Proteomics has great potential in discovering potential biomarkers for several diseases that could aid in diagnosis and management of diseases. Blood plasma is usually used as it remains in contact with nearly all cells of the organism and is also easily accessible. After immuno-depletion of the abundant proteins, identification of low abundant proteins that are differentially expressed in diseased conditions compared to healthy controls is achieved through various quantitative techniques.
Both unlabelled and labelled approach could be used. The unlabelled approach is promising. We compared Sequential windowed acquisition of all theoretical fragments (SWATH-MS unlabelled) to the isobaric tag for relative and absolute quantitation (iTRAQ). We observed that SWATH had the advantage of quantifying a larger percentage of low abundance proteins (below 60 ppm). We believe that SWATH's ability to quantify low abundant proteins could aid in biomarker discoveries.