Depletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics by Tu, Chengjian, Rudnick, Paul A, Martinez, Misti Y, Cheek, Kristin L, Stein, Stephen E, Slebos, Robbert J. C, Liebler, Daniel C

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Comprehensive Analysis of Protein Digestion Using Six Trypsins Reveals the Origin of Trypsin As a Significant Source of Variability in Proteomics by Walmsley, Scott J, Rudnick, Paul A, Liang, Yuxue, Dong, Qian, Stein, Stephen E, Nesvizhskii, Alexey I

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Proteome Analysis of Microdissected Formalin-fixed and Paraffin-embedded Tissue Specimens by Guo, Tong, Wang, Weijie, Rudnick, Paul A, Song, Tao, Li, Jie, Zhuang, Zhengping, Weil, Robert J, DeVoe, Don L, Lee, Cheng S, Balgley, Brian M

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Interlaboratory studies and initiatives developing standards for proteomics by Ivanov, Alexander R., Colangelo, Christopher M., Dufresne, Craig P., Friedman, David B., Lilley, Kathryn S., Mechtler, Karl, Phinney, Brett S., Rose, Kristie L., Rudnick, Paul A., Searle, Brian C., Shaffer, Scott A., Weintraub, Susan T.

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MRM as a discovery tool? by Rudnick, Paul A.

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Metabolite Profiling of a NIST Standard Reference Material for Human Plasma (SRM 1950): GC-MS, LC-MS, NMR, and Clinical Laboratory Analyses, Libraries, and Web-Based Resources by Simón-Manso, Yamil, Lowenthal, Mark S, Kilpatrick, Lisa E, Sampson, Maureen L, Telu, Kelly H, Rudnick, Paul A, Mallard, W. Gary, Bearden, Daniel W, Schock, Tracey B, Tchekhovskoi, Dmitrii V, Blonder, Niksa, Yan, Xinjian, Liang, Yuxue, Zheng, Yufang, Wallace, William E, Neta, Pedatsur, Phinney, Karen W, Remaley, Alan T, Stein, Stephen E

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A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline by Rudnick, Paul A, Markey, Sanford P, Roth, Jeri, Mirokhin, Yuri, Yan, Xinjian, Tchekhovskoi, Dmitrii V, Edwards, Nathan J, Thangudu, Ratna R, Ketchum, Karen A, Kinsinger, Christopher R, Mesri, Mehdi, Rodriguez, Henry, Stein, Stephen E

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Quantitative Mass Spectrometry to Interrogate Proteomic Heterogeneity in Metastatic Lung Adenocarcinoma and Validate a Novel Somatic Mutation CDK12-G879V[S] by Zhang, Xu, Nguyen, Khoa Dang, Rudnick, Paul A., Roper, Nitin, Kawaler, Emily, Maity, Tapan K., Awasthi, Shivangi, Gao, Shaojian, Biswas, Romi, Venugopalan, Abhilash, Cultraro, Constance M., Fenyö, David, Guha, Udayan

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Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry by Tabb, David L, Vega-Montoto, Lorenzo, Rudnick, Paul A, Variyath, Asokan Mulayath, Ham, Amy-Joan L, Bunk, David M, Kilpatrick, Lisa E, Billheimer, Dean D, Blackman, Ronald K, Cardasis, Helene L, Carr, Steven A, Clauser, Karl R, Jaffe, Jacob D, Kowalski, Kevin A, Neubert, Thomas A, Regnier, Fred E, Schilling, Birgit, Tegeler, Tony J, Wang, Mu, Wang, Pei, Whiteaker, Jeffrey R, Zimmerman, Lisa J, Fisher, Susan J, Gibson, Bradford W, Kinsinger, Christopher R, Mesri, Mehdi, Rodriguez, Henry, Stein, Stephen E, Tempst, Paul, Paulovich, Amanda G, Liebler, Daniel C, Spiegelman, Cliff

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Refining spectral library searching by Rudnick, Paul A.

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Improved Normalization of Systematic Biases Affecting Ion Current Measurements in Label-free Proteomics Data by Rudnick, Paul A., Wang, Xia, Yan, Xinjian, Sedransk, Nell, Stein, Stephen E.

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Characterization of the Human Salivary Proteome by Capillary Isoelectric Focusing/Nanoreversed-Phase Liquid Chromatography Coupled with ESI-Tandem MS by Guo, Tong, Rudnick, Paul A, Wang, Weijie, Lee, Cheng S, DeVoe, Don L, Balgley, Brian M

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Tandem Mass Spectral Libraries of Peptides in Digests of Individual Proteins: Human Serum Albumin (HSA) by Dong, Qian, Yan, Xinjian, Kilpatrick, Lisa E., Liang, Yuxue, Mirokhin, Yuri A., Roth, Jeri S., Rudnick, Paul A., Stein, Stephen E.

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Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance by Paulovich, Amanda G., Billheimer, Dean, Ham, Amy-Joan L., Vega-Montoto, Lorenzo, Rudnick, Paul A., Tabb, David L., Wang, Pei, Blackman, Ronald K., Bunk, David M., Cardasis, Helene L., Clauser, Karl R., Kinsinger, Christopher R., Schilling, Birgit, Tegeler, Tony J., Variyath, Asokan Mulayath, Wang, Mu, Whiteaker, Jeffrey R., Zimmerman, Lisa J., Fenyo, David, Carr, Steven A., Fisher, Susan J., Gibson, Bradford W., Mesri, Mehdi, Neubert, Thomas A., Regnier, Fred E., Rodriguez, Henry, Spiegelman, Cliff, Stein, Stephen E., Tempst, Paul, Liebler, Daniel C.

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NCI's Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data by Thangudu, Ratna R, Holck, Michael, Singhal, Deepak, Pilozzi, Alexander, Edwards, Nathan, Rudnick, Paul A, Domagalski, Marcin J, Chilappagari, Padmini, Ma, Lei, Xin, Yi, Le, Toan, Nyce, Kristen, Chaudhary, Rekha, Ketchum, Karen A, Maurais, Aaron, Connolly, Brian, Riffle, Michael, Chambers, Matthew C, MacLean, Brendan, MacCoss, Michael J, McGarvey, Peter B, Basu, Anand, Otridge, John, Casas-Silva, Esmeralda, Venkatachari, Sudha, Rodriguez, Henry, Zhang, Xu

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Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy by 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.

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Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer by Zhang, Hui, 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, 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., Carr, Steven A., Gillette, Michael A., Klauser, Karl R., Kuhn, Eric, Mani, D.R., 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, 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, Zhao, Yingming, 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

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Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities by 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, Zhang, Bing, 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

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glnD and mviN Are Genes of an Essential Operon in Sinorhizobium meliloti by Rudnick, P A, Arcondéguy, T, Kennedy, C K, Kahn, D

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Proteome Analysis of Microdissected Tumor Tissue Using a Capillary Isoelectric Focusing-Based Multidimensional Separation Platform Coupled with ESI-Tandem MS by Wang, Yueju, Rudnick, Paul A, Evans, Erin L, Li, Jie, Zhuang, Zhengping, DeVoe, Don L, Lee, Cheng S, Balgley, Brian M

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