Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides by Daniel J. Geiszler, Daniel A. Polasky, Fengchao Yu, Alexey I. Nesvizhskii

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

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

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

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Unraveling the glycosylated immunopeptidome with HLA-Glyco by Georges Bedran, Daniel A. Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier A. Alfaro, Marcin Cieslik, Alexey I. Nesvizhskii

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

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Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars by Atieh Moradi, Shuaijian Dai, Emily Oi Ying Wong, Guang Zhu, Fengchao Yu, Hon-Ming Lam, Zhiyong Wang, Al Burlingame, Chengtao Lin, Alireza Afsharifar, Weichuan Yu, Tingliang Wang, Ning Li

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Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides by Humberto J. Ferreira, Brian J. Stevenson, HuiSong Pak, Fengchao Yu, Jessica Almeida Oliveira, Florian Huber, Marie Taillandier-Coindard, Justine Michaux, Emma Ricart-Altimiras, Anne I. Kraemer, Lana E. Kandalaft, Daniel E. Speiser, Alexey I. Nesvizhskii, Markus Müller, Michal Bassani-Sternberg

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