DICP OpenIR
The Null-Test for peptide identification algorithm in Shotgun proteomics
Zhang, Shu-Rong1; Shan, Yi-Chu1; Jiang, Hao1,2; Liu, Jian-Hui1,2; Zhou, Yuan1; Zhang, Li-Hua1; Zhang, Yu-Kui1
KeywordNull-test Shotgun Proteomics Peptide Identification Target-decoy Search Fdr Estimation
Source PublicationJOURNAL OF PROTEOMICS
2017-06-23
DOI10.1016/j.jprot.2017.05.010
Volume163Pages:118-125
Indexed BySCI
SubtypeArticle
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
WOS SubjectBiochemical Research Methods
WOS Research AreaBiochemistry & Molecular Biology
WOS KeywordTANDEM MASS-SPECTROMETRY ; FALSE-DISCOVERY RATE ; POSTTRANSLATIONAL MODIFICATIONS ; PROTEIN IDENTIFICATION ; DATABASE SEARCH ; SEQUENCE ; CELL ; INFERENCE ; SPECTRA ; RATES
AbstractThe 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.
Language英语
WOS IDWOS:000404709600010
Citation statistics
Document Type期刊论文
Identifierhttp://cas-ir.dicp.ac.cn/handle/321008/152085
Collection中国科学院大连化学物理研究所
Affiliation1.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
GB/T 7714
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.
APA Zhang, Shu-Rong.,Shan, Yi-Chu.,Jiang, Hao.,Liu, Jian-Hui.,Zhou, Yuan.,...&Zhang, Yu-Kui.(2017).The Null-Test for peptide identification algorithm in Shotgun proteomics.JOURNAL OF PROTEOMICS,163,118-125.
MLA Zhang, Shu-Rong,et al."The Null-Test for peptide identification algorithm in Shotgun proteomics".JOURNAL OF PROTEOMICS 163(2017):118-125.
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