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

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MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics von Kong, Andy T, Leprevost, Felipe V, Avtonomov, Dmitry M, Mellacheruvu, Dattatreya, Nesvizhskii, Alexey I

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MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics von Kong, Andy T, Leprevost, Felipe V, Avtonomov, Dmitry M, Mellacheruvu, Dattatreya, Nesvizhskii, Alexey I

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

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Philosopher: a versatile toolkit for shotgun proteomics data analysis von da Veiga Leprevost, Felipe, Haynes, Sarah E., Avtonomov, Dmitry M., Chang, Hui-Yin, Shanmugam, Avinash K., Mellacheruvu, Dattatreya, Kong, Andy T., Nesvizhskii, Alexey I.

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PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results von Geiszler, Daniel J., Kong, Andy T., Avtonomov, Dmitry M., Yu, Fengchao, Leprevost, Felipe da Veiga, Nesvizhskii, Alexey I.

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PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results von Geiszler, Daniel J, Kong, Andy T, Avtonomov, Dmitry M, Yu, Fengchao, Leprevost, Felipe da Veiga, Nesvizhskii, Alexey I

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BatMass: a Java Software Platform for LC–MS Data Visualization in Proteomics and Metabolomics von Avtonomov, Dmitry M, Raskind, Alexander, Nesvizhskii, Alexey I

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DeltaMass: Automated Detection and Visualization of Mass Shifts in Proteomic Open-Search Results von Avtonomov, Dmitry M, Kong, Andy, Nesvizhskii, Alexey I

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Crystal-C: A Computational Tool for Refinement of Open Search Results von Chang, Hui-Yin, Kong, Andy T, da Veiga Leprevost, Felipe, Avtonomov, Dmitry M, Haynes, Sarah E, Nesvizhskii, Alexey I

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IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry von Avtonomov, Dmitry M, Polasky, Daniel A, Ruotolo, Brandon T, Nesvizhskii, Alexey I

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Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma von 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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Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma von 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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MSFragger: ultrafast and comprehensive peptide identification in shotgun proteomics von Kong, Andy T., Leprevost, Felipe V., Avtonomov, Dmitry M., Mellacheruvu, Dattatreya, Nesvizhskii, Alexey I.

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

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