Proteins and peptides that undergo variations in concentration or state as a result of a biological process or disease may be used as biomarkers for the diagnosis or prognosis of diseases and/or for the monitoring of therapy. Serum/plasma is one of the most easily obtained patient specimens and contains thousands of proteins produced and secreted from cells and tissues. While serum/plasma is a valuable specimen for protein biomarker research, especially in the area of infectious diseases, the dynamic range of the proteome presents a technical challenge. Serum/plasma is dominated by high abundance proteins, such as albumin, immunoglobulins, haptogloblulin, which constitute almost 90% of the total serum/plasma protein by weight and make the detection of the low abundance proteins difficult. Therefore, effective fractionation and separation methods are essential to detect potential biomarker proteins present in small quantities for mass spectrometry.The current tests for blood-borne protozoan diseases are inadequate by monitoring treatment efficacy or for prognosis and also lack sensitivity and specificity. To overcome these limitations, we began a program to develop novel assays for infectious diseases using mass spectrometric data directly as well as "next generation" assays that exploit the richness of the MS data converted to standard platforms. Here we focus on high-throughput fractionation and proteomic analysis using Surface Enhanced Laser Desorption Ionization Time of Flight (SELDI-TOF) mass spectrometry platform. Separation and enrichment is achieved using stepwise anion exchange fractionation prior to analysis on multiple ProteinChip array chemistries. We have used this approach successfully to identify proteins/peptides or protein "profiles" (biomarkers) in subjects chronically infected with blood-borne protozoan parasites (i.e. Chagas disease, babesia, toxoplasma, malaria), fascioliosis, and cysticercosis.