Improvement of peptide identification with considering the abundance of mRNA and peptide

BMC Bioinformatics

Methodology Article

Xin Liu¹  Chunwei Ma¹  Shaohang Xu¹  Siqi Liu¹  Geng Liu¹  Xun Xu¹  Bo Wen¹ 

[1] BGI-Shenzhen, 518083, Shenzhen, China;

关键词: Bioinformatics;    Mass spectrometry;    RNA-Seq;    Machine learning;    Shotgun proteomics;    Proteogenomics;   

DOI  :  10.1186/s12859-017-1491-5

 received in 2016-07-07, accepted in 2017-01-20,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundTandem 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.ResultsHerein, 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.ConclusionsWe have demonstrated that this strategy could enable improvement of peptide/protein identification and discovery of novel peptides, as compared with the traditional search methods.

【 授权许可】

CC BY   
© The Author(s). 2017