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A similar pre-processing analysis as the o … A similar pre-processing analysis as the one described for the standard mixture dataset was performed. We used a fatty acid methyl esters (FAMEs) as RI marker standards (Additional file 8) and an in-house reference library composed of 153 metabolites (Additional file 9). This library was manually curated and in addition to known metabolites includes several unknown metabolites that have been observed in previous experiments.<br />
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After running TargetSearch, we manually compared the final profile with the deconvoluted peak profiles obtained with LECO (see Additional file 10 for full profile with manual annotations). The profile list contained 138 entries in total, of which 131 metabolites were unambiguously assigned. The 7 ambiguous assignments corresponded to 14 metabolites (2 metabolites per entry). The remaining 8 metabolites (of the 153) were neither present in the final profile nor in the chromatograms as confirmed by manual inspection. Based on our previous experience, we routinely only consider metabolites to be present if at least 3 correlating masses at the correct RI are identified (this excludes the duplicate isotope pairs that are often observed to correlate). Taking this into account, we would consider 101 metabolites to be identified in this experiment. We thus checked these manually and found that 96 were correctly assigned (these were all assigned a similarity score above 600), 1 ambiguity was wrongly resolved, i.e., the correct metabolite was not the one suggested; 1 ambiguity could not be resolved manually, due to similar RIs and reference spectra; 1 metabolite was not found in the chromatograms; and 2 metabolites were not found but 2 peaks (unknowns) were found at their expected retention time. The later could be anticipated in the profile since the similarity score reported by TargetSearch was below 400. re reported by TargetSearch was below 400.
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