Protein is essential for human physiological processes and signalling pathways. Mass spectrometry (MS) is an important tool for ligand identification against protein target. This project aims to establish an MS-based ligand identification method towards neurodegenerative disease-related protein targets, including cytosolic LRRK2 protein, adenosine A2A receptor (A2AR), and α2-adrenergic receptor (α2AR). The LRRK2 subdomains (Roc/GTPase, COR, and MAPKKK/kinase) and GPCRs (A2AR, A2AR-GFP, and α2AR) were cloned, sequenced, expressed and purified for MS assay. The proteins were solubilised in different types of detergents (such as Triton X-100 and n-dodecyl-β- D-maltoside). Moreover, the A2AR, A2AR-GFP, and α2AR were reconstituted into selfassembled phospholipid bilayers (or nanodisc) to improve the solubility and stability. Because LRRK2 subdomains and α2AR had solubility and yield problems that would limit the MS analysis, the A2AR nanodisc was consequently demonstrated as a suitable protein target for MS method development. Two MS methods, native ESI MS and ultrafiltrationbased affinity LC/MS, were attempted for ligand identification against A2AR nanodisc. The ultrafiltration-based affinity LC/MS was successfully developed to assay the interactions (binding affinities) between A2AR nanodiscs and 15-ligand mixture (eight known ligands with seven unrelated negative ligands). The ultrafiltration-based affinity LC/MS allowed identification of ligands to a relatively stable unliganded/apo GPCR in nanodisc environment.