Quality control of single amino acid variations detected by tandem mass spectrometry
文献类型：期刊论文
| 作者 | Yi, Xinpei1,3; Wang, Bo2; An, Zhiwu1,3; Gong, Fuzhou1,3 ; Li, Jing2; Fu, Yan1,3
|
| 刊名 | JOURNAL OF PROTEOMICS
 |
| 出版日期 | 2018-09-15 |
| 卷号 | 187页码:144-151 |
| 关键词 | Single amino acid variations Mass spectrometry Peptide identification False discovery rate Unrestrictive mass shift relocalization |
| ISSN号 | 1874-3919 |
| DOI | 10.1016/j.jprot.2018.07.004 |
| 英文摘要 | Study of single amino acid variations (SAVs) of proteins, resulting from single nucleotide polymorphisms, is of great importance for understanding the relationships between genotype and phenotype. In mass spectrometry based shotgun proteomics, identification of peptides with SAVs often suffers from high error rates on the variant sites detected. These site errors are due to multiple reasons and can be confirmed by manual inspection or genomic sequencing. Here, we present a software tool, named SAVControl, for site-level quality control of variant peptide identifications. It mainly includes strict false discovery rate control of variant peptide identifications and variant site verification by unrestrictive mass shift relocalization. SAVControl was validated on three colorectal adenocarcinoma cell line datasets with genomic sequencing evidences and tested on a colorectal cancer dataset from The Cancer Genome Atlas. The results show that SAVControl can effectively remove false detections of SAVs. Significance: Protein sequence variations caused by single nucleotide polymorphisms (SNPs) are single amino acid variations (SAVs). The investigation of SAVs may provide a chance for understanding the relationships between genotype and phenotype. Mass spectrometry (MS) based proteomics provides a large-scale way to detect SAVs. However, using the current analysis strategy to detect SAVs may lead to high rate of false positives. The SAVControl we present here is a computational workflow and software tool for site-level quality control of SAVs detected by MS. It accesses the confidence of detected variant sites by relocating the mass shift responsible for an SAV to search for alternative interpretations. In addition, it uses a strict false discovery rate control method for variant peptide identifications. The advantages of SAVControl were demonstrated on three colorectal adenocarcinoma cell line datasets and a colorectal cancer dataset. We believe that SAVControl will be a powerful tool for computational proteomics and proteogenomics. |
| 资助项目 | Strategic Priority Research Program of CAS[XDB13040600] ; National Natural Science Foundation of China[31271416] ; National Key Basic Research Program of China[2015CB554406] ; Natural Science Foundation of Shanghai[17ZR1413900] ; International S&T Cooperation Program of China[2014DFB30010] ; NCMIS CAS |
| WOS研究方向 | Biochemistry & Molecular Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:000444789800013 |
| 出版者 | ELSEVIER SCIENCE BV |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/31288]  |
| 专题 | 应用数学研究所 |
| 通讯作者 | Gong, Fuzhou; Li, Jing; Fu, Yan |
| 作者单位 | 1.Chinese Acad Sci, Acad Math & Syst Sci, RCSDS, NCMIS, Beijing 100190, Peoples R China 2.Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Dept Bioinformat & Biostat, Shanghai 200240, Peoples R China 3.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Yi, Xinpei,Wang, Bo,An, Zhiwu,et al. Quality control of single amino acid variations detected by tandem mass spectrometry[J]. JOURNAL OF PROTEOMICS,2018,187:144-151. |
| APA | Yi, Xinpei,Wang, Bo,An, Zhiwu,Gong, Fuzhou,Li, Jing,&Fu, Yan.(2018).Quality control of single amino acid variations detected by tandem mass spectrometry.JOURNAL OF PROTEOMICS,187,144-151. |
| MLA | Yi, Xinpei,et al."Quality control of single amino acid variations detected by tandem mass spectrometry".JOURNAL OF PROTEOMICS 187(2018):144-151. |
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。