Wen-Feng Zeng @ Westlake University

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AlphaDIA enables DIA transfer learning for feature-free proteomics
Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sophia Steigerwald, Mohamed Kotb, Oscar Despard, Tim Heymann, Xie-Xuan Zhou, Maximilian T. Strauss, Constantin Ammar, Sander Willems, Magnus Schwörer, Wen-Feng Zeng^✉ & Matthias Mann^✉
Nature Biotechnology 2025

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Uncovering missing glycans and unexpected fragments with pGlycoNovo for site-specific glycosylation analysis across species
Wen-Feng Zeng^†, Guoquan Yan, Huan-huan Zhao, Chao Liu, Weiqian Cao^✉
Nature Communications 2024, 15, 8055

1

Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3
Wen-Feng Zeng^†,✉, Wei-Qian Cao^†, Ming-Qi Liu, Si-Min He, Peng-Yuan Yang
Nature Methods 2021, 18, 1515–1523

2

AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics
Wen-Feng Zeng^†, Xie-Xuan Zhou, Sander Willems, Constantin Ammar, Maria Wahle, Isabell Bludau, Eugenia Voytik, Maximillian T. Strauss, Matthias Mann^✉
Nature Commununications 2022, 13, 7238

3

pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification
Ming-Qi Liu^†, Wen-Feng Zeng^†, Pan Fang^†, Wei-Qian Cao^†, Chao Liu^†, Guo-Quan Yan, Yang Zhang, Chao Peng, Jian-Qiang Wu, Xiao-Jin Zhang, Hui-Jun Tu, Hao Chi, Rui-Xiang Sun, Yong Cao, Meng-Qiu Dong, Bi-Yun Jiang, Jiang-Ming Huang, Hua-Li Shen, Catherine CL Wong^✉, Si-Min He^✉, Peng-Yuan Yang^✉
Nature Commununications 2017, 8, 438

4

pDeep3: toward more accurate spectrum prediction with fast few-shot learning
Ching Tarn^†, Wen-Feng Zeng^†,✉
Analytical Chemistry 2021, 93(14), 5815–5822

5

MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning
Wen-Feng Zeng^†,✉, Xie-Xuan Zhou, Wen-Jing Zhou, Hao Chi, Jianfeng Zhan, and Si-Min He
Analytical Chemistry 2019, 91(15), 9724–9731

6

Artificial intelligence for proteomics and biomarker discovery
Matthias Mann^†,✉, Chanchal Kumar^✉, Wen-Feng Zeng^✉, Maximilian T Strauss^✉
Cell Systems 2021, 12(8), 759-770

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Publications (selected)

Prior publications (selected)