Abstract: Mass spectrometry (MS) based systems and methods of implementing multi-stage MS/MS analysis for identification of experimental glycolipid samples. A processor communicatively coupled to a memory and a reference spectral database (1) implements a first stage analysis of glycan fragment data including determining, based on a matching reference glycan of a candidate reference glycolipid, a glycan structure of a glycan portion of the experimental glycolipid. The processor further (2) implements a second stage analysis of lipid/glycolipid fragment data including determining a lipid structure of a lipid portion of the experimental glycolipid by performing a spectral comparison of one or more MS/MS spectral values of a shifted experimental lipid fragment data with one or more MS/MS spectral values of matching reference lipid/glycolipid fragment data of the candidate reference glycolipid.