AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility

doi:10.1021/acs.analchem.9b02520

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	AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility
	Gao, Zhiqiang 3,4; Chang, Cheng 2; Yang, Jinghan 3,4; Zhu, Yunping 1,2; Fu, Yan3,4
刊名	ANALYTICAL CHEMISTRY
	2019-07-02
卷号	91 期号:13 页码:8705-8711
ISSN号	0003-2700
DOI	10.1021/acs.analchem.9b02520
英文摘要	The selection of proteotypic peptides, that is, detectable unique representatives of proteins of interest, is a key step in targeted proteomics. To date, much effort has been made to understand the mechanisms underlying peptide detection in liquid chromatography-tandem mass spectrometry (LC-MS/MS) based shotgun proteomics and to predict proteotypic peptides in the absence of experimental LC-MS/MS data. However, the prediction accuracy of existing tools is still unsatisfactory. We find that one crucial reason is their neglect of the significant influence of protein proteolytic digestion on peptide detectability in shotgun proteomics. Here, we present an Advanced Proteotypic Peptide Predictor (AP3), which explicitly takes peptide digestibility into account for the prediction of proteotypic peptides. Specifically, peptide digestibility is first predicted for each peptide and then incorporated as a feature into the peptide detectability prediction model. Our results demonstrated that peptide digestibility is the most important feature for the accurate prediction of proteotypic peptides in our model. Compared with the existing available algorithms, AP3 showed 10.3-34.7% higher prediction accuracy. On a targeted proteomics data set, AP3 accurately predicted the proteotypic peptides for proteins of interest, showing great potential for assisting the design of targeted proteomics experiments.
资助项目	National Basic Research Program of China[2017YEA0505002] ; National Basic Research Program of China[2015CB554406] ; International S&T Cooperation Program of China[2014DFB30010] ; Strategic Priority Research Program of CAS[XDB13040600] ; National Natural Science Foundation of China[21605159] ; NCMIS CAS
WOS研究方向	Chemistry
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000474477900098
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/35175]
专题	应用数学研究所
通讯作者	Zhu, Yunping; Fu, Yan
作者单位	1.Anhui Med Univ, Hefei 230032, Anhui, Peoples R China 2.Beijing Inst Life, Natl Ctr Prot Sci Beijing, Beijing Proteome Res Ctr, State Key Lab Prote, Beijing 102206, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Key Lab Random Complex Struct & Data Sci, Beijing 100190, Peoples R China 4.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Gao, Zhiqiang,Chang, Cheng,Yang, Jinghan,et al. AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility[J]. ANALYTICAL CHEMISTRY,2019,91(13):8705-8711.
APA	Gao, Zhiqiang,Chang, Cheng,Yang, Jinghan,Zhu, Yunping,&Fu, Yan.(2019).AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility.ANALYTICAL CHEMISTRY,91(13),8705-8711.
MLA	Gao, Zhiqiang,et al."AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility".ANALYTICAL CHEMISTRY 91.13(2019):8705-8711.