Novel peptide identification from tandem mass spectra using ESTs and sequence database compression

Peptide identification by tandem mass spectrometry is the dominant proteomics workflow for protein characterization in complex samples. Traditional search engines, which match peptide sequences with tandem mass spectra to identify the samples' proteins, use protein sequence databases to suggest peptide candidates for consideration. Although the acquisition of tandem mass spectra is not biased toward well-understood protein isoforms, this computational strategy is failing to identify peptides from alternative splicing and coding SNP protein isoforms despite the acquisition of good-quality tandem mass spectra. We propose, instead, that expressed sequence tags (ESTs) be searched. Ordinarily, such a strategy would be computationally infeasible due to the size of EST sequence databases; however, we show that a sophisticated sequence database compression strategy, applied to human ESTs, reduces the sequence database size approximately 35-fold. Once compressed, our EST sequence database is comparable in size to other commonly used protein sequence databases, making routine EST searching feasible. We demonstrate that our EST sequence database enables the discovery of novel peptides in a variety of public data sets.