Abstract
This document contains the basics to compute the data obtained by gas chromatography coupled to mass spectrometry. We will learn how to convert the manufacturer files to open format files, create a reproducible pipeline to batch clean, integrate and align your chromatograms. At last, I'll give you some tips to annotate the molecules. I won't consider ESI, HRMS, MS2 spectra nor statistical analysis on the obtained data but MZmine can do it too!