Byonic is a new proteomics search engine that can identify peptides carrying N- and O-linked glycans. Byonic offers a number of ways to search for glycopeptides, including preset glycan tables and manually entered glycan masses, and the search strategy affects the quality and quantity of spectrum assignments. Here we show how a progression of searches, from wider to narrower in both proteins and glycans, can improve sensitivity and specificity for glycopeptide identification.