The compositions of paradoxin and taipoxin (PDx and TPx, respectively) were investigated using size exclusion chromatography (SEC) and nano-electrospray ionization mass spectrometry (nano-ESI-MS). The elution profiles from size exclusion chromatography of the venoms from Oxyuranus microlepidotus and Oxyuranus scutellatus were similar. Fractions corresponding to the trimeric toxins were treated with guanidinium hydrochloride and the individual subunits were separated by HPLC. In this report we present the size exclusion chromatography profiles for these toxins, and the nano-ESI mass spectra of the subunits after separation by HPLC: the first such comparative study of these toxins at the protein level. Data in this article are associated with the research article published in Toxicon: "Insight into the subunit arrangement and diversity of paradoxin and taipoxin" (J.A. Harrison, J.A. Aquilina, 2016).