Mass spectrometry-based investigation of clinical samples enables the
high-throughput identification of protein biomarkers. We provide an overview of
mass spectrometry-based proteomic techniques that are applicable to the
investigation of clinical samples. We address sample collection, protein
extraction and fractionation, mass spectrometry modalities, and quantitative
proteomics. Finally, we examine the limitations and further potential of such
technologies. Liquid chromatography fractionation coupled with tandem mass
spectrometry is well suited to handle mixtures of hundreds or thousands of
proteins. Mass spectrometry-based proteome elucidation can reveal potential
biomarkers and aid in the development of hypotheses for downstream investigation
of the molecular mechanisms of disease
