This work describes a versatile analytical approach, which combines the proxy ligand electrospray ionization mass spectrometry (ESI-MS) assay and model membranes of defined composition, to quantify the influence of lipid bilayer composition on protein-glycolipid binding in vitro. To illustrate the implementation of the assay (experimental design and data analysis), affinities of the monosialoganglioside ligand GM1, incorporated into nanodiscs (NDs), for cholera toxin B subunit homopentamer (CTB5) were measured. A series of NDs containing GM1 and cholesterol were prepared using three different phospholipids (1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)), and the average GM1 and cholesterol content of each ND were determined. The intrinsic affinities of GM1-containing NDs prepared with the three phospholipids are found to be similar in magnitude, indicating that small differences in the fatty acid chain length and the number of unsaturated bonds do not significantly affect the CTB5-GM1 interaction. Moreover, the measured affinities are similar to the value measured for GM1 pentasaccharide, indicating that neither the ceramide moiety nor the surface of the phospholipid membrane plays a significant role in CTB5 binding. The intrinsic (per binding site) affinity of the CTB5-GM1 interaction was found to decrease with increasing GM1 content of the ND, consistent with the occurrence of GM1 clustering in the membrane, which sterically hinders binding to CTB5. Notably, the addition of cholesterol to GM1-containing NDs did not have a significant effect on the strength of the CTB5-GM1 interaction. This result, which is at odds with the findings of a previous study of CTB5 binding to GM1 in vesicles, suggests that cholesterol does not "mask" GM1, at least not in NDs. These data, in addition to providing new insights into the influence of membrane composition on CTB5-GM1 binding, demonstrate the potential of the proxy ligand ESI-MS approach for comprehensive and quantitative studies of lectin interactions with glycolipids in native-like, membrane environments.