PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq

BMC Bioinformatics

Software

Xin Liu¹  Shaohang Xu¹  Ruo Zhou¹  Bo Wen¹  Xun Xu¹  Siqi Liu²  Bing Zhang³  Xiaojing Wang³ 

[1] BGI-Shenzhen, 518083, Shenzhen, China;BGI-Shenzhen, 518083, Shenzhen, China;Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China;Department of Biomedical Informatics, Vanderbilt University School of Medicine, 37232, Nashville, TN, USA;

关键词: Proteomics;    RNA-Seq;    MS/MS;    Peptide identification;    Proteogenomics;   

DOI  :  10.1186/s12859-016-1133-3

 received in 2015-06-27, accepted in 2016-06-09,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundPeptide identification based upon mass spectrometry (MS) is generally achieved by comparison of the experimental mass spectra with the theoretically digested peptides derived from a reference protein database. Obviously, this strategy could not identify peptide and protein sequences that are absent from a reference database. A customized protein database on the basis of RNA-Seq data is thus proposed to assist with and improve the identification of novel peptides. Correspondingly, development of a comprehensive pipeline, which provides an end-to-end solution for novel peptide detection with the customized protein database, is necessary.ResultsA pipeline with an R package, assigned as a PGA utility, was developed that enables automated treatment to the tandem mass spectrometry (MS/MS) data acquired from different MS platforms and construction of customized protein databases based on RNA-Seq data with or without a reference genome guide. Hence, PGA can identify novel peptides and generate an HTML-based report with a visualized interface. On the basis of a published dataset, PGA was employed to identify peptides, resulting in 636 novel peptides, including 510 single amino acid polymorphism (SAP) peptides, 2 INDEL peptides, 49 splice junction peptides, and 75 novel transcript-derived peptides. The software is freely available from http://bioconductor.org/packages/PGA/, and the example reports are available at http://wenbostar.github.io/PGA/.ConclusionsThe pipeline of PGA, aimed at being platform-independent and easy-to-use, was successfully developed and shown to be capable of identifying novel peptides by searching the customized protein database derived from RNA-Seq data.

【 授权许可】

CC BY   
© The Author(s). 2016