So I am very new to analysing metabolomics data, so please forgive me if this is a silly question.
Following preprocessing of LC-MS data of 3 different sets (so three separate mass spec runs i.e 3 files from different sources with replicates within) I have identified metabolites common to each run. I have found log fold changes of each metabolite of each run and have found that the same metabolite has been identified multiple times within each run.
e.g of how the data looks
L.Arginine..........."peak intensities"...."fold change" L.Arginine.1........"peak intensities"...."fold change" L.Arginine.2........"peak intensities"...."fold change"
From these names I have looked back to the raw data and I have different retention times and different masses.
How do I determine which is the "real" peak intensities that I should be looking at for the named metabolite? Since the fold change is calculated from peak intensity and I am looking at differences between common metabolites of my samples I need to know how I can determine which resultant fold change is most likely true.