Purpose The objective of this study was to quantitatively assess the concentration of human tear proteins in patients wearing contact lenses of various ionicities and determine whether differences were related to the incidence of corneal infiltrative events (CIE). Methods 24 subjects (samples) were randomly selected for spectral count analysis to obtain protein concentrations using LCMS analysis. The subjects were neophyte and ametropic with ages between 18 and 40; 6 wore control lenses, 8 wore TestLens1, and 10 wore TestLens2. 16 subjects experienced CIEs during the study. Results A pairwise multiple hypothesis test identified 7 proteins that significantly differed in concentration between TestLens1 and control, and 11 proteins that differed between TestLens2 and control. Of the 12 unique proteins, 9 were at increased concentration and 3 were at lower concentration in the tears of test lens wearers compared to the control lens group. Bootstrap clustering confirmed these findings, showing 3 similar clusters to the original sample groups which separated people wearing control lenses from those wearing TestLens1 or TestLens2 with 83% accuracy and between TestLens1 and TestLens2 with 45% accuracy. Permutation testing identified 5 proteins that had significantly changed in concentration between people wearing TestLens2 and Control lenses. There was no difference in protein concentrations between those subjects who experienced a CIE and those who did not. Conclusion Wearing contact lenses of different ionicities can affect the concentration of proteins in the tear film. The current study did not find any associations of the concentration of proteins with CIEs. Future tests with increased sample size are needed to establish any relations between these changes and clinical performance.