This data article restrains data associated to the Choudhary et al. [1]. Nemopilema nomurai Jellyfish venom (NnV) can lead to cardiac toxicity. Here we analyzed the effect of NnV on rat cardiomyocytes cell line H9c2 at the proteome level using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). This analysis resulted in 34 proteins with differential expression. Here we provide the dataset for the proteins with amplified or reduced level as compare to control.