title: A note on the false discovery rate of novel peptides in proteogenomics.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  yfu@amss.ac.cn or xupingghy@gmail.com or smhe@ict.ac.cn
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190, University of Chinese Academy of Sciences, Beijing 100049.
authors.forename: Kun
authors.initials: K
authors.lastname: Zhang
authors.affiliation: National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190 and.
authors.forename: Yan
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190, University of Chinese Academy of Sciences, Beijing 100049.
authors.forename: Wen-Feng
authors.initials: WF
authors.lastname: Zeng
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190, University of Chinese Academy of Sciences, Beijing 100049.
authors.forename: Kun
authors.initials: K
authors.lastname: He
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190.
authors.forename: Hao
authors.initials: H
authors.lastname: Chi
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190.
authors.forename: Chao
authors.initials: C
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China.
authors.forename: Yan-Chang
authors.initials: YC
authors.lastname: Li
authors.affiliation: State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Gao
authors.affiliation: State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Xu
authors.affiliation: Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190.
authors.forename: Si-Min
authors.initials: SM
authors.lastname: He
mesh_terms: D004926:Escherichia coli / Q000235:genetics; D058977:Molecular Sequence Annotation; D009169:Mycobacterium tuberculosis / Q000235:genetics; D010455:Peptides / Q000737:chemistry*; D040901:Proteomics
chemical_list: D010455:Peptides