Although the field of mass spectrometry-based proteomics is still in its infancy, recent developments in targeted proteomic techniques have left the field poised to impact the clinical protein biomarker pipeline now more than at any other time in history. for proteomics to meet its potential for finding biomarkers, clinicians, statisticians, epidemiologists and chemists must work together in an interdisciplinary approach. These interdisciplinary efforts will have the greatest chance for success if participants from each discipline have a basic working knowledge of the other disciplines. To that end, the purpose of this review is to provide a nontechnical overview of the emerging/evolving roles that mass spectrometry (especially targeted modes of mass spectrometry) can play in the biomarker pipeline, in hope of making the technology more accessible to the broader community for biomarker discovery efforts. Additionally, the technologies discussed are broadly applicable to proteomic studies, and are not restricted to biomarker discovery.