I am doing LCMS data analysis in MetaboAnalyst. Example of a metabolite..
3-Hydroxy-3-methylglutaric acid
Positive ion mode, 0.771 (FC), -0.374 (log2(FC))
Negative ion mode, 1.168 (FC), 0.225 (log2(FC))
*correction: ..upregulated in positive and downregulated in negative ion mode
The difference is ionization efficiency. Some ions 'fly' better than others in the same mode in MS. There is lots of speculation about why this is so, which occasionally breaks out in shouting matches (reaching the point of fist-a-cuffs) at ASMS and other MS conferences. Consequentliy, I will leave my speculations out of this response. However, just like some ions will only be seen in positive ion mode and others only in negative ion mode, the differences in relative ionization between molecules in a single mode can easily give you the result you see. If you really want to see if the molecule is upregulated or downregulated, you can spike the sample with a 13C or 18O-analog of the compound and deconvolve the isotopic patterns quantitatively. see reference attached.
Method Isotopic Vector Angle Analysis in Mass Spectrometry v2
Unregulations makes more sense for quick decisions as lack of ionisation in the other mode hindered its detection.
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