AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility
文献类型：期刊论文
| 作者 | Gao, Zhiqiang3,4; Chang, Cheng2; Yang, Jinghan3,4; Zhu, Yunping1,2; Fu, Yan3,4
|
| 刊名 | ANALYTICAL CHEMISTRY
 |
| 出版日期 | 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 |
| WOS记录号 | WOS:000474477900098 |
| 出版者 | AMER CHEMICAL SOC |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。