Pipeline predictions.

All 118,184 spectra were searched against a concatenated database comprising all Celera accessions, target and decoy hits from the pre-screening search (Table 1). Peptides that were uniquely identified by the six-frame search are referred as ‘orphan’ peptides. These peptides were classified according to their genomic position. ΣR – averaged conserved GERP score for the region from which the peptide originated. FDR was computed using the reverse decoy hits, as described in the methods.