Figure 6

Assessment of the fold change confidence interval. a) To assess the fold change 95% confidence interval estimate it has been plotted for a subset of fold changes and noise levels as shown. The confidence interval was seen to tighten up when the noise level decreases, which illustrates its value as an assessment parameter of spectral quality. The asymmetry in the confidence interval reflects how the uncertainty and multivariate dependencies between the estimated isotope intensities influence the fold change estimate. Furthermore the confidence interval widens when the fold change increases, in accordance with the increased fold change error (see Fig. 4). b) The confidence interval was also found to mirror the uncertainty caused by noise and low labeling efficiency, thus in total capturing important aspects of spectral quality.