A method was developed using enhanced liquid chromatography coupled with electrospray ionization mass spectrometry for the analysis and quantitation of 2 main potato glycoalkaloids, $alpha$-chaconine, and $alpha$-solanine, without any pre-concentration or derivatisation steps. Calibration curves generated by this technique exhibited a linear dynamic range from 0.025 to $50{mu}g/mL$ and from 0.05 to $50{mu}g/mL$ for $alpha$-chaconine and $alpha$-solanine, respectively. Matrix effects were evaluated by comparing calibration curves measured in matrix-matched and solvent-based systems. Ion suppression due to matrix effects was weak and extraction recoveries of 88 to 114% were obtained in different sample matrices spiked with analyte concentrations ranging from 15 to $35{mu}g/mL$. Potatoes that had been genetically modified to tolerate glufosinate contained the same glycoalkaloid levels as their non-transgenic counterpart. We suggest complementing compositional comparison assessment strategy by validating quantitative analytical methods for the toxic glycoalkaloids in potato plants.