For each group studied by MS, there were two technical replicates and two sample replicates, resulting in four ratios for each comparison. Because of the variability observed between replicates, a measure, termed the 'regulation score' [Equation (1)] was used to summarize the magnitude and consistency of differential abundance across multiple derives log2(ratios) 21. Proteins located in the top 40 most consistently regulated, proteins identified with ≥ 2 peptides and significant (p<0.05) were selected as high confidence proteins. High confidence proteins with fold change (≥2 or <0.5) across groups were used for further validating markers. The differences in the intensities of proteins in different groups were compared using the Kruskal-Wallis rank sum test. SNK (q-test) was utilized to compare the difference between every pair of groups. Area under the receiver operating characteristic (AUC) analysis and correct prediction rate were used to evaluate predictive performance.

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