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BMC Bioinformatics. 2017 Feb 16;18(1):109. doi: 10.1186/s12859-017-1491-5.

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

Author information

1
BGI-Shenzhen, Shenzhen, 518083, China.
2
BGI-Shenzhen, Shenzhen, 518083, China. wenbo@genomics.cn.
3
BGI-Shenzhen, Shenzhen, 518083, China. siqiliu@genomics.cn.

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.

KEYWORDS:

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

PMID:
28201984
PMCID:
PMC5311845
DOI:
10.1186/s12859-017-1491-5
[Indexed for MEDLINE]
Free PMC Article

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