Single-walled-carbon-nanohorns (SNH) exhibit huge application prospects. Notably, spherical SNH possess different morphology from conventional carbon nanotubes (CNT). However, there is a tremendous lack of studies on the nanotoxicity and mechanism of SNH, and their comparison with nanotubes. Here, the dissimilarity between SNH and CNT is found in nano-protein interaction. To validate the potential protein-mediated membrane disturbance caused by different nanocarbons, LC-MS/MS based on LFQ proteomics technology is utilized to compare the differences of total cellular proteins after different nanocarbon incubations and evaluate the impact of nanocarbons on protein expressions.The incubation concentrations of nanocarbons were normalized to assure the identical intracellular amount of nanomaterials.