CSpace  > 应用数学研究所
Quality control of single amino acid variations detected by tandem mass spectrometry
Yi, Xinpei1,3; Wang, Bo2; An, Zhiwu1,3; Gong, Fuzhou1,3; Li, Jing2; Fu, Yan1,3
2018-09-15
Source PublicationJOURNAL OF PROTEOMICS
ISSN1874-3919
Volume187Pages:144-151
AbstractStudy 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.
KeywordSingle amino acid variations Mass spectrometry Peptide identification False discovery rate Unrestrictive mass shift relocalization
DOI10.1016/j.jprot.2018.07.004
Language英语
Funding ProjectStrategic 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 Research AreaBiochemistry & Molecular Biology
WOS SubjectBiochemical Research Methods
WOS IDWOS:000444789800013
PublisherELSEVIER SCIENCE BV
Citation statistics
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/31289
Collection应用数学研究所
Affiliation1.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
Recommended Citation
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.
Files in This Item:
There are no files associated with this item.
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Yi, Xinpei]'s Articles
[Wang, Bo]'s Articles
[An, Zhiwu]'s Articles
Baidu academic
Similar articles in Baidu academic
[Yi, Xinpei]'s Articles
[Wang, Bo]'s Articles
[An, Zhiwu]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Yi, Xinpei]'s Articles
[Wang, Bo]'s Articles
[An, Zhiwu]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.