KMS Of Academy of mathematics and systems sciences, CAS
| AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility | |
Gao, Zhiqiang1,3; Chang, Cheng2; Yang, Jinghan1,3; Zhu, Yunping2,4; Fu, Yan1,3
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| 2019-07-02 | |
| Source Publication | ANALYTICAL CHEMISTRY
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| ISSN | 0003-2700 |
| Volume | 91Issue:13Pages:8705-8711 |
| Abstract | 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. |
| DOI | 10.1021/acs.analchem.9b02520 |
| Language | 英语 |
| Funding Project | 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 Research Area | Chemistry |
| WOS Subject | Chemistry, Analytical |
| WOS ID | WOS:000474477900098 |
| Publisher | AMER CHEMICAL SOC |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/35176 |
| Collection | 应用数学研究所 |
| Corresponding Author | Zhu, Yunping; Fu, Yan |
| Affiliation | 1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Key Lab Random Complex Struct & Data Sci, Beijing 100190, 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.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China 4.Anhui Med Univ, Hefei 230032, Anhui, Peoples R China |
| Recommended Citation 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. |
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