This dataset is from a study where we investigated the enzymatic hydrolysis and degree of isomerisation of diacylglycerols (DAG) and monoacylglycerols (MAG) during in vitro digestion of a triacylglycerol standard (TAG-C14:0/C18:1n-9cis9/C14:0) and bovine milk. The data provides information on the fatty acid (FA) profile of several lipid fractions: triacylglycerols (TAG), DAGs, MAGs, free fatty acids (FFA) and polar lipids (PL), isolated after the in vitro digestion of the TAG standard and commercial whole milk. Data on the lipid profile after gastric digestion of whole milk is also included. In addition, the degree of isomerisation of a sn-2 MAG standard at room temperature and at -20 degrees celcius, during solid phase extraction using amino propyl columns was studied. The data includes chromatograms from the GC_MS analysis of the MAG-samples. Moreover, a direct infusion electrospray ionisation (ESI)-MS/MS method was used to study the difference in the collision induced dissociation (CID) mass spectra between sn-1/sn-3 MAGs and sn-2 MAGs, for the purpose of analysing different MAG isomers. The data includes CID mass spectra for several different standards of 1-MAG and 2-MAG.