FIGURE 6.

Quantity of proteins identified and quantified in TDA/DDA and DDA control method experiments. (A) Average numbers of proteins identified (from ≥ 2 significantly scoring peptide spectrum matches) per technical replicate in each batch of LC-MS/MS experiments conducted on sample 1 (left) and sample 2 (right); identified and quantified proteins are differentiated from proteins that are identified but not quantified; standard errors are shown for these two categories of identified protein. (B) Average percentages of identified proteins that are also quantified (from ≥ 2 heavy/light peptide pairs) per technical replicate in each batch of LC-MS/MS experiments conducted on sample 1 (left) and sample 2 (right). Statistically significant differences between TDA/DDA and DDA control method experiments, as determined using 2-tailed t-tests, are labeled ^∗p < 0.05.