Osteoporosis is a common disease among older people, especially postmenopausal women. Calcium supplementation is effective in decreasing the occurrence of osteoporosis. We tested the effect of different calcium sources (i.e., calcium carbonate chew, milk mineral chew, milk drink and placebo chew) by direct mass spectrometry (dMS) profiling and cathepsin K measurement in the serum of subjects. The dMS method is promising for plasma biomarker discovery, and cathepsin K level in the plasma is an indicator for osteoporosis. Our result shows that dMS detected characteristic ion peaks after different calcium supplement interventions; ion peak 4281.0 m/z was commonly inhibited by all three treatments. This ion peak was identified to be a fragment of follistatin-related protein 3 precursor by means of the "Lift" mode of MS/MS. The other differential ion peaks were also successfully identified: 1786.5 m/z (upregulated after calcium carbonate chew) was shown to be one fragment of transcription factor jun-B; the parent protein of 3504.7 m/z (upregulated after milk drink) was a collagen alpha-2 (type I) chain precursor; the ion peak of 3359.6 m/z (downregulated after milk mineral chew) was one fragment of family 31 glucosidase. Cathepsin K is significantly inhibited only by calcium carbonate chew treatment, indicating this form of calcium supplement has some advantage over other sources of supplementation.