ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules

Marcus Ludwig; Louis-Félix Nothias; Kai Dührkop; Irina Koester; Markus Fleischauer; Martin A. Hoffmann; Daniel Petras; Fernando Vargas; Mustafa Morsy; Lihini Aluwihare; Pieter C. Dorrestein; Sebastian Böcker

Third, we removed features from the beginning and end of the chromatography run and features with low relative or absolute intensity; and we removed MS/MS spectra which could not be assigned to an MS1 feature, MS/MS of a precursor peak with low absolute or relative intensity, and chimeric MS/MS. See Table 2 for dataset-specic parameter values. Chimeric spectra contain fragments of multiple precursor ions; we detected chimeric spectra as follows: All peaks within the isolation window, excluding isotope peaks, were considered to contribute their intensity to the measured MS/MS. We estimated the relative intensity that the target precursor ion contributes to the MS/MS; if the target precursor ion contributed to less than 50 % of the MS/MS intensity or if a second precursor ion contributed more than 33 % of the target precursor ion intensity, the MS/MS was marked as chimeric and excluded. The Isolation window width for the Orbitrap mass spectrometer used for the dendroides, NIST1950, tomato and diatoms is 1 Da; for the mice stool dataset analyzed on a QTOF mass spectrometer an isolation window of 3 Da width and shifted by 1 Da to the right, centered at the +1 isotope peak, was assumed.