GenoMS is a tool for sequencing a small set of proteins using an imperfect database and tandem mass spectra. The database need not contain full protein sequence, but instead can contain exons or partial sequences. The database can also be a small region of the genome. Tandem mass spectra should be from overlapping peptides produced from digestion by multiple proteases.
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Template Proteogenomics: sequencing whole proteins using an imperfect database.
NE Castellana, V Pham, D Arnott, JR Lill, V Bafna. (2010).
Mol. Cell. Proteomics, 9, 6:1260-70.