PNNL

Abstract

RATIONALE Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a preferred technique for analyzing complex organic mixtures. Currently, there is no consensus normalization approach, nor an objective method for selecting one, for quantitative analyses of FT-ICR-MS data. We investigate a method to evaluate and score the amount of bias various normalization approaches introduce into the data. METHODS We evaluate the ability of the Statistical Procedure for the Analysis of Normalization Strategies (SPANS) to guide selection of appropriate normalization approaches for two different FT-ICR-MS datasets. Further, we test the robustness of SPANS results to changes in SPANS parameter values and assess the impact of using various normalization approaches on downstream statistical analyses. RESULTS The normalization approach identified by SPANS differed for the two datasets. Normalization methods impacted the statistical significance of peaks differently, underscoring the importance of carefully evaluating potential methods. More consistent SPANS scores resulted when at least 120 significant peaks are used, where larger sets of peaks were obtained by increasing the p-value threshold. Interestingly, we show that Total Sum Scaling and highest peak normalization, used in previous studies, underperformed relative to SPANS-recommended normalization approaches. CONCLUSIONS While there is no single, best normalization method for all datasets, SPANS provides a mechanism to identify an appropriate normalization method for analyzing FT-ICR-MS data quantitatively. The number of peaks used in the background distributions of SPANS contributes more significantly to the reproducibility of results than the p-value thresholds used to obtain those peaks.