Fig. 1. Overview of the PepQueryDB, PepQuery2 workflow, and some possible applications.

The workflow involves five major steps as described in the previous publication (ref. ¹⁶): (1) peptide preparation and initial filtering; (2) candidate spectra retrieval and PSM scoring; (3) competitive filtering based on reference sequences; (4) statistical evaluation based on shuffled peptides; and (5) competitive filtering based on unrestricted modification searching. Query peptides and PSMs are classified into seven categories (C1-C7) on the basis of query results.