schnaubelt, Michael, additional, Chen, Lijun, additional, da Veiga Leprevost, Felipe, additional, Eguez, Rodrigo Vargas, additional, Yang, Weiming, additional, Pan, Jianbo, additional, Wen, Bo, additional, Dou, Yongchao, additional, Jiang, Wen, additional, Liao, Yuxing, additional, Shi, Zhiao, additional, Terekhanova, Nadezhda V., additional, Cao, Song, additional, Lu, Rita Jui-Hsien, additional, Li, Yize, additional, Liu, Ruiyang, additional, Zhu, Houxiang, additional, Ronning, Peter, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Easwaran, Hariharan, additional, Danilova, Ludmila, additional, Mer, Arvind Singh, additional, Yoo, Seungyeul, additional, Wang, Joshua M., additional, Liu, Wenke, additional, Haibe-Kains, Benjamin, additional, Thiagarajan, Mathangi, additional, Jewell, Scott D., additional, Hostetter, Galen, additional, Newton, Chelsea J., additional, Li, Qing Kay, additional, Roehrl, Michael H., additional, Fenyö, David, additional, Wang, Pei, additional, Nesvizhskii, Alexey I., additional, Mani, D.R., additional, Omenn, Gilbert S., additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Bathe, Oliver F., additional, Chan, Daniel W., additional, Hruban, Ralph H., additional, Ding, Li, additional, Zhang, Bing, additional, Zhang, Hui, additional, Amin, Mitual, additional, An, Eunkyung, additional, Ayad, Christina, additional, Bauer, Thomas, additional, Birger, Chet, additional, Birrer, Michael J., additional, Boca, Simina M., additional, Bocik, William, additional, Borucki, Melissa, additional, Cai, Shuang, additional, Carr, Steven A., additional, Cerda, Sandra, additional, Chen, Huan, additional, Chen, Steven, additional, Chesla, David, additional, Chinnaiyan, Arul M., additional, Colaprico, Antonio, additional, Cottingham, Sandra, additional, Derejska, Magdalena, additional, Dhanasekaran, Saravana M., additional, Domagalski, Marcin J., additional, Druker, Brian J., additional, Duffy, Elizabeth, additional, Dyer, Maureen A., additional, Edwards, Nathan J., additional, Ellis, Matthew J., additional, Eschbacher, Jennifer, additional, Francis, Alicia, additional, Francis, Jesse, additional, Gabriel, Stacey, additional, Gabrovski, Nikolay, additional, Gardner, Johanna, additional, Getz, Gad, additional, Gillette, Michael A., additional, Goldthwaite, Charles A., additional, Grady, Pamela, additional, Guo, Shuai, additional, Hariharan, Pushpa, additional, Hiltke, Tara, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Huang, Jasmine, additional, Jones, Corbin D., additional, Ketchum, Karen A., additional, Kinsinger, Christopher R., additional, Koziak, Jennifer M., additional, Kusnierz, Katarzyna, additional, Liu, Tao, additional, Long, Jiang, additional, Mallery, David, additional, Mareedu, Sailaja, additional, Matteotti, Ronald, additional, Maunganidze, Nicollette, additional, McGarvey, Peter B., additional, Minoo, Parham, additional, Paklina, Oxana V., additional, Paulovich, Amanda G., additional, Payne, Samuel H., additional, Potapova, Olga, additional, Pruetz, Barbara, additional, Qi, Liqun, additional, Roche, Nancy, additional, Rodland, Karin D., additional, Rohrer, Daniel C., additional, Schadt, Eric E., additional, Shabunin, Alexey V., additional, Shelton, Troy, additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Smith, Michael, additional, Smith, Richard D., additional, Sokoll, Lori J., additional, Suh, James, additional, Thangudu, Ratna R., additional, Tsang, Shirley X., additional, Um, Ki Sung, additional, Valley, Dana R., additional, Vatanian, Negin, additional, Wang, Wenyi, additional, Wilson, George D., additional, Wiznerowicz, Maciej, additional, Zhang, Zhen, additional, and Zhao, Grace, additional

Published
2021
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38. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics

Author

Aderinwale, Tunde, Afyounian, Ebrahim, Agrawal, Piyush, Ali, Mehreen, Amadoz, Alicia, Azuaje, Francisco, Bachman, John, Bae, Seohui, Bhalla, Sherry, Carbonell-Caballero, José, Chakraborty, Priyanka, Chaudhary, Kumardeep, Choi, Yonghwa, Choi, Yoonjung, Çubuk, Cankut, Dhanda, Sandeep Kumar, Dopazo, Joaquín, Elo, Laura L., Fóthi, Ábel, Gevaert, Olivier, Granberg, Kirsi, Greiner, Russell, Heo, Eunji, Hidalgo, Marta R., Jayaswal, Vivek, Jeon, Hwisang, Jeon, Minji, Kalmady, Sunil V., Kambara, Yasuhiro, Kang, Jaewoo, Kang, Keunsoo, Kaoma, Tony, Kaur, Harpreet, Kazan, Hilal, Kesar, Devishi, Kesseli, Juha, Kim, Daehan, Kim, Keonwoo, Kim, Sang-Yoon, Kim, Sunkyu, Kumar, Sajal, Lee, Bora, Lee, Heewon, Liu, Yunpeng, Luethy, Roland, Mahajan, Swapnil, Mahmoudian, Mehrad, Muller, Arnaud, Nazarov, Petr V., Nguyen, Hien, Nykter, Matti, Okuda, Shujiro, Park, Sungsoo, Pal Singh Raghava, Gajendra, Rajapakse, Jagath C., Rantapero, Tommi, Ryu, Hobin, Salavert, Francisco, Saraei, Sohrab, Sharma, Ruby, Siitonen, Ari, Sokolov, Artem, Subramanian, Kartik, Suni, Veronika, Suomi, Tomi, Tranchevent, Léon-Charles, Usmani, Salman Sadullah, Välikangas, Tommi, Vega, Roberto, Zhong, Hua, Yang, Mi, Petralia, Francesca, Li, Zhi, Li, Hongyang, Ma, Weiping, Song, Xiaoyu, Yu, Han, Kaczmarczyk, Jan, Stępniak, Piotr, Warchoł, Michał, Yu, Thomas, Calinawan, Anna P., Boutros, Paul C., Payne, Samuel H., Reva, Boris, Boja, Emily, Rodriguez, Henry, Stolovitzky, Gustavo, Guan, Yuanfang, Wang, Pei, Fenyö, David, and Saez-Rodriguez, Julio

Published
2020
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39. Proteogenomic characterization of human colon and rectal cancer

Author

Zhang, Bing, Wang, Jing, Wang, Xiaojing, Zhu, Jing, Liu, Qi, Shi, Zhiao, Chambers, Matthew C., Zimmerman, Lisa J., Shaddox, Kent F., Kim, Sangtae, Davies, Sherri R., Wang, Sean, Wang, Pei, Kinsinger, Christopher R., Rivers, Robert C., Rodriguez, Henry, Townsend, Reid R., Ellis, Matthew J. C., Carr, Steven A., Tabb, David L., Coffey, Robert J., Slebos, Robbert J. C., Liebler, Daniel C., Gillette, Michael A., Klauser, Karl R., Kuhn, Eric, Mani, D. R., Mertins, Philipp, Ketchum, Karen A., Paulovich, Amanda G., Whiteaker, Jeffrey R., Edwards, Nathan J., McGarvey, Peter B., Madhavan, Subha, Chan, Daniel, Pandey, Akhilesh, Shih, Ie-Ming, Zhang, Hui, Zhang, Zhen, Zhu, Heng, Whiteley, Gordon A., Skates, Steven J., White, Forest M., Levine, Douglas A., Boja, Emily S., Hiltke, Tara, Mesri, Mehdi, Shaw, Kenna M., Stein, Stephen E., Fenyo, David, Liu, Tao, McDermott, Jason E., Payne, Samuel H., Rodland, Karin D., Smith, Richard D., Rudnick, Paul, Snyder, Michael, Zhao, Yingming, Chen, Xian, Ransohoff, David F., Hoofnagle, Andrew N., Sanders, Melinda E., Wang, Yue, Ding, Li, and Reid Townsend, R.

Published
2014
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40. Proteogenomic and metabolomic characterization of human glioblastoma

Author

Wang, Liang-Bo, primary, Karpova, Alla, additional, Gritsenko, Marina A., additional, Kyle, Jennifer E., additional, Cao, Song, additional, Li, Yize, additional, Rykunov, Dmitry, additional, Colaprico, Antonio, additional, Rothstein, Joseph H., additional, Hong, Runyu, additional, Stathias, Vasileios, additional, Cornwell, MacIntosh, additional, Petralia, Francesca, additional, Wu, Yige, additional, Reva, Boris, additional, Krug, Karsten, additional, Pugliese, Pietro, additional, Kawaler, Emily, additional, Olsen, Lindsey K., additional, Liang, Wen-Wei, additional, Song, Xiaoyu, additional, Dou, Yongchao, additional, Wendl, Michael C., additional, Caravan, Wagma, additional, Liu, Wenke, additional, Cui Zhou, Daniel, additional, Ji, Jiayi, additional, Tsai, Chia-Feng, additional, Petyuk, Vladislav A., additional, Moon, Jamie, additional, Ma, Weiping, additional, Chu, Rosalie K., additional, Weitz, Karl K., additional, Moore, Ronald J., additional, Monroe, Matthew E., additional, Zhao, Rui, additional, Yang, Xiaolu, additional, Yoo, Seungyeul, additional, Krek, Azra, additional, Demopoulos, Alexis, additional, Zhu, Houxiang, additional, Wyczalkowski, Matthew A., additional, McMichael, Joshua F., additional, Henderson, Brittany L., additional, Lindgren, Caleb M., additional, Boekweg, Hannah, additional, Lu, Shuangjia, additional, Baral, Jessika, additional, Yao, Lijun, additional, Stratton, Kelly G., additional, Bramer, Lisa M., additional, Zink, Erika, additional, Couvillion, Sneha P., additional, Bloodsworth, Kent J., additional, Satpathy, Shankha, additional, Sieh, Weiva, additional, Boca, Simina M., additional, Schürer, Stephan, additional, Chen, Feng, additional, Wiznerowicz, Maciej, additional, Ketchum, Karen A., additional, Boja, Emily S., additional, Kinsinger, Christopher R., additional, Robles, Ana I., additional, Hiltke, Tara, additional, Thiagarajan, Mathangi, additional, Nesvizhskii, Alexey I., additional, Zhang, Bing, additional, Mani, D.R., additional, Ceccarelli, Michele, additional, Chen, Xi S., additional, Cottingham, Sandra L., additional, Li, Qing Kay, additional, Kim, Albert H., additional, Fenyö, David, additional, Ruggles, Kelly V., additional, Rodriguez, Henry, additional, Mesri, Mehdi, additional, Payne, Samuel H., additional, Resnick, Adam C., additional, Wang, Pei, additional, Smith, Richard D., additional, Iavarone, Antonio, additional, Chheda, Milan G., additional, Barnholtz-Sloan, Jill S., additional, Rodland, Karin D., additional, Liu, Tao, additional, Ding, Li, additional, Agarwal, Anupriya, additional, Amin, Mitual, additional, An, Eunkyung, additional, Anderson, Matthew L., additional, Andrews, David W., additional, Bauer, Thomas, additional, Birger, Chet, additional, Birrer, Michael J., additional, Blumenberg, Lili, additional, Bocik, William E., additional, Borate, Uma, additional, Borucki, Melissa, additional, Burke, Meghan C., additional, Cai, Shuang, additional, Calinawan, Anna P., additional, Carr, Steven A., additional, Cerda, Sandra, additional, Chan, Daniel W., additional, Charamut, Alyssa, additional, Chen, Lin S., additional, Chesla, David, additional, Chinnaiyan, Arul M., additional, Chowdhury, Shrabanti, additional, Cieślik, Marcin P., additional, Clark, David J., additional, Culpepper, Houston, additional, Czernicki, Tomasz, additional, D'Angelo, Fulvio, additional, Day, Jacob, additional, De Young, Stephanie, additional, Demir, Emek, additional, Dhanasekaran, Saravana Mohan, additional, Dhir, Rajiv, additional, Domagalski, Marcin J., additional, Druker, Brian, additional, Duffy, Elizabeth, additional, Dyer, Maureen, additional, Edwards, Nathan J., additional, Edwards, Robert, additional, Elburn, Kimberly, additional, Ellis, Matthew J., additional, Eschbacher, Jennifer, additional, Francis, Alicia, additional, Gabriel, Stacey, additional, Gabrovski, Nikolay, additional, Garofano, Luciano, additional, Getz, Gad, additional, Gillette, Michael A., additional, Godwin, Andrew K., additional, Golbin, Denis, additional, Hanhan, Ziad, additional, Hannick, Linda I., additional, Hariharan, Pushpa, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Hostetter, Galen, additional, Huang, Chen, additional, Jaehnig, Eric, additional, Jewell, Scott D., additional, Ji, Nan, additional, Jones, Corbin D., additional, Karz, Alcida, additional, Kaspera, Wojciech, additional, Kim, Lyndon, additional, Kothadia, Ramani B., additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan, additional, Leprevost, Felipe D., additional, Li, Kai, additional, Liao, Yuxing, additional, Lilly, Jena, additional, Liu, Hongwei, additional, Lubínski, Jan, additional, Madan, Rashna, additional, Maggio, William, additional, Malc, Ewa, additional, Malovannaya, Anna, additional, Mareedu, Sailaja, additional, Markey, Sanford P., additional, Marrero-Oliveras, Annette, additional, Martinez, Nina, additional, Maunganidze, Nicollette, additional, McDermott, Jason E., additional, McGarvey, Peter B., additional, McGee, John, additional, Mieczkowski, Piotr, additional, Migliozzi, Simona, additional, Modugno, Francesmary, additional, Montgomery, Rebecca, additional, Newton, Chelsea J., additional, Omenn, Gilbert S., additional, Ozbek, Umut, additional, Paklina, Oxana V., additional, Paulovich, Amanda G., additional, Perou, Amy M., additional, Pico, Alexander R., additional, Piehowski, Paul D., additional, Placantonakis, Dimitris G., additional, Polonskaya, Larisa, additional, Potapova, Olga, additional, Pruetz, Barbara, additional, Qi, Liqun, additional, Ramkissoon, Shakti, additional, Resnick, Adam, additional, Richey, Shannon, additional, Riggins, Gregory, additional, Robinson, Karna, additional, Roche, Nancy, additional, Rohrer, Daniel C., additional, Rood, Brian R., additional, Rossell, Larissa, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Shi, Yan, additional, Shi, Zhiao, additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Skelly, Tara, additional, Sokoll, Lori J., additional, Stawicki, Jakub, additional, Stein, Stephen E., additional, Suh, James, additional, Szopa, Wojciech, additional, Tabor, Dave, additional, Tan, Donghui, additional, Tansil, Darlene, additional, Thangudu, Ratna R., additional, Tognon, Cristina, additional, Traer, Elie, additional, Tsang, Shirley, additional, Tyner, Jeffrey, additional, Um, Ki Sung, additional, Valley, Dana R., additional, Vasaikar, Suhas, additional, Vatanian, Negin, additional, Velvulou, Uma, additional, Vernon, Michael, additional, Wan, Weiqing, additional, Wang, Junmei, additional, Webster, Alex, additional, Wen, Bo, additional, Whiteaker, Jeffrey R., additional, Wilson, George D., additional, Zakhartsev, Yuriy, additional, Zelt, Robert, additional, Zhang, Hui, additional, Zhang, Liwei, additional, Zhang, Zhen, additional, Zhao, Grace, additional, and Zhu, Jun, additional

Published
2021
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41. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma

Author

Huang, Chen, primary, Chen, Lijun, additional, Savage, Sara R., additional, Eguez, Rodrigo Vargas, additional, Dou, Yongchao, additional, Li, Yize, additional, da Veiga Leprevost, Felipe, additional, Jaehnig, Eric J., additional, Lei, Jonathan T., additional, Wen, Bo, additional, Schnaubelt, Michael, additional, Krug, Karsten, additional, Song, Xiaoyu, additional, Cieślik, Marcin, additional, Chang, Hui-Yin, additional, Wyczalkowski, Matthew A., additional, Li, Kai, additional, Colaprico, Antonio, additional, Li, Qing Kay, additional, Clark, David J., additional, Hu, Yingwei, additional, Cao, Liwei, additional, Pan, Jianbo, additional, Wang, Yuefan, additional, Cho, Kyung-Cho, additional, Shi, Zhiao, additional, Liao, Yuxing, additional, Jiang, Wen, additional, Anurag, Meenakshi, additional, Ji, Jiayi, additional, Yoo, Seungyeul, additional, Zhou, Daniel Cui, additional, Liang, Wen-Wei, additional, Wendl, Michael, additional, Vats, Pankaj, additional, Carr, Steven A., additional, Mani, D.R., additional, Zhang, Zhen, additional, Qian, Jiang, additional, Chen, Xi S., additional, Pico, Alexander R., additional, Wang, Pei, additional, Chinnaiyan, Arul M., additional, Ketchum, Karen A., additional, Kinsinger, Christopher R., additional, Robles, Ana I., additional, An, Eunkyung, additional, Hiltke, Tara, additional, Mesri, Mehdi, additional, Thiagarajan, Mathangi, additional, Weaver, Alissa M., additional, Sikora, Andrew G., additional, Lubiński, Jan, additional, Wierzbicka, Małgorzata, additional, Wiznerowicz, Maciej, additional, Satpathy, Shankha, additional, Gillette, Michael A., additional, Miles, George, additional, Ellis, Matthew J., additional, Omenn, Gilbert S., additional, Rodriguez, Henry, additional, Boja, Emily S., additional, Dhanasekaran, Saravana M., additional, Ding, Li, additional, Nesvizhskii, Alexey I., additional, El-Naggar, Adel K., additional, Chan, Daniel W., additional, Zhang, Hui, additional, Zhang, Bing, additional, Agarwal, Anupriya, additional, Anderson, Matthew L., additional, Avanessian, Shayan C., additional, Avtonomov, Dmitry, additional, Bathe, Oliver F., additional, Birger, Chet, additional, Birrer, Michael J., additional, Blumenberg, Lili, additional, Bocik, William E., additional, Borate, Uma, additional, Borucki, Melissa, additional, Burke, Meghan C., additional, Cai, Shuang, additional, Calinawan, Anna Pamela, additional, Cerda, Sandra, additional, Charamut, Alyssa, additional, Chen, Lin S., additional, Chowdhury, Shrabanti, additional, Clauser, Karl R., additional, Culpepper, Houston, additional, Czernicki, Tomasz, additional, D'Angelo, Fulvio, additional, Day, Jacob, additional, De Young, Stephanie, additional, Demir, Emek, additional, Ding, Fei, additional, Domagalski, Marcin J., additional, Dort, Joseph C., additional, Druker, Brian, additional, Duffy, Elizabeth, additional, Dyer, Maureen, additional, Edwards, Nathan J., additional, Elburn, Kimberly, additional, Ermakova, Tatiana S., additional, Fenyo, David, additional, Ferrarotto, Renata, additional, Francis, Alicia, additional, Gabriel, Stacey, additional, Garofano, Luciano, additional, Geffen, Yifat, additional, Getz, Gad, additional, Goldthwaite, Charles A., additional, Hannick, Linda I., additional, Hariharan, Pushpa, additional, Hayes, David N., additional, Heiman, David, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Hostetter, Galen, additional, Hyrcza, Martin, additional, Jewell, Scott D., additional, Jones, Corbin D., additional, Kane, M. Harry, additional, Karz, Alicia, additional, Kothadia, Ramani B., additional, Krek, Azra, additional, Kumar-Sinha, Chandan, additional, Liu, Tao, additional, Liu, Hongwei, additional, Ma, Weiping, additional, Malc, Ewa, additional, Malovannaya, Anna, additional, Mareedu, Sailaja, additional, Markey, Sanford P., additional, Marrero-Oliveras, Annette, additional, Maunganidze, Nicollette, additional, McDermott, Jason E., additional, McGarvey, Peter B., additional, McGee, John, additional, Mieczkowski, Piotr, additional, Migliozzi, Simona, additional, Montgomery, Rebecca, additional, Newton, Chelsea J., additional, Ozbek, Umut, additional, Paulovich, Amanda G., additional, Payne, Samuel H., additional, Pazardzhikliev, Dimitar Dimitrov, additional, Perou, Amy M., additional, Petralia, Francesca, additional, Petrenko, Lyudmila, additional, Piehowski, Paul D., additional, Placantonakis, Dmitris, additional, Polonskaya, Larisa, additional, Ponomareva, Elena V., additional, Potapova, Olga, additional, Qi, Liqun, additional, Qu, Ning, additional, Ramkissoon, Shakti, additional, Reva, Boris, additional, Richey, Shannon, additional, Robinson, Karna, additional, Roche, Nancy, additional, Rodland, Karin, additional, Rohrer, Daniel C., additional, Rykunov, Dmitry, additional, Schadt, Eric E., additional, Shi, Yan, additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Skelly, Tara, additional, Smith, Richard, additional, Sokoll, Lori J., additional, Stawicki, Jakub, additional, Stein, Stephen E., additional, Suh, James, additional, Szopa, Wojciech, additional, Tabor, Dave, additional, Tan, Donghui, additional, Tansil, Darlene, additional, Teo, Guo Ci, additional, Thangudu, Ratna R., additional, Tognon, Cristina, additional, Traer, Elie, additional, Tsang, Shirley, additional, Tyner, Jeffrey, additional, Um, Ki Sung, additional, Valley, Dana R., additional, Vasilev, Lyubomir Valkov, additional, Vatanian, Negin, additional, Velvulou, Uma, additional, Vernon, Michael, additional, Westbrook, Thomas F., additional, Whiteaker, Jeffrey R., additional, Wu, Yige, additional, Xu, Midie, additional, Yao, Lijun, additional, Yi, Xinpei, additional, Yu, Fengchao, additional, Zaalishvili, Kakhaber, additional, Zakhartsev, Yuriy, additional, Zelt, Robert, additional, Zhao, Grace, additional, and Zhu, Jun, additional

Published
2021
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42. Structural conservation of mouse and rat zona pellucida glycoproteins. Probing the native rat zona pellucida proteome by mass spectrometry

Author

Boja, Emily S., Hoodbhoy, Tanya, Garfield, Mark, and Fales, Henry M.

Subjects
Glycoproteins -- Chemical properties, Proteomics -- Research, Mass spectrometry -- Usage, Biological sciences, Chemistry
Abstract

Mouse zonae are composed of three glycoproteins (ZP1, ZP2, and ZP3), while rat zonae contain four (ZP1, ZP2, ZP3, and ZP4/ZPB). Rat sperm are shown to bind with the zonae, indicating that ZP2 and ZP3 contain a 'minimum structure(s)' to which rodent sperm can bind, and ZP1 and ZP4/ZPB are dispensable in these two rodents.

Published
2005

43. Testis brain ribonucleic acid-binding protein/translin possesses both single-stranded and double-stranded ribonuclease activities

Author

Jun Wang, Boja, Emily A., Oubrahim, Hammou, and Chock, P. Boon

Subjects
Protein binding -- Research, RNA -- Research, Biological sciences, Chemistry
Abstract

A (super 32)P- and photoaffinity moiety-labeled 22 bp dsRNA fragment is synthesized and is used as bait to fish out proteins directly interacting with the double stranded RNA (dsRNA) fragment. The analysis of DNA/RNA binding protein showed that it possesses both ssRNase and dsRNase activities but not DNase activity.

Published
2004

44. Mass spectrometry analysis of recombinant human ZP3 expressed in glycosylation-deficient CHO cells

Author

Ming Zhao, Hoodbhoy, Tanya, Kaufman, Jeanne B., Ghirlando, Rodolfo, Pannell, Lewis;, Boja, Emily S., Nawrocki, Joseph, Dean, Jurrien, Kresge, Nicole, Shiloach, Joseph, Fales, Henry M., and Levine, Rodney L.

Subjects
Proteins -- Chemical properties, Mass spectrometry -- Usage, Biological sciences, Chemistry
Abstract

The proteins of native mouse zona pellucid are previously analyzed by mass spectrometry, but the difficulty in obtaining biological material precludes a similar analysis of native human zona proteins. Therefore taking advantage of earlier success in expressing mouse ZP3 in CHO cells, human ZP3 is expressed in glycosylation-deficient CHO cells to minimize heterogeneity and analyzed by microscale mass spectrometry.

Published
2004

45. Divinyl sulfone as a postdigestion modifier for enhancing the [a.sub.1] ion in MS/MS and postsource decay: potential applications in proteomics

Author

Boja, Emily S., Sokoloski, Edward A., and Fales, Henry M.

Subjects
Chemistry, Analytic -- Research, Chemistry
Abstract

Divinyl sulfone reacts at pH 8-9 with the [alpha]-amino groups of N-terminal residues, proline, the [epsilon]-amino groups of lysine, and the histidine side chains of peptides. This reaction leads to great enhancement of the abundance of the normally weak or missing '[a.sub.1]' fragment ion in MS/MS analysis defining the N-terminal residue of a peptide in a digest. This provides 'one-step Edman-like' information that, together with a fairly accurately determined mass, often enables one to correctly identify a protein or family of proteins. The applicability of this procedure in proteomics was demonstrated with several peptides and tryptic digests of protein mixtures by LC-MS/MS experiments using a QTOF and MALDI-PSD analyses. Advantages of this approach are its simple chemistry, retention of charge multiplicity, and possibly, shortening of database search time. Used with other MS/MS data, it provides higher confidence in the scores and identification of a protein found in peptide mass fingerprinting. Moreover, this approach has an advantage in 'de novo' sequencing due to its ability to decipher the first amino acid of a peptide whose information is normally unavailable in MS/MS spectra.

Published
2004

47. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer

Author

Petralia, Francesca, primary, Tignor, Nicole, additional, Reva, Boris, additional, Koptyra, Mateusz, additional, Chowdhury, Shrabanti, additional, Rykunov, Dmitry, additional, Krek, Azra, additional, Ma, Weiping, additional, Zhu, Yuankun, additional, Ji, Jiayi, additional, Calinawan, Anna, additional, Whiteaker, Jeffrey R., additional, Colaprico, Antonio, additional, Stathias, Vasileios, additional, Omelchenko, Tatiana, additional, Song, Xiaoyu, additional, Raman, Pichai, additional, Guo, Yiran, additional, Brown, Miguel A., additional, Ivey, Richard G., additional, Szpyt, John, additional, Guha Thakurta, Sanjukta, additional, Gritsenko, Marina A., additional, Weitz, Karl K., additional, Lopez, Gonzalo, additional, Kalayci, Selim, additional, Gümüş, Zeynep H., additional, Yoo, Seungyeul, additional, da Veiga Leprevost, Felipe, additional, Chang, Hui-Yin, additional, Krug, Karsten, additional, Katsnelson, Lizabeth, additional, Wang, Ying, additional, Kennedy, Jacob J., additional, Voytovich, Uliana J., additional, Zhao, Lei, additional, Gaonkar, Krutika S., additional, Ennis, Brian M., additional, Zhang, Bo, additional, Baubet, Valerie, additional, Tauhid, Lamiya, additional, Lilly, Jena V., additional, Mason, Jennifer L., additional, Farrow, Bailey, additional, Young, Nathan, additional, Leary, Sarah, additional, Moon, Jamie, additional, Petyuk, Vladislav A., additional, Nazarian, Javad, additional, Adappa, Nithin D., additional, Palmer, James N., additional, Lober, Robert M., additional, Rivero-Hinojosa, Samuel, additional, Wang, Liang-Bo, additional, Wang, Joshua M., additional, Broberg, Matilda, additional, Chu, Rosalie K., additional, Moore, Ronald J., additional, Monroe, Matthew E., additional, Zhao, Rui, additional, Smith, Richard D., additional, Zhu, Jun, additional, Robles, Ana I., additional, Mesri, Mehdi, additional, Boja, Emily, additional, Hiltke, Tara, additional, Rodriguez, Henry, additional, Zhang, Bing, additional, Schadt, Eric E., additional, Mani, D.R., additional, Ding, Li, additional, Iavarone, Antonio, additional, Wiznerowicz, Maciej, additional, Schürer, Stephan, additional, Chen, Xi S., additional, Heath, Allison P., additional, Rokita, Jo Lynne, additional, Nesvizhskii, Alexey I., additional, Fenyö, David, additional, Rodland, Karin D., additional, Liu, Tao, additional, Gygi, Steven P., additional, Paulovich, Amanda G., additional, Resnick, Adam C., additional, Storm, Phillip B., additional, Rood, Brian R., additional, Wang, Pei, additional, Francis, Alicia, additional, Morgan, Allison M., additional, Waanders, Angela J., additional, Viaene, Angela N., additional, Buccoliero, Anna Maria, additional, Chinnaiyan, Arul M., additional, Leonard, Carina A., additional, Kline, Cassie N., additional, Caporalini, Chiara, additional, Kinsinger, Christopher R., additional, Li, Chunde, additional, Kram, David E., additional, Hanson, Derek, additional, Appert, Elizabeth, additional, Kawaler, Emily A., additional, Raabe, Eric H., additional, Jackson, Eric M., additional, Greenfield, Jeffrey P., additional, Stone, Gabrielle S., additional, Getz, Gad, additional, Grant, Gerald, additional, Teo, Guo Ci, additional, Pollack, Ian F., additional, Cain, Jason E., additional, Foster, Jessica B., additional, Phillips, Joanna J., additional, Palma, July E., additional, Ketchum, Karen A., additional, Ruggles, Kelly V., additional, Blumenberg, Lili, additional, Cornwell, Macintosh, additional, Sarmady, Mahdi, additional, Domagalski, Marcin J., additional, Cieślik, Marcin P., additional, Santi, Mariarita, additional, Li, Marilyn M., additional, Ellis, Matthew J., additional, Wyczalkowski, Matthew A., additional, Connors, Meghan, additional, Scagnet, Mirko, additional, Gupta, Nalin, additional, Edwards, Nathan J., additional, Vitanza, Nicholas A., additional, Vaske, Olena M., additional, Becher, Oren, additional, McGarvey, Peter B., additional, Firestein, Ron, additional, Mueller, Sabine, additional, Winebrake, Samuel G., additional, Dhanasekaran, Saravana Mohan, additional, Cai, Shuang, additional, Partap, Sonia, additional, Patton, Tatiana, additional, Le, Toan, additional, Lorentzen, Travis D., additional, Liu, Wenke, additional, and Bocik, William E., additional

Published
2020
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48. precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

Author

Olson, Nathan D., primary, Wagner, Justin, additional, McDaniel, Jennifer, additional, Stephens, Sarah H., additional, Westreich, Samuel T., additional, Prasanna, Anish G., additional, Johanson, Elaine, additional, Boja, Emily, additional, Maier, Ezekiel J., additional, Serang, Omar, additional, Jáspez, David, additional, Lorenzo-Salazar, José M., additional, Muñoz-Barrera, Adrián, additional, Rubio-Rodríguez, Luis A., additional, Flores, Carlos, additional, Kyriakidis, Konstantinos, additional, Malousi, Andigoni, additional, Shafin, Kishwar, additional, Pesout, Trevor, additional, Jain, Miten, additional, Paten, Benedict, additional, Chang, Pi-Chuan, additional, Kolesnikov, Alexey, additional, Nattestad, Maria, additional, Baid, Gunjan, additional, Goel, Sidharth, additional, Yang, Howard, additional, Carroll, Andrew, additional, Eveleigh, Robert, additional, Bourgey, Mathieu, additional, Bourque, Guillaume, additional, Li, Gen, additional, ChouXian, MA, additional, Tang, LinQi, additional, YuanPing, DU, additional, Zhang, ShaoWei, additional, Morata, Jordi, additional, Tonda, Raúl, additional, Parra, Genís, additional, Trotta, Jean-Rémi, additional, Brueffer, Christian, additional, Demirkaya-Budak, Sinem, additional, Kabakci-Zorlu, Duygu, additional, Turgut, Deniz, additional, Kalay, Özem, additional, Budak, Gungor, additional, Narcı, Kübra, additional, Arslan, Elif, additional, Brown, Richard, additional, Johnson, Ivan J, additional, Dolgoborodov, Alexey, additional, Semenyuk, Vladimir, additional, Jain, Amit, additional, Tetikol, H. Serhat, additional, Jain, Varun, additional, Ruehle, Mike, additional, Lajoie, Bryan, additional, Roddey, Cooper, additional, Catreux, Severine, additional, Mehio, Rami, additional, Ahsan, Mian Umair, additional, Liu, Qian, additional, Wang, Kai, additional, Sahraeian, Sayed Mohammad Ebrahim, additional, Fang, Li Tai, additional, Mohiyuddin, Marghoob, additional, Hung, Calvin, additional, Jain, Chirag, additional, Feng, Hanying, additional, Li, Zhipan, additional, Chen, Luoqi, additional, Sedlazeck, Fritz J., additional, and Zook, Justin M., additional

Published
2020
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49. Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy

Author

Krug, Karsten, primary, Jaehnig, Eric J., additional, Satpathy, Shankha, additional, Blumenberg, Lili, additional, Karpova, Alla, additional, Anurag, Meenakshi, additional, Miles, George, additional, Mertins, Philipp, additional, Geffen, Yifat, additional, Tang, Lauren C., additional, Heiman, David I., additional, Cao, Song, additional, Maruvka, Yosef E., additional, Lei, Jonathan T., additional, Huang, Chen, additional, Kothadia, Ramani B., additional, Colaprico, Antonio, additional, Birger, Chet, additional, Wang, Jarey, additional, Dou, Yongchao, additional, Wen, Bo, additional, Shi, Zhiao, additional, Liao, Yuxing, additional, Wiznerowicz, Maciej, additional, Wyczalkowski, Matthew A., additional, Chen, Xi Steven, additional, Kennedy, Jacob J., additional, Paulovich, Amanda G., additional, Thiagarajan, Mathangi, additional, Kinsinger, Christopher R., additional, Hiltke, Tara, additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Westbrook, Thomas F., additional, Ding, Li, additional, Getz, Gad, additional, Clauser, Karl R., additional, Fenyö, David, additional, Ruggles, Kelly V., additional, Zhang, Bing, additional, Mani, D.R., additional, Carr, Steven A., additional, Ellis, Matthew J., additional, Gillette, Michael A., additional, Avanessian, Shayan C., additional, Cai, Shuang, additional, Chan, Daniel, additional, Chen, Xian, additional, Edwards, Nathan J., additional, Hoofnagle, Andrew N., additional, Kane, M. Harry, additional, Ketchum, Karen A., additional, Kuhn, Eric, additional, Levine, Douglas A., additional, Li, Shunqiang, additional, Liebler, Daniel C., additional, Liu, Tao, additional, Luo, Jingqin, additional, Madhavan, Subha, additional, Maher, Chris, additional, McDermott, Jason E., additional, McGarvey, Peter B., additional, Oberti, Mauricio, additional, Pandey, Akhilesh, additional, Payne, Samuel H., additional, Ransohoff, David F., additional, Rivers, Robert C., additional, Rodland, Karin D., additional, Rudnick, Paul, additional, Sanders, Melinda E., additional, Shaw, Kenna M., additional, Shih, Ie-Ming, additional, Slebos, Robbert J.C., additional, Smith, Richard D., additional, Snyder, Michael, additional, Stein, Stephen E., additional, Tabb, David L., additional, Thangudu, Ratna R., additional, Thomas, Stefani, additional, Wang, Yue, additional, White, Forest M., additional, Whiteaker, Jeffrey R., additional, Whiteley, Gordon A., additional, Zhang, Hui, additional, Zhang, Zhen, additional, Zhao, Yingming, additional, Zhu, Heng, additional, and Zimmerman, Lisa J., additional

Published
2020
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50. Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma

Author

Hu, Yingwei, primary, Pan, Jianbo, additional, Shah, Punit, additional, Ao, Minghui, additional, Thomas, Stefani N., additional, Liu, Yang, additional, Chen, Lijun, additional, Schnaubelt, Michael, additional, Clark, David J., additional, Rodriguez, Henry, additional, Boja, Emily S., additional, Hiltke, Tara, additional, Kinsinger, Christopher R., additional, Rodland, Karin D., additional, Li, Qing Kay, additional, Qian, Jiang, additional, Zhang, Zhen, additional, Chan, Daniel W., additional, Zhang, Hui, additional, Pandey, Akhilesh, additional, Paulovich, Amanda, additional, Hoofnagle, Andrew, additional, Zhang, Bing, additional, Mani, D.R., additional, Liebler, Daniel C., additional, Ransohoff, David F., additional, Fenyo, David, additional, Tabb, David L., additional, Levine, Douglas A., additional, Kuhn, Eric, additional, White, Forest M., additional, Whiteley, Gordon A., additional, Zhu, Heng, additional, Shih, Ie-Ming, additional, Bavarva, Jasmin, additional, McDermott, Jason E., additional, Whiteaker, Jeffrey, additional, Ketchum, Karen A., additional, Clauser, Karl R., additional, Ruggles, Kelly, additional, Elburn, Kimberly, additional, Ding, Li, additional, Hannick, Linda, additional, Zimmerman, Lisa J., additional, Watson, Mark, additional, Thiagarajan, Mathangi, additional, Ellis, Matthew J.C., additional, Oberti, Mauricio, additional, Mesri, Mehdi, additional, Sanders, Melinda E., additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Snyder, Michael, additional, Edwards, Nathan J., additional, Vatanian, Negin, additional, Rudnick, Paul A., additional, McGarvey, Peter B., additional, Mertins, Philip, additional, Townsend, R. Reid, additional, Thangudu, Ratna R., additional, Smith, Richard D., additional, Rivers, Robert C., additional, Slebos, Robert J.C., additional, Payne, Samuel H., additional, Davies, Sherri R., additional, Cai, Shuang, additional, Stein, Stephen E., additional, Carr, Steven A., additional, Skates, Steven J., additional, Madhavan, Subha, additional, Liu, Tao, additional, Chen, Xian, additional, Zhao, Yingming, additional, Wang, Yue, additional, and Shi, Zhiao, additional

Published
2020
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