Highlights UHPLC-ESI-MS/MS method for quantitative amino acids analysis in cells developed Data-independent acquisition allows simultaneous untargeted metabolic profiling PLS reveals a correlation between metabolic profiles and toxicity of ILs The most toxic ILs tested were [P 4441 ][OAc], [P 14444 ][OAc] and [P 14444 ]Cl LC-MS metabolic profiling seems to be a useful strategy to classify the toxicity of ILs