OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics

Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version of the database was created from the results of 27 nanoLC-MS/MS runs on a hybrid ion trap-orbitrap mass spectrometer, which offers high accuracy for analyzing tryptic digests from undifferentiated cultured rice cells. Peptides were identified by searching the product ion spectra against the protein, cDNA, transcript and genome databases from Michigan State University, and were mapped to the rice genome. Approximately 3200 genes were covered by these peptides and 40 of them contained novel genomic features. Users can search, download or navigate the database per chromosome, gene, protein, cDNA or transcript and download the updated annotations in standard GFF3 format, with visualization in PNG format. In addition, the database scheme of OryzaPG was designed to be generic and can be reused to host similar proteogenomic information for other species. OryzaPG is the first proteogenomics-based database of the rice proteome, providing peptide-based expression profiles, together with the corresponding genomic origin, including the annotation of novelty for each peptide.The OryzaPG database was constructed and is freely available at http://oryzapg.iab.keio.ac.jp/ webcite.Among high-throughput experimental methods, genome sequencing represents a turning point in the understanding of biological systems. Nevertheless, the biological significance of the sequenced genome cannot be understood unless the protein-coding genes and their products are accurately identified. Thus, genome annotation has become major issue [1-3]. Genome annotation is the process of gene structure and function determination, and it usually takes place after genome sequencing and before data deposition in a database or databank [2,4,5].In typical genome annotation work, experimental and computational methods are integrated to an