Wen-Feng Zeng


I am a assistant researcher in Insitute of Computing Technology (ICT), Chinese Academy of Sciences. I am from Xiapu, Fujian Province. It is a very beautiful place where is famous for its sea and sunrise.

I am a pFinder, who works in pFind team. pFind is a software solution suite for mass spectrometry based proteomics, you are welcome to try it. Enjoy your research career with pFind and pFinders.

My recent research interest is in machine learning for proteomics and glycoproteomics. I have developed pDeep and pGlyco.

Selected Publications

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

    The idea of pDeep originated in 2012, when I first learned the RNN/LSTM networks. At that time, the best deep learning platform was Theano, but it was not easy to be used. I then switched to develop pGlyco from 2013 becuase Prof. Pengyuan Yang and pFind had a collaborative project for glycopeptide search engines. But I still kept paying attention to new deep learning methods and platforms during that time. Then I learned Keras, which provides very simple APIs to access different neural networks based on different platforms. Because of developing pGlyco, I do not have enough time to try Keras-based pDeep until 2016. In the spring of 2016, my wife Xie-Xuan and I took Prof. Hong Chang's machine learning course, and we had to do a machine learning project as the final examination. Prof. Chang gave us some choices, most of them were computer vision problems, but we thought why not trying pDeep. This is the starting of pDeep. Untill now, I always believe that machine learning will play a very important role in MS.

  • Ming-Qi Liu, Wen-Feng Zeng(co-first author, major developer and maintainer of pGlyco software), 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 C. L. 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, 2017, volume 8, Article number: 438.
  • 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 C. L. 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, 2016, volume 6, Article number: 25102.


Education Background

  • I received my bachelor's degree in department of software engineering of Xidian University, 2010.09.
  • I received my Ph.D. degree in Insitute of Computing Technology (ICT), Chinese Academy of Sciences, 2017.03, supervised by associate professor Ruixiang Sun and professor Si-Min He.
  • I am currently a assistant researcher in ICT.


Research Interests

  • Algorithms & Bioinformatics
  • Statistical Learning
  • My current research interest is mass spectrometry-based proteomics, especially glycopeptides identification problems, machine learning based resoring methods and novel mass spectrometry technologies like DIA method.


  • Reading. I like reading web fiction, kungfu stories and computer science materials.
  • Sports. I like basketball very much. I also played baseball for a short time.

Contact me

  • Address: Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100090, China
  • Email: zengwenfeng%AT%ict.ac.cn
  • Tel: 010-62600822