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A note on the false discovery rate of novel peptides in proteogenomics.

ABSTRACT:

Motivation

Proteogenomics has been well accepted as a tool to discover novel genes. In most conventional proteogenomic studies, a global false discovery rate is used to filter out false positives for identifying credible novel peptides. However, it has been found that the actual level of false positives in novel peptides is often out of control and behaves differently for different genomes.

Results

To quantitatively model this problem, we theoretically analyze the subgroup false discovery rates of annotated and novel peptides. Our analysis shows that the annotation completeness ratio of a genome is the dominant factor influencing the subgroup FDR of novel peptides. Experimental results on two real datasets of Escherichia coli and Mycobacterium tuberculosis support our conjecture.

Contact

yfu@amss.ac.cn or xupingghy@gmail.com or smhe@ict.ac.cn

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Zhang K

PROVIDER: S-EPMC4595894 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

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A note on the false discovery rate of novel peptides in proteogenomics.

Zhang Kun K Fu Yan Y Zeng Wen-Feng WF He Kun K Chi Hao H Liu Chao C Li Yan-Chang YC Gao Yuan Y Xu Ping P He Si-Min SM

Bioinformatics (Oxford, England) 20150614 20

<h4>Motivation</h4>Proteogenomics has been well accepted as a tool to discover novel genes. In most conventional proteogenomic studies, a global false discovery rate is used to filter out false positives for identifying credible novel peptides. However, it has been found that the actual level of false positives in novel peptides is often out of control and behaves differently for different genomes.<h4>Results</h4>To quantitatively model this problem, we theoretically analyze the subgroup false d ...[more]

PMID: 26076724

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