customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. A previous study showed that a sample-specific protein database derived from RNA-Seq data can better approximate the real protein pool in the sample and thus improve protein identification. More importantly, single nucleotide variations (SNVs), short insertion and deletions (INDELs) and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here scientists at the Vanderbilt University School of Medicine report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration.

rna-seq

Availability – customProDB and related documents are freely available at http://bioconductor.org/packages/2.13/bioc/html/customProDB.html

Contact: bing.zhang@vanderbilt.edu

  • Wang X, Zhang B. (2013) customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search. Bioinformatics [epub ahead of print]. [article]