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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

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OryzaPG-DB: rice proteome database based on shotgun proteogenomics.

Mohamed Helmy¹, Masaru Tomita, Yasushi Ishihama

¹Institute for Advanced Biosciences, Keio University, 403-1 Daihoji, Tsuruoka, Yamagata 997-0017, Japan.

BMC Plant Biology

|April 14, 2011

Summary

OryzaPG-DB is a new rice proteome database using shotgun proteogenomics to improve genome annotation. It provides peptide-based expression data and identifies novel genomic features, aiding in gene re-annotation.

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Area of Science:

Proteomics and Genomics
Bioinformatics and Database Development

Background:

Proteogenomics enhances genome annotation using experimental proteome data.
Mass spectrometry-based shotgun proteomics generates high-throughput peptide sequencing data.
A dedicated data repository is crucial for translational gene expression evidence.

Purpose of the Study:

To present OryzaPG-DB, a novel rice proteome database.
To integrate genomic features with experimental shotgun proteomics data.
To provide a valuable resource for genome re-annotation.

Main Methods:

Developed OryzaPG-DB using shotgun proteogenomics data from 27 nanoLC-MS/MS runs.
Identified peptides by searching against multiple rice databases (protein, cDNA, transcript, genome).
Mapped identified peptides to the rice genome, identifying novel genomic features.

Main Results:

OryzaPG-DB covers approximately 3200 rice genes.
Identified 40 novel genomic features within these genes.
Database provides peptide-based expression profiles and genomic origins.

Conclusions:

OryzaPG-DB is the first proteogenomics-based rice proteome database.
The database offers updated annotations in GFF3 format and visualization.
Its generic design allows adaptation for other species.