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

Xiaojing Wang, Bing Zhang, Jonathan Wren

Research output: Contribution to journalArticlepeer-review

86 Scopus citations

Abstract

Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we 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 crossomics data integration.

Original languageEnglish (US)
Pages (from-to)3235-3237
Number of pages3
JournalBioinformatics
Volume29
Issue number24
DOIs
StatePublished - Dec 15 2013
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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