A Deep Learning-Based Tumor Classifier Directly Using MS Raw Data

doi:10.1002/pmic.201900344

	A Deep Learning-Based Tumor Classifier Directly Using MS Raw Data
	Dong, Hao 1,2,4; Liu, Yi 1,3; Zeng, Wen-Feng 5,6; Shu, Kunxian 2,4; Zhu, Yunping 1; Chang, Cheng 1
	2020-07-26
发表期刊	PROTEOMICS
ISSN	1615-9853
页码	7
摘要	Since the launch of Chinese Human Proteome Project (CNHPP) and Clinical Proteomic Tumor Analysis Consortium (CPTAC), large-scale mass spectrometry (MS) based proteomic profiling of different kinds of human tumor samples have provided huge amount of valuable data for both basic and clinical researchers. Accurate prediction for tumor and non-tumor samples, as well as the tumor types has become a key step for biological and medical research, such as biomarker discovery, diagnosis, and monitoring of diseases. The traditional MS-based classification strategy mainly depends on the identification and quantification results of MS data, which has some inherent limitations, such as the low identification rate of MS data. Here, a deep learning-based tumor classifier directly using MS raw data is proposed, which is independent of the identification and quantification results of MS data. The potential precursors with intensities and retention times from MS data as input is first detected and extracted. Then, a deep learning-based classifier is trained, which can accurately distinguish between the tumor and non-tumor samples. Finally, it is demonstrated the deep learning-based classifier has a good performance compared with other machine learning methods and may help researchers find the potential biomarkers which are likely to be missed by the traditional strategy.
关键词	deep learning MS data proteomics tumor classifier
DOI	10.1002/pmic.201900344
收录类别	SCI
语种	英语
资助项目	State Key Laboratory of Proteomics[SKLP-Y201802] ; National Natural Science Foundation of China[21605159]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods ; Biochemistry & Molecular Biology
WOS记录号	WOS:000552293400001
出版者	WILEY
引用统计	被引频次：12[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/2XEOYT63/15911
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Shu, Kunxian; Zhu, Yunping; Chang, Cheng
作者单位	1.Beijing Inst Life, Natl Ctr Prot Sci Beijing, Beijing Proteome Res Ctr, State Key Lab Prote, Beijing 102206, Peoples R China 2.Chongqing Univ Posts & Telecommun, Sch Comp Sci & Technol, Chongqing 400065, Peoples R China 3.Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100023, Peoples R China 4.Chongqing Univ Posts & Telecommun, Chongqing Key Lab Big Data Bio Intelligence, Chongqing 400065, Peoples R China 5.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China 6.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Dong, Hao,Liu, Yi,Zeng, Wen-Feng,et al. A Deep Learning-Based Tumor Classifier Directly Using MS Raw Data[J]. PROTEOMICS,2020:7.
APA	Dong, Hao,Liu, Yi,Zeng, Wen-Feng,Shu, Kunxian,Zhu, Yunping,&Chang, Cheng.(2020).A Deep Learning-Based Tumor Classifier Directly Using MS Raw Data.PROTEOMICS,7.
MLA	Dong, Hao,et al."A Deep Learning-Based Tumor Classifier Directly Using MS Raw Data".PROTEOMICS (2020):7.