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PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome
An, Zhiwu1,5; Zhai, Linhui2; Ying, Wantao3,4; Qian, Xiaohong3,4; Gong, Fuzhou1,5; Tan, Minjia2; Fu, Yan1,5
2019-02-01
Source PublicationMOLECULAR & CELLULAR PROTEOMICS
ISSN1535-9476
Volume18Issue:2Pages:391-405
AbstractThe open (mass tolerant) search of tandem mass spectra of peptides shows great potential in the comprehensive detection of post-translational modifications (PTMs) in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms for automated and reliable post-processing of the coarse and error-prone search results. Here we present PTMiner, a software tool for confident filtering and localization of modifications (mass shifts) detected in an open search. After mass-shift-grouped false discovery rate (FDR) control of peptide-spectrum matches (PSMs), PTMiner uses an empirical Bayesian method to localize modifications through iterative learning of the prior probabilities of each type of modification occurring on different amino acids. The performance of PTMiner was evaluated on three data sets, including simulated data, chemically synthesized peptide library data and modified-peptide spiked-in proteome data. The results showed that PTMiner can effectively control the PSM FDR and accurately localize the modification sites. At 1% real false localization rate (FLR), PTMiner localized 93%, 84 and 83% of the modification sites in the three data sets, respectively, far higher than two open search engines we used and an extended version of the Ascore localization algorithm. We then used PTMiner to analyze a draft map of human proteome containing 25 million spectra from 30 tissues, and confidently identified over 1.7 million modified PSMs at 1% FDR and 1% FLR, which provided a system-wide view of both known and unknown PTMs in the human proteome.
DOI10.1074/mcp.RA118.000812
Language英语
Funding ProjectNational Key Basic Research Program of China[2017YFC0908400] ; National Key Basic Research Program of China[2017YFC0906600] ; National Key Basic Research Program of China[2015CB554406] ; Natural Science Foundation of China[81872888] ; Natural Science Foundation of China[31670066] ; Natural Science Foundation of China[31700724] ; Natural Science Foundation of China[91630314] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDB13040600] ; International SAMP;T Cooperation Program of China[2014DFB30010] ; NCMIS CAS
WOS Research AreaBiochemistry & Molecular Biology
WOS SubjectBiochemical Research Methods
WOS IDWOS:000457454000016
PublisherAMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
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Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/32418
Collection应用数学研究所
Affiliation1.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.Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, Shanghai 201203, Peoples R China
3.Natl Engn Res Ctr Prot Drugs, Beijing Proteome Res Ctr, Natl Ctr Prot Sci Beijing, State Key Lab Prote, Beijing 102206, Peoples R China
4.Beijing Inst Life, Beijing 100850, Peoples R China
5.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
Recommended Citation
GB/T 7714
An, Zhiwu,Zhai, Linhui,Ying, Wantao,et al. PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome[J]. MOLECULAR & CELLULAR PROTEOMICS,2019,18(2):391-405.
APA An, Zhiwu.,Zhai, Linhui.,Ying, Wantao.,Qian, Xiaohong.,Gong, Fuzhou.,...&Fu, Yan.(2019).PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome.MOLECULAR & CELLULAR PROTEOMICS,18(2),391-405.
MLA An, Zhiwu,et al."PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome".MOLECULAR & CELLULAR PROTEOMICS 18.2(2019):391-405.
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