Our study of the Arabidopsis proteome through tandem mass spectrometry revealed over 18,000 novel peptides not in the TAIR7 genome annotation release. Using Inspect, we identified over 144,000 peptides from 3 sequence databases; the six-frame translation of the Arabidopsis genome, an exon-graph based on ab initio gene predictions, and the TAIR7 proteome. From the novel peptides we predicted over 700 new gene models and over 600 corrections to current gene models. The peptides and predicted models can be accessed here.