Carbonic anhydrases (CA) are a family of metalloenzymes that catalyse the reversible hydration of CO2, to form bicarbonate and a proton, contributing to pH homeostasis in the human body. CA3 is less well characterised among the 16 human CA isoforms, possibly due to its low catalytic activity minimising research interest, but unlike other CAs, it is reported to have surface-exposed cysteine residues and antioxidant activity. To better understand the cellular role of CA3, this project focuses on identifying and characterising binding partners for CA3, as well as exploring the role of the cysteine residues in CA3. We employed native mass spectrometry (nMS), also known as intact mass spectrometry, to assess ligand binding to CA II and CA III and discovered two novel compounds that for the first time display strong binding to CA III. A compound library constructed with 993 mildly electrophilic fragments was also used to identify potential CA3 inhibitors that target the surface exposed cysteine residues in CA3 rather than the normal catalytic site. We present a new data visualization and quantification tool developed to display native mass spectra as an intuitive stacked heat map representation for rapidly interpreting the results of ligand-protein binding from nMS screening.