FIGURE 6.

Advantages of multiple scans and database search engines. A combination of neutral-loss scanning and multiple database search engines resulted in a greater number of confident identifications of phosphopeptides. (A) The bar graph compares the number of phosphopeptides identified from each enrichment protocol using data derived from the MS² scan only (black bars), MS³ scan only (gray bars), and MS² and MS³ scans (white bars). (B) Venn diagram showing the total phosphopeptides identified from the DIMAC enrichment protocol using the Mascot or SEQUEST database search engines. (C) The bar graph compares the total phosphopeptides identified by each search engine from the MS² scan only (black bars), MS³ scan only (white bars), and MS² and MS³ scans (gray bars).