Figure 7.

(A) In four subsequent nano-LC–MS/MS experiments, only 810 of 1500 mouse peptide targets were identified with DDA. The identifications improve to 1072 when IDA is used (error bars represent 1 σ). (B) In total, 826 target peptides were identified in all four mice when IDA was used to target. This number falls to only 459 peptides when DDA is used. (C) The number of statistically significant differences (p value <0.05) quantified when each tissue is compared with liver is greater with IDA than DDA. (D) When comparing target peptides identified in the muscle versus the liver, IDA quantified 826 statistically significant peptides compared with only 531 when DDA was used, a 56% increase.