Identification of modified peptides using localization-aware open search by Yu, Fengchao, Teo, Guo Ci, Kong, Andy T., Haynes, Sarah E., Avtonomov, Dmitry M., Geiszler, Daniel J., Nesvizhskii, Alexey I.

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dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts by Demichev, Vadim, Szyrwiel, Lukasz, Yu, Fengchao, Teo, Guo Ci, Rosenberger, George, Niewienda, Agathe, Ludwig, Daniela, Decker, Jens, Kaspar-Schoenefeld, Stephanie, Lilley, Kathryn S., Mülleder, Michael, Nesvizhskii, Alexey I., Ralser, Markus

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Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine by Teo, Guo Ci, Polasky, Daniel A, Yu, Fengchao, Nesvizhskii, Alexey I

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MSBooster: improving peptide identification rates using deep learning-based features by Yang, Kevin L., Yu, Fengchao, Teo, Guo Ci, Li, Kai, Demichev, Vadim, Ralser, Markus, Nesvizhskii, Alexey I.

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Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform by Yu, Fengchao, Teo, Guo Ci, Kong, Andy T., Fröhlich, Klemens, Li, Ginny Xiaohe, Demichev, Vadim, Nesvizhskii, Alexey I.

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Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers by Tsou, Chih-Chiang, Tsai, Chia-Feng, Teo, Guo Ci, Chen, Yu-Ju, Nesvizhskii, Alexey I.

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Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant by Yu, Fengchao, Haynes, Sarah E., Teo, Guo Ci, Avtonomov, Dmitry M., Polasky, Daniel A., Nesvizhskii, Alexey I.

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Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer by Reva, Boris, Chowdhury, Shrabanti, Ji, Jiayi, Whiteaker, Jeffrey R., Colaprico, Antonio, Raman, Pichai, Guo, Yiran, Brown, Miguel A., Ivey, Richard G., Szpyt, John, Guha Thakurta, Sanjukta, Lopez, Gonzalo, Kalayci, Selim, Gümüş, Zeynep H., Yoo, Seungyeul, da Veiga Leprevost, Felipe, Katsnelson, Lizabeth, Wang, Ying, Kennedy, Jacob J., Voytovich, Uliana J., Zhao, Lei, Baubet, Valerie, Tauhid, Lamiya, Lilly, Jena V., Mason, Jennifer L., Farrow, Bailey, Young, Nathan, Leary, Sarah, Moon, Jamie, Petyuk, Vladislav A., Nazarian, Javad, Palmer, James N., Lober, Robert M., Rivero-Hinojosa, Samuel, Wang, Joshua M., Broberg, Matilda, Chu, Rosalie K., Moore, Ronald J., Monroe, Matthew E., Zhao, Rui, Zhu, Jun, Mesri, Mehdi, Boja, Emily, Hiltke, Tara, Rodriguez, Henry, Zhang, Bing, Mani, D.R., Iavarone, Antonio, Schürer, Stephan, Chen, Xi S., Heath, Allison P., Rokita, Jo Lynne, Nesvizhskii, Alexey I., Fenyö, David, Rodland, Karin D., Liu, Tao, Paulovich, Amanda G., Resnick, Adam C., Storm, Phillip B., Rood, Brian R., Wang, Pei, Morgan, Allison M., Waanders, Angela J., Buccoliero, Anna Maria, Leonard, Carina A., Kline, Cassie N., Li, Chunde, Kram, David E., Hanson, Derek, Appert, Elizabeth, Kawaler, Emily A., Raabe, Eric H., Jackson, Eric M., Greenfield, Jeffrey P., Pollack, Ian F., Cain, Jason E., Foster, Jessica B., Palma, July E., Ketchum, Karen A., Blumenberg, Lili, Cornwell, Macintosh, Sarmady, Mahdi, Domagalski, Marcin J., Cieślik, Marcin P., Li, Marilyn M., Wyczalkowski, Matthew A., Connors, Meghan, Gupta, Nalin, Edwards, Nathan J., Vaske, Olena M., Becher, Oren, Firestein, Ron, Mueller, Sabine, Winebrake, Samuel G., Dhanasekaran, Saravana Mohan, Cai, Shuang, Patton, Tatiana, Lorentzen, Travis D., Liu, Wenke, Bocik, William E.

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Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma by Pan, Jianbo, Hu, Yingwei, Krek, Azra, Li, Yize, Chen, Lin S., Vasaikar, Suhas, Wu, Yige, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Kong, Andy, Sethuraman, Sunantha, Avtonomov, Dmitry M., Colaprico, Antonio, Cao, Song, Cho, Kyung-Cho, Kalayci, Selim, Ma, Shiyong, Ruggles, Kelly, Kawaler, Emily, Wen, Bo, Chen, Feng, Edwards, Nathan, Pierorazio, Phillip M., Pavlovich, Christian P., Brominski, Gabriel, Hsieh, James J., Lubinski, Jan, Wiznerowicz, Maciej, Kinsinger, Christopher R., Thiagarajan, Mathangi, Mesri, Mehdi, Hiltke, Tara, Ding, Li, Zhang, Zhen, Omenn, Gilbert S., Cieslik, Marcin, Nesvizhskii, Alexey I., Zhang, Hui, Hashimi, Abdul Samad, Charamut, Alyssa, Druker, Brian J., Tognon, Cristina, Mani, D.R., Rohrer, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Wheeler, David, Chan, Doug, Demir, Emek, Wilson, George D., Liu, Hongwei, Zhou, Hua, Day, Jacob, Suh, James, Whiteaker, Jeffrey R., Eschbacher, Jennifer, Chen, Jin, Ketchum, Karen A., Rodland, Karin D., Krug, Karsten, Holloway, Kimberly, Sokoll, Lori J., Cornwell, MacIntosh, Loriaux, Marc, Anderson, Matthew, Ellis, Matthew J., Dyer, Maureen, Burke, Meghan C., Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Smith, Michael, Khan, Munziba, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Tignor, Nicole, Piehowski, Paul, McGarvey, Peter B., Hariharan, Pushpa, Gao, Qingsong, Thangudu, Ratna R., Montgomery, Rebecca, Bremner, Ross, Liu, Ruiyang, Hong, Runyu, Payne, Samuel H., Patel, Shalin, Satpathy, Shankha, Davies, Sherri R., Patil, Snehal, Carter, Sonya, Gabriel, Stacey, Thomas, Stefani N., Carr, Steven A., Skelly, Tara, Borate, Uma, Maruvka, Yosef, Li, Zhi

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MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics by Polasky, Daniel A., Geiszler, Daniel J., Yu, Fengchao, Li, Kai, Teo, Guo Ci, Nesvizhskii, Alexey I.

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Proteogenomic Characterization of Endometrial Carcinoma by Kawaler, Emily A., Cui Zhou, Daniel, Huang, Chen, Blumenberg, Lili, Karpova, Alla, Petyuk, Vladislav A., Wen, Bo, Li, Zhi, Cao, Song, Moon, Jamie, Shi, Zhiao, Cornwell, MacIntosh, Wyczalkowski, Matthew A., Chu, Rosalie K., Gao, Qingsong, Moore, Ronald J., Li, Kai, Zhao, Rui, Clauser, Karl, Maruvka, Yosef, Pico, Alexander R., Beecroft, Sean J.I., Adams, David W., Liao, Yuxing, Rykunov, Dmitry, Czekański, Andrzej, Jędryka, Marcin, Kinsinger, Christopher R., Mesri, Mehdi, Ellis, Matthew J., Thiagarajan, Mathangi, Noble, Michael, Wang, Pei, Anderson, Matthew L., Levine, Douglas A., Rodland, Karin D., Liu, Tao, Birger, Chet, Birrer, Michael J., Bocik, William E., Borate, Uma, Cai, Shuang, Carter, Sonya, Castro, Patricia, Chaikin, Michelle, Chen, Jin, Chesla, David, Chheda, Milan G., Culpepper, Houston, Demir, Emek, Dhir, Rajiv, Domagalski, Marcin J., Edwards, Robert, Elburn, Kim, Field, Jayson B., Gabriel, Stacey, Godwin, Andrew K., Grady, Pamela, Hariharan, Pushpa, Hoadley, Katherine A., Hostetter, Galen, Hu, Yingwei, Jaehnig, Eric, Jewell, Scott D., Ji, Jiayi, Jones, Corbin D., Karabon, Renee, Ketchum, Karen A., Krubit, Tanya, Leprevost, Felipe D., Lewis, Michael, Ma, Weiping, Madan, Rashna, Markey, Sanford P., McDermott, Jason, McGarvey, Peter B., Modugno, Francesmary, Montgomery, Rebecca, Piehowski, Paul, Polonskaya, Larisa, Qi, Liqun, Schadt, Eric E., Shi, Yan, Skelly, Tara, Stein, Stephen E., Tan, Donghui, Teo, Guo Ci, Thangudu, Ratna R., Valley, Dana R., Vernon, Michael, Wang, Ying, Webster, Alex, Westbrook, Thomas, Wheeler, David, Wilson, George D., Zelt, Robert, Zhang, Hui, Zhang, Yuping, Zhang, Zhen, Zhao, Grace

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Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors by Kacen, Assaf, Javitt, Aaron, Kramer, Matthias P., Morgenstern, David, Tsaban, Tomer, Shmueli, Merav D., Teo, Guo Ci, da Veiga Leprevost, Felipe, Barnea, Eilon, Yu, Fengchao, Admon, Arie, Eisenbach, Lea, Samuels, Yardena, Schueler-Furman, Ora, Levin, Yishai, Nesvizhskii, Alexey I., Merbl, Yifat

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Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry by Cho, Kyung-Cho, Clark, David J, Schnaubelt, Michael, Teo, Guo Ci, Leprevost, Felipe da Veiga, Bocik, William, Boja, Emily S, Hiltke, Tara, Nesvizhskii, Alexey I, Zhang, Hui

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Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma by Clark, David J., Petralia, Francesca, Pan, Jianbo, Hu, Yingwei, Lih, Tung-Shing M., Chang, Hui-Yin, Ma, Weiping, Krek, Azra, Li, Yize, Ozbek, Umut, Wu, Yige, Chowdhury, Shrabanti, Wyczalkowski, Matthew A., Schnaubelt, Michael, Avtonomov, Dmitry M., Kalayci, Selim, Ma, Shiyong, Ruggles, Kelly, Gümüş, Zeynep H., Kawaler, Emily, Edwards, Nathan, Chen, Xi Steven, Antczak, Andrzej, Omelchenko, Tatiana, Kinsinger, Christopher R., Thiagarajan, Mathangi, Mesri, Mehdi, Robles, Ana I., Qian, Jiang, Fenyö, David, Zhang, Bing, Zhang, Zhen, Cieslik, Marcin, Chan, Daniel W., Nesvizhskii, Alexey I., Hashimi, Abdul Samad, Charamut, Alyssa, Druker, Brian J., Tognon, Cristina, Mani, D.R., Rohrer, Daniel C., Tansil, Darlene, Chesla, David, Heiman, David, Wheeler, David, Chan, Doug, Demir, Emek, Modugno, Francesmary, Getz, Gaddy, Wilson, George D., Liu, Hongwei, Zhou, Hua, Day, Jacob, Suh, James, Whiteaker, Jeffrey R., Eschbacher, Jennifer, Chen, Jin, Ketchum, Karen A., Rodland, Karin D., Krug, Karsten, Holloway, Kimberly, Sokoll, Lori J., Cornwell, MacIntosh, Loriaux, Marc, Anderson, Matthew, Ellis, Matthew J., Dyer, Maureen, Burke, Meghan C., Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Smith, Michael, Khan, Munziba, Roche, Nancy, Edwards, Nathan J., Vatanian, Negin, Tignor, Nicole, Grady, Pamela, Piehowski, Paul, McGarvey, Peter B., Hariharan, Pushpa, Gao, Qingsong, Thangudu, Ratna R., Montgomery, Rebecca, Bremner, Ross, Liu, Ruiyang, Hong, Runyu, Payne, Samuel H., Patel, Shalin, Satpathy, Shankha, Davies, Sherri R., Patil, Snehal, Carter, Sonya, Gabriel, Stacey, Thomas, Stefani N., Carr, Steven A., Skelly, Tara, Borate, Uma, Maruvka, Yosef, Li, Zhi

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Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant by Yu, Fengchao, Haynes, Sarah E, Teo, Guo Ci, Avtonomov, Dmitry M, Polasky, Daniel A, Nesvizhskii, Alexey I

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High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe by Demichev, Vadim, Yu, Fengchao, Teo, Guo Ci, Szyrwiel, Lukasz, Rosenberger, George A, Decker, Jens, Kaspar-Schoenefeld, Stephanie, Lilley, Kathryn S, Mülleder, Michael, Nesvizhskii, Alexey I, Ralser, Markus

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