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Validation Methods of Peptide Identification Results in Proteomics br 期刊论文
PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS, 2023, 卷号: 50, 期号: 1, 页码: 109-125
作者:  Zhou, Wen-Jing;  Zeng, Wen-Feng;  Chi, Hao;  He, Si-Min
收藏  |  浏览/下载:23/0  |  提交时间:2023/12/04
proteomics  mass spectrometry  target-decoy approach  false discovery rate  validation methods  
Confident software-driven identification of intact glycopeptides by integrating complementary peptide- and glycan-first search strategies in efficient mining of MS2 data 期刊论文
GLYCOBIOLOGY, 2021, 卷号: 31, 期号: 12, 页码: 1725-1726
作者:  Chien, Yu-Chun;  Kuo, Chu-Wei;  Zeng, Wen-Feng;  Khoo, Kay-Hooi
收藏  |  浏览/下载:18/0  |  提交时间:2022/12/07
Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3 期刊论文
NATURE METHODS, 2021, 页码: 15
作者:  Zeng, Wen-Feng;  Cao, Wei-Qian;  Liu, Ming-Qi;  He, Si-Min;  Yang, Peng-Yuan
收藏  |  浏览/下载:29/0  |  提交时间:2022/06/21
pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning 期刊论文
JOURNAL OF PROTEOME RESEARCH, 2021, 卷号: 20, 期号: 5, 页码: 2570-2582
作者:  Chen, Zhen-Lin;  Mao, Peng-Zhi;  Zeng, Wen-Feng;  Chi, Hao;  He, Si-Min
收藏  |  浏览/下载:39/0  |  提交时间:2021/12/01
cross-linking mass spectrometry  spectrum prediction  deep learning  transfer learning  online fine-tuning  
pDeep3: Toward More Accurate Spectrum Prediction with Fast Few-Shot Learning 期刊论文
ANALYTICAL CHEMISTRY, 2021, 卷号: 93, 期号: 14, 页码: 5815-5822
作者:  Tarn, Ching;  Zeng, Wen-Feng
收藏  |  浏览/下载:31/0  |  提交时间:2021/12/01
Deep Learning in Proteomics 期刊论文
PROTEOMICS, 2020, 页码: 21
作者:  Wen, Bo;  Zeng, Wen-Feng;  Liao, Yuxing;  Shi, Zhiao;  Savage, Sara R.;  Jiang, Wen;  Zhang, Bing
收藏  |  浏览/下载:30/0  |  提交时间:2021/12/01
bioinformatics  deep learning  proteomics  
A Deep Learning-Based Tumor Classifier Directly Using MS Raw Data 期刊论文
PROTEOMICS, 2020, 页码: 7
作者:  Dong, Hao;  Liu, Yi;  Zeng, Wen-Feng;  Shu, Kunxian;  Zhu, Yunping;  Chang, Cheng
收藏  |  浏览/下载:59/0  |  提交时间:2020/12/10
deep learning  MS data  proteomics  tumor classifier  
MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning 期刊论文
ANALYTICAL CHEMISTRY, 2019, 卷号: 91, 期号: 15, 页码: 9724-9731
作者:  Zeng, Wen-Feng;  Zhou, Xie-Xuan;  Zhou, Wen-Jing;  Chi, Hao;  Zhan, Jianfeng;  He, Si-Min
收藏  |  浏览/下载:77/0  |  提交时间:2019/12/10
A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides 期刊论文
NATURE COMMUNICATIONS, 2019, 卷号: 10, 页码: 12
作者:  Chen, Zhen-Lin;  Meng, Jia-Ming;  Cao, Yong;  Yin, Ji-Li;  Fang, Run-Qian;  Fan, Sheng-Bo;  Liu, Chao;  Zeng, Wen-Feng;  Ding, Yue-He;  Tan, Dan;  Wu, Long;  Zhou, Wen-Jing;  Chi, Hao;  Sun, Rui-Xiang;  Dong, Meng-Qiu;  He, Si-Min
收藏  |  浏览/下载:91/0  |  提交时间:2019/12/10
pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework 期刊论文
BIOINFORMATICS, 2019, 卷号: 35, 期号: 14, 页码: I183-I190
作者:  Yang, Hao;  Chi, Hao;  Zeng, Wen-Feng;  Zhou, Wen-Jing;  He, Si-Min
收藏  |  浏览/下载:71/0  |  提交时间:2019/12/10