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.