Fig. 2.

The template proteogenomic method reconstructs a target protein sequence using tandem mass spectra and a template database in three steps: template-chain selection, anchor extension, and sequence construction. The template database specifies ordering and mutual exclusion constraints between templates. A set of templates is selected that obeys these constraints based on peptides identified on them. Anchors are peptides identified by searching spectra against the template database. Anchors are extended by aligning spectra that overlap the anchor. Finally, the sequence is reconstructed by merging the extended anchor sequences.