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题名: The Null-Test for peptide identification algorithm in Shotgun proteomics
作者: Zhang, Shu-Rong1;  Shan, Yi-Chu1;  Jiang, Hao1, 2;  Liu, Jian-Hui1, 2;  Zhou, Yuan1;  Zhang, Li-Hua1;  Zhang, Yu-Kui1
关键词: Null-Test ;  Shotgun proteomics ;  Peptide identification ;  Target-Decoy search ;  FDR estimation
刊名: JOURNAL OF PROTEOMICS
发表日期: 2017-06-23
DOI: 10.1016/j.jprot.2017.05.010
卷: 163, 页:118-125
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ;  Life Sciences & Biomedicine
类目[WOS]: Biochemical Research Methods
研究领域[WOS]: Biochemistry & Molecular Biology
英文摘要: The present research proposed general evaluation strategy named Null-Test for peptide identification algorithm in Shotgun proteomics. The Null-Test method based on random matching can be utilized to check whether the algorithm has a tendency to make a mistake or has potential bugs, faultiness, errors etc., and to validate the reliability of the identification algorithm. Unfortunately, none of the five famous identification software could pass the most stringent Null-Test. PatternLab had good performance in both Null-Test and routine search by making a good control on the overfitting with sound design. The fuzzy logics based method presented as another candidate strategy could pass the Null-Test and has competitive efficiency in peptide identification. Filtering the results by appropriate FDR would increase the number of discoveries in an experiment, at the cost of losing control of Type I errors. Thus, it is necessary to utilize some more stringent criteria when someone wants to design or analyze an algorithm/software. The more stringent criteria will facilitate the discovery of latent bugs, faultiness, errors etc. in the algorithm/software. It would be recommended to utilize independent search combining random database with statistics theorem to estimate the accurate FDR of the identified results.
关键词[WOS]: TANDEM MASS-SPECTROMETRY ;  FALSE-DISCOVERY RATE ;  POSTTRANSLATIONAL MODIFICATIONS ;  PROTEIN IDENTIFICATION ;  DATABASE SEARCH ;  SEQUENCE ;  CELL ;  INFERENCE ;  SPECTRA ;  RATES
语种: 英语
WOS记录号: WOS:000404709600010
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/152085
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Dalian Inst Chem Phys, Key Lab Separat Sci Analyt Chem, Natl Chromatog Res & Anal Ctr, Dalian, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China

Recommended Citation:
Zhang, Shu-Rong,Shan, Yi-Chu,Jiang, Hao,et al. The Null-Test for peptide identification algorithm in Shotgun proteomics[J]. JOURNAL OF PROTEOMICS,2017,163:118-125.
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