GUIDE FOR CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY DATA PROCESSING

In this work, a discussed and step-wise tutorial for LC-MS and GC-MS data processing using the open-access software MZMine2 is presented and discussed. The rationale behind each step was demonstrated to enable the readers to go through their own data and process it accordingly. The main lesson to be learned is that each parameter must be chosen in light of the raw data and no guidelines should suggest a predetermined value. Still, it is worth mentioning that ideal values for each parameter do not exist, and that the user might end up investing too much time futilely optimizing values. Our suggestion is to process your data in light of the raw data (and the study design) following the preview figure result and the resulting feature list generated in each processing step, interpret your data, and go back to process it again to tune the detection of important features.