Dear Eldin,

Without any further information on the structure of metabolites shown in the XIC, from a qualitative point of view the largest peak is the most abundant metabolite, however from a quantitative point of view the largest peak may (or not!) be the most abundant metabolite.

When using mass spectrometry as the detection mode, the intensity is related to the molecule's affinity to protonation (formation of [M+H]+ in the (+)ve ion mode) or to deprotonation (formation of [M-H]- in the (-)ve ion mode). So the largest peak in the XIC only means it has higher affinity to form the ion, not necessarily the most abundnat metabolite in your sample.

To determine the quantity (concentration) of your metabolite you'll need to build a cal curve (peak area vs conc) for each metabolite (peaks in your XIC) and plot the peak area in the cal curve.

Hope this helps,

Ana

Hello,

The principal problem here is that there are not enough data points in your scans, so you should probably increase the dwell time. To mee, it seems that you do not have enough peaks to define a good chromatographic peak. I guess the problem comes for having several parent ions scans running at the same time. My advice is to do create different methods with the different parent ion scans.

Also, I see that all your molecules are eluting quite early and depending on the size of your column it could mean that you are not able to retain your compounds with this column and that could be also a problem.

Regards,

Andreu