(# indicates first author; * indicates corresponding author)

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

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

3. Ching Tarn^*, Wen-Feng Zeng^#,*. pDeep3: Toward More Accurate Spectrum Prediction with Fast Few-Shot Learning. Analytical Chemistry 93 (14), 5815-5822.

4. Matthias Mann^*, Chanchal Kumar^*, Wen-Feng Zeng^*, Maximilian T.

Strauss^*. Artificial intelligence for proteomics and biomarker discovery. Cell Systems 12 (8), 759-770 (2021).

5. Bo Wen^#,*, Wen-Feng Zeng^#, Yuxing Liao, Zhiao Shi, Sara R. Savage, Wen Jiang, Bing Zhang^*. Deep Learning in Proteomics. Proteomics 20 (21-22), 1900335.

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

7. Siyuan Kong^#, Pengyun Gong^#, Wen-Feng Zeng^#, Biyun Jiang^#, Xinhang Hou, Yang Zhang, Huanhuan Zhao, Mingqi Liu, Guoquan Yan, Xinwen Zhou, Xihua Qiao, Mengxi Wu, Pengyuan Yang, Chao Liu^*, Weiqian Cao^*. pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level. Nature Communications 13, 7539 (2022).

8. Ming-Qi Liu^#, Wen-Feng Zeng^#,Pan Fang^#, Wei-Qian Cao^#, Cao 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^*. pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification. Nature Communications , 438 (2017).

9. Wen-Feng Zeng^#, Ming-Qi Liu^#, Yang Zhang^#, Jian-Qiang Wu^#, Pan Fang, Chao Peng, Aiying Nie, Guoquan Yan, Weiqian Cao, Chao Liu, Hao Chi, Rui-Xiang Sun, Catherine CL Wong, Si-Min He^*, Pengyuan Yang^*. pGlyco: a pipeline for the identification of intact N-glycopeptides by using HCD- and CID-MS/MS and MS3. Scientific Reports 6, 25102 (2016).

10. Xie-Xuan Zhou^#, Wen-Feng Zeng^#, Hao Chi, Chunjie Luo, Chao Liu, Jianfeng Zhan^*, Si-Min He^*, Zhifei Zhang^*. pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning. Analytical Chemistry 89 (23), 12690-12697 (2017).