Fig. 4

Bland-Altman type plots showing differences in normalized lipid levels calculated using different methods and ions. The panels show the percent differences in normalized lipid levels calculated using smoothed versus non-smoothed peak heights (smoothing was done as the final step in MZmine) (a), peak area versus peak height (b), positive versus negative polarity using peak area (c), and sodium adducts versus the major adduct observed in positive polarity using peak area (d). Note that orange lines represent 1.96 x standard deviation (the 95% limits), and hence are a measure of where you would expect 95% of the percent differences to fall for each comparison. See Formula 1 for relative percent difference calculation. Arrows delineate the direction of difference. *Note that the differences between major adducts and [M + Na]⁺ were drastic and ranged over several orders of magnitude. Therefore, the log of the absolute percent difference was used and then multiplied by − 1 when the [M + Na]⁺ normalized lipid level was calculated higher than the major ion