Comparison of normalization methods for the identification of biomarkers using MALDI-TOF and SELDI-TOF mass spectra

Proteomic profiling by mass spectrometry has tremendous potential for identifying disease biomarkers. A key limitation of mass spectrometry is that the information provided on the abundance of the various peptides is only relative. Thus, normalization is typically employed. Several normalization methods have been proposed and implemented in the literature. However, it is not clear if there is any reason to prefer one method over another. The goal of this study was to investigate the effect of normalization strategy on the identification of putative biomarkers from MALDI-TOF and SELDI-TOF mass spectra. Our results demonstrate that many of the putative biomarkers identified by mass spectrometry will be the same regardless of which data normalization scheme is applied. However, there can be substantial differences in the m/z values identified as being most discriminatory based on choice of normalization method. As there is no consistent pattern as to which normalization method yields the most promising targets for follow up study, we recommend that investigators routinely repeat their analysis with multiple normalization methods and consider the top several candidates identified in each case.