Figure 5.

Subset of 500 mouse peptides were targeted with DDA, an accurate mass inclusion list (INC), and our intelligent data acquisition (IDA) method in hexplicate. (A) IDA identified the most target peptides of the three methods (error bars represent the 1 σ). (B) Discovery identifications by three methods show only a slight decline in the total number of peptides identified using IDA. (C) 74% of the targets were observed in all six technical replicates when IDA was used compared with <20% for the inclusion list or data-dependent acquisition.