In this work, three modified CDs (mCDs), namely 6-deoxy-6-[1-(2-amino)ethylamino]-beta-CD, 6-deoxy-6-[N-(2-methylamino)pyridine)]-beta-CD and 3-monodeoxy-3-monoamino-beta-CD, are investigated as chiral selectors for CE with LIF (CE-LIF) and CE-TOF-MS. The potential of these three mCDs as chiral selectors in CE was also compared with the unmodified beta-CD and gamma-CD. A group of ten different D- and L-amino acids derivatized with FITC was selected as case-study for CE-LIF and CE-MS comparison. The analyte group includes negatively (D/L-Glu and D/L-Asp), neutral (D/L-Ala and D/L-Asn) and positively (D/L-Arg) charged amino acids. Chiral separation conditions compatible with CE-TOF-MS could be achieved based on the figures of merit obtained by CE-LIF using the different CDs. Interestingly, LOD values obtained by chiral CE-TOF-MS were in the nM range comparable or only slightly worse to those obtained by CE-LIF. Moreover, the time of analysis using mCDs was reduced more than 30% compared with the non-chiral conditions (19.2 versus 28.4 min, respectively), with resolution and efficiency values as high as 5.15 and 843 000 plates/m, respectively. The usefulness of this chiral CE-TOF-MS method was corroborated through the detection of the main D- and L-amino acids found in different real samples including transgenic versus wild soy and vinegar.