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pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning
文献类型：期刊论文
| 作者 | Zhou, Xie-Xuan2,3; Zeng, Wen-Feng1,3; Chi, Hao1,3; Luo, Chunjie2,3; Liu, Chao1,3; Zhan, Jianfeng2,3; He, Si-Min1,3; Zhang, Zhifei4 |
| 刊名 | ANALYTICAL CHEMISTRY
 |
| 出版日期 | 2017-12-05 |
| 卷号 | 89期号:23页码:12690-12697 |
| ISSN号 | 0003-2700 |
| DOI | 10.1021/acs.analchem.7b02566 |
| 英文摘要 | In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate prediction of the theoretical spectra of peptides appears to be particularly important. Here, we present pDeep, a deep neural network based model for the spectrum prediction of peptides. Using the bidirectional long short-term memory (BiLSTM), pDeep can predict higher-energy collisional dissociation, electrontransfer dissociation, and electron-transfer and higher-energy collision dissociation MS/MS spectra of peptides with >0.9 median Pearson correlation coefficients. Further, we showed that intermediate layer of the neural network could reveal physicochemical properties of amino acids, for example the similarities of fragmentation behaviors between amino acids. We also showed the potential of pDeep to distinguish extremely similar peptides (peptides that contain isobaric amino acids, for example, GG = N, AG = Q or even I = L), which were very difficult to distinguish using traditional search engines. |
| 资助项目 | National Key Research and Development Program of China[2016YFA0501301] ; National Key Research Program of China[2016YFB1000605] ; National Natural Science Foundation of China[31470805] ; CAS Interdisciplinary Innovation Team Program |
| WOS研究方向 | Chemistry |
| 语种 | 英语 |
| WOS记录号 | WOS:000417549600014 |
| 出版者 | AMER CHEMICAL SOC |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/5500]  |
| 专题 | 中国科学院计算技术研究所期刊论文_英文 |
| 通讯作者 | Zhan, Jianfeng; He, Si-Min; Zhang, Zhifei |
| 作者单位 | 1.Chinese Acad Sci, ICT, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing 100190, Peoples R China 3.Univ Chinese Acad Sci, Beijing, Peoples R China 4.Capital Med Univ, Beijing 100069, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhou, Xie-Xuan,Zeng, Wen-Feng,Chi, Hao,et al. pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning[J]. ANALYTICAL CHEMISTRY,2017,89(23):12690-12697. |
| APA | Zhou, Xie-Xuan.,Zeng, Wen-Feng.,Chi, Hao.,Luo, Chunjie.,Liu, Chao.,...&Zhang, Zhifei.(2017).pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning.ANALYTICAL CHEMISTRY,89(23),12690-12697. |
| MLA | Zhou, Xie-Xuan,et al."pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning".ANALYTICAL CHEMISTRY 89.23(2017):12690-12697. |
入库方式： OAI收割
来源：计算技术研究所
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