An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry
文献类型：期刊论文
| 作者 | Xiong, Yun1; Guo, Yufeng1; Xiao, Weidi2; Cao, Qichen1; Li, Shanshan1; Qi, Xianni1; Zhang, Zhidan1; Wang, Qinhong1; Shui, Wenqing1 |
| 刊名 | ANALYTICAL CHEMISTRY
 |
| 出版日期 | 2016-03-01 |
| 卷号 | 88期号:5页码:2784-2791 |
| 英文摘要 | Detection of proteins containing single amino acid polymorphisms (SAPs) encoded by nonsynonymous SNPs (nsSNPs) can aid researchers in studying the functional significance of protein variants. Most proteogenomic approaches for large-scale SAPs mapping require construction of a sample specific database containing protein variants predicted from the next-generation sequencing (NGS) data. Searching shotgun proteomic data sets against these NGS-derived databases allowed for identification of SAP peptides, thus validating the proteome-level sequence variation. Contrary to the conventional approaches, our study presents a novel strategy for proteome-wide SAP detection without relying on sample-specific NGS data. By searching a deep-coverage proteomic data set from an industrial thermotolerant yeast strain using our strategy, we identified 337 putative SAPs compared to the reference genome. Among the SAP peptides identified with stringent criteria, 85.2% of SAP sites were validated using whole-genome sequencing data obtained for this organism, which indicates high accuracy of SAP identification with our strategy. More interestingly, for certain SAP peptides that cannot be predicted by genomic sequencing, we used synthetic peptide standards to verify expression of peptide variants in the proteome. Our study has provided a unique tool for proteogenomics to enable proteome-wide direct SAP identification and capture nongenetic protein variants not linked to nsSNPs. |
| WOS标题词 | Science & Technology ; Physical Sciences |
| 类目[WOS] | Chemistry, Analytical |
| 研究领域[WOS] | Chemistry |
| 关键词[WOS] | DATABASE SEARCH ; PEPTIDES ; SPECTRA ; VARIANT ; ENGINE |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000371371400040 |
| 源URL | [http://124.16.173.210/handle/834782/1526]  |
| 专题 | 天津工业生物技术研究所_生物质谱与定量生物学研究 水雯箐_期刊论文 |
| 作者单位 | 1.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Key Lab Syst Microbial Biotechnol, Tianjin 300308, Peoples R China 2.Nankai Univ, Coll Life Sci, Tianjin 300071, Peoples R China |
| 推荐引用方式 GB/T 7714 | Xiong, Yun,Guo, Yufeng,Xiao, Weidi,et al. An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry[J]. ANALYTICAL CHEMISTRY,2016,88(5):2784-2791. |
| APA | Xiong, Yun.,Guo, Yufeng.,Xiao, Weidi.,Cao, Qichen.,Li, Shanshan.,...&Shui, Wenqing.(2016).An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry.ANALYTICAL CHEMISTRY,88(5),2784-2791. |
| MLA | Xiong, Yun,et al."An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry".ANALYTICAL CHEMISTRY 88.5(2016):2784-2791. |
入库方式： OAI收割
来源：天津工业生物技术研究所
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