Biomarker profiling and reproducibility study of MALDI-MS measurements of Escherichia coli by analysis of variance-principal component analysis.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has proved useful for the characterization of bacteria and the detection of biomarkers. Key challenges for MALDI-MS measurements of bacteria are overcoming the relatively large variability in peak intensities. A soft tool, combining analysis of variance and principal component analysis (ANOVA-PCA) (Harrington, P. D.; Vieira, N. E.; Chen, P.; Espinoza, J.; Nien, J. K.; Romero, R.; Yergey, A. L. Chemom. Intell. Lab. Syst. 2006, 82, 283-293. Harrington, P. D.; Vieira, N. E.; Espinoza, J.; Nien, J. K.; Romero, R.; Yergey, A. L. Anal. Chim. Acta. 2005, 544, 118-127) was applied to investigate the effects of the experimental factors associated with MALDI-MS studies of microorganisms. The variance of the measurements was partitioned with ANOVA and the variance of target factors combined with the residual error was subjected to PCA to provide an easy to understand statistical test. The statistical significance of these factors can be visualized with 95% Hotelling T2 confidence intervals. ANOVA-PCA is useful to facilitate the detection of biomarkers in that it can remove the variance corresponding to other experimental factors from the measurements that might be mistaken for a biomarker. Four strains of Escherichia coli at four different growth ages were used for the study of reproducibility of MALDI-MS measurements. ANOVA-PCA was used to disclose potential biomarker proteins associated with different growth stages.