pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning

doi:10.1021/acs.jproteome.0c01004

	pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning
	Chen, Zhen-Lin; Mao, Peng-Zhi; Zeng, Wen-Feng; Chi, Hao; He, Si-Min
	2021-05-07
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	20 期号:5 页码:2570-2582
摘要	In cross-linking mass spectrometry, the identification of cross-linked peptide pairs heavily relies on the ability of a database search engine to measure the similarities between experimental and theoretical MS/MS spectra. However, the lack of accurate ion intensities in theoretical spectra impairs the performance of search engines, in particular, on proteome scales. Here we introduce pDeepXL, a deep neural network to predict MS/MS spectra of cross-linked peptide pairs. To train pDeepXL, we used the transfer-learning technique because it facilitated the training with limited benchmark data of cross-linked peptide pairs. Test results on more than ten data sets showed that pDeepXL accurately predicted the spectra of both noncleavable DSS/BS3/Leiker crosslinked peptide pairs (>80% of predicted spectra have Pearson's r values higher than 0.9) and cleavable DSSO/DSBU cross-linked peptide pairs (>75% of predicted spectra have Pearson's r values higher than 0.9). pDeepXL also achieved the accurate prediction on unseen data sets using an online fine-tuning technique. Lastly, integrating pDeepXL into a database search engine increased the number of identified cross-link spectra by 18% on average.
关键词	cross-linking mass spectrometry spectrum prediction deep learning transfer learning online fine-tuning
DOI	10.1021/acs.jproteome.0c01004
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[32071435] ; National Key Research and Development Program of China[2016YFA0501300]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000649269600036
出版者	AMER CHEMICAL SOC
引用统计	被引频次：8[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/17710
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	He, Si-Min
作者单位	Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, CAS, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Chen, Zhen-Lin,Mao, Peng-Zhi,Zeng, Wen-Feng,et al. pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning[J]. JOURNAL OF PROTEOME RESEARCH,2021,20(5):2570-2582.
APA	Chen, Zhen-Lin,Mao, Peng-Zhi,Zeng, Wen-Feng,Chi, Hao,&He, Si-Min.(2021).pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning.JOURNAL OF PROTEOME RESEARCH,20(5),2570-2582.
MLA	Chen, Zhen-Lin,et al."pDeepXL: MS/MS Spectrum Prediction for Cross-Linked Peptide Pairs by Deep Learning".JOURNAL OF PROTEOME RESEARCH 20.5(2021):2570-2582.