pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

doi:10.1021/acs.analchem.7b02566

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	pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning
	Zhou, Xie-Xuan 2,3; Zeng, Wen-Feng 1,3; Chi, Hao 1,3; Luo, Chunjie 2,3; Liu, Chao 1,3; Zhan, Jianfeng 2,3; He, Si-Min 1,3; Zhang, Zhifei 4
刊名	ANALYTICAL CHEMISTRY
	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
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000417549600014
内容类型	期刊论文
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.