Mass spectrometry is being increasingly used in biomarker research mainly due to its ability to achieve high selectivity coupled with high sensitivity. This dissertation focuses on quantitative mass spectrometric investigations of two protein biomarkers i.e. serum thymidine kinase 1 (TK1) and human osteopontin (OPN). First part of this research was focused on developing a liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) method for measuring the activity of TK1 in serum by monitoring the conversion of a TK1 specific exogenous substrate, 3’-deoxy-3’-fluorothymidine (FLT), to its mono-phosphorylated form 3’-deoxy-3’-fluorothymidine monophosphate (FLT-MP). A method to quantify FLT-MP on LC-MS/MS was developed and validated. The method was linear over the range of 2.5-2000 ng/mL with a mean correlation coefficient of 0.9935. Using the developed method, serum TK1 activity was measured in serum from hepatocellular carcinoma (HCC) patients and age-matched controls under standardized conditions. A sub-population of the HCC patient samples showed an almost 20-fold enhanced TK1 activity compared to the controls. A method was developed and validated for quantifying human osteopontin from plasma using immunoaffinity isolations coupled with microflow liquid chromatography and tandem mass spectrometry (MFLC-MS/MS). A biologically relevant tryptic peptide ‘GDSVVYGLR’ which is unique to hOPN was identified and used as a signature peptide for this method. The method was validated over a range of 25-600 ng/mL. The performance of the method was compliant with USFDA validation guidance. In addition, a stable isotope labeled (SIL) peptide GDSVVYGLR* and an extended SIL peptide TYDGRGDSVV*YGLRSKSKKF’ were evaluated as internal standards (IS) to account for signature peptide digestion instability and variability. In the digestion variability studies, the use of extended SIL peptide as internal standard limited the total variability within ±30%. Alternatively, when SIL peptide was used as internal standard the variability ranged from -67.4% to +50.6 %. The applicability of the validated method was demonstrated by analyzing plasma samples obtained from 10 healthy individuals and 10 breast cancer patients. More than 9-fold increase in the mean plasma hOPN concentration was seen in 30% of the breast cancer patient samples (n=10) in comparison to the healthy volunteer samples. In a proof of concept investigation, a stable isotope labeled signature peptide was evaluated as an internal standard to compensate for immunocapture variability during quantification of human osteopontin (hOPN) by immunoaffinity coupled LC-MS/MS. Immunocapture variability was induced by varying the antibody amount per well. The immunocapture variability ranged from -80.9 % to +77.0 % when the IS was added after immunocapture and from -37.5% to +20.3% when the IS was added before immunocapture. The lower variability demonstrates the ability of SIL-IS peptide to compensate for variation during immunocapture.