Specific Protein Database Creation from Transcriptomics Data in Nonmodel Species: Holm Oak (Quercus ilex L.)

Abstract

Proteomics encompasses efforts to identify all the proteins of a proteome, with most of studies about plant proteomics based on a bottom-up mass spectrometry (MS) strategy, in which the proteins are subjected to digestion by trypsin and the tryptic fragments are subjected to MS analysis. The identification of proteins from MS/MS spectra has been performed using different algorithms (Mascot, Sequest) against plant protein sequence databases such as UniProtKB or NCBI_Viridiplantae. But these databases are not the best choice for nonmodel species where they are underrepresented, resulting in poor identification rates. A high identification rate requires a sequenced and well-annotated genome of the species under investigation. For nonmodel organisms, the identification of proteins is challenging since, in the best of the cases, only hits or orthologs instead of gene products are identified. However, in the absence of a sequenced genome, this situation can be improved using transcriptome data to generate a specific species database to compare proteins. In this chapter, we report the protein database construction from RNA-Seq data in a nonmodel species, in this particular case Holm oak (Q. ilex).