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Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments

Title
Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments
Author
백은옥
Keywords
proteogenomic search; novel peptide identification; spike-in data; simulation; false discovery rate control
Issue Date
2017-06
Publisher
AMER CHEMICAL SOC
Citation
JOURNAL OF PROTEOME RESEARCH, v. 16, no. 6, page. 2231-2239
Abstract
Proteogenoinit searches are useful for novel peptide identification from tandem mass spectra. Usually, separate and multistage approaches are adopted to accurately control the false discovery rate (FDR) for: proteogenomic search. Their performance on novel peptide identification has not been thoroughly evaluated; however, mainly due to the. difficulty in Confirming existence of identified novel peptides.' We, simulated a proteogenomic search controlled, spike-in proteomic data set. After confirming that the results of the simulated proteogenomic search were similar to those of a real proteogenomic search using,a human cell line data set, we evaluated the performance of six FDR Control methods-global, separate, and multistage FDR estimation) respectively, coupled to a target-decoy search and a mixture model-based: method on novel peptide identification. The multistage approach showed the highest accuracy for FDR. estimation. However, global and separate FDR estimation with the mixture model-based method showed higher sensitivities than others at the same true FDR. Furthermore, the mixture model based method performed equally well when applied without or with a reduced set of decoy sequences: Considering different prior probabilities for novel and known protein identification, we recommend using mixture model-based methods with separate FDR estimation for sensitive and reliable identification of novel peptides from proteogenomic searches.
URI
https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00033https://repository.hanyang.ac.kr/handle/20.500.11754/114530
ISSN
1535-3893; 1535-3907
DOI
10.1021/acs.jproteome.7b00033
Appears in Collections:
COLLEGE OF ENGINEERING[S](공과대학) > COMPUTER SCIENCE(컴퓨터소프트웨어학부) > Articles
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