We determined the gas-phase acidities of two cysteine-polyalanine peptides, HSCA3 and HSCA4, using a triple-quadrupole mass spectrometer through application of the extended kinetic method with full entropy analysis. Five halogenated carboxylic acids were used as the reference acids. The negatively charged proton-bound dimers of the deprotonated peptides with the conjugate bases of the reference acids were generated by electrospray ionization. Collision-induced dissociation (CID) experiments were carried out at three collision energies. The enthalpies of deprotonation (ΔacidH) of the peptides were derived according to the linear relationship between the logarithms of the CID product ion branching ratios and the differences of the gas-phase acidities. The values were determined to be ΔacidH(HSCA3)=317.3 ± 2.4 kcal/mol and ΔacidH (HSCA4)=316.2±3.9 kcal/mol. Large entropy effects (Δ(ΔS)=13–16 cal/mol K) were observed for these systems. Combining the enthalpies of deprotonation with the entropy term yielded the apparent gas-phase acidities (ΔacidGapp) of 322.1±2.4 kcal/mol (HSCA3) and 320.1±3.9 kcal/mol (HSCA4), in agreement with the results obtained from the CID-bracketing experiments. Compared with that in the isolated cysteine residue, the thiol group in HSCA3,4 has a stronger gas-phase acidity by about 20 kcal/mol. This increased acidity is likely due to the stabilization of the negatively charged thiolate group through internal solvation.