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

文献类型：期刊论文

作者Chen, Zhen-Lin; Mao, Peng-Zhi; Zeng, Wen-Feng; Chi, Hao; He, Si-Min
刊名JOURNAL OF PROTEOME RESEARCH
出版日期2021-05-07
卷号20期号:5页码:2570-2582
关键词cross-linking mass spectrometry spectrum prediction deep learning transfer learning online fine-tuning
ISSN号1535-3893
DOI10.1021/acs.jproteome.0c01004
英文摘要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.
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
语种英语
WOS记录号WOS:000649269600036
出版者AMER CHEMICAL SOC
源URL[http://119.78.100.204/handle/2XEOYT63/17709]  
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.

入库方式： OAI收割

来源：计算技术研究所

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