title: Improvement of peptide identification with considering the abundance of mRNA and peptide.
abstract: BACKGROUND
  Tandem mass spectrometry (MS/MS) followed by database search is a main approach to identify peptides/proteins in proteomic studies. A lot of effort has been devoted to improve the identification accuracy and sensitivity for peptides/proteins, such as developing advanced algorithms and expanding protein databases.
  
  
  RESULTS
  Herein, we described a new strategy for enhancing the sensitivity of protein/peptide identification through combination of mRNA and peptide abundance in Percolator. In our strategy, a new workflow for peptide identification is established on the basis of the abundance of transcripts and potential novel transcripts derived from RNA-Seq and abundance of peptides towards the same life species. We demonstrate the utility of this strategy by two MS/MS datasets and the results indicate that about 5% ~ 8% improvement of peptide identification can be achieved with 1% FDR in peptide level by integrating the peptide abundance, the transcript abundance and potential novel transcripts from RNA-Seq data. Meanwhile, 181 and 154 novel peptides were identified in the two datasets, respectively.
  
  
  CONCLUSIONS
  We have demonstrated that this strategy could enable improvement of peptide/protein identification and discovery of novel peptides, as compared with the traditional search methods.
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Chunwei
authors.initials: C
authors.lastname: Ma
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Shaohang
authors.initials: S
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Geng
authors.initials: G
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. wenbo@genomics.cn.
authors.forename: Bo
authors.initials: B
authors.lastname: Wen
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China. siqiliu@genomics.cn.
authors.forename: Siqi
authors.initials: S
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D010455:Peptides / Q000032:analysis / Q000737:chemistry / Q000235:genetics; D040901:Proteomics / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; D012333:RNA, Messenger
keywords: Bioinformatics; Machine learning; Mass spectrometry; Proteogenomics; RNA-Seq; Shotgun proteomics