Fig. 1

Bayes plot showing the posterior probabilities revised in light of the screening study data. The prior probabilities (p = 0.20) are indicated by the red horizontal line. Note the large increase in probability for the number of SWATH windows. The LogWorth value corresponding to a statistically significant effect at the p < 0.05 level of significance is indicated by the blue horizontal line. While the Number of SWATH windows, MS range and Gradient length are all statistically significant, the posterior probability increases only for the Number of SWATH windows. Increasing the number of precursor windows from 20 to 83 increases the number of proteins recovered. Note that within the experimental ranges used the method is relatively robust to variation in protein amount, choice of fixed or variable window, MS/MS range and MS accumulation times