Mass Spectrometry Data Preprocessing

Mass spectra were obtained by summarizing one-minute signals using DataAnalysis version 4.1 (Bruker Daltonics). Mass spectra preprocessing including recalibration, peak detection, and peak intensity calculation were carried out by DataAnalysis software using the following parameters: peak width, 2; signal-to-noise ratio, 2; relative and absolute threshold intensity, 0.01% and 100, respectively. The resulting mass spectrometry peak masses were pooled and processed using Matlab version R2010a (MathWorks, Natick, MA, USA). The alignment of mass spectrometry data was performed as described previously [25 (link)]. If mass difference was not exceeding 0.01 Da the peaks were considered as related to the same metabolite ion. Peaks that were below the detection limit in <80% of samples in each group were removed from the analysis. Mass peak intensities were normalized as described previously [24 (link)].