There is growing interest to use mass spectrometry data to search genome sequences directly. Previous work by other authors demonstrated that this approach is able to correct and complement available genome annotations. We discuss the practical difficulty of searching large eukaryotic genomes with peptide ion trap tandem mass spectra of small proteins (<40 kDa). The challenging problem of automatically identifying peptides that span across exon/intron boundaries is explored for the first time by using experimental data. In a human genome search, we find that roughly 30% of the peptides are missed, due to various reasons, compared to a Swiss-Prot search. We show that this percentage is significantly reduced with improved parent mass accuracy. We finally provide several examples of predicted gene structures that could be improved by proteomics data, in particular by peptides spanning across exon/intron boundaries.