221 Christopher Peacock (ed.), Parasite Genomics Protocols, Methods in Molecular Biology, vol. 1201, DOI 10.1007/978-1-4939-1438-8_13, © Springer Science+Business Media New York 2015 Chapter 13 Protein Microarrays for Parasite Antigen Discovery Patrick Driguez, Denise L. Doolan, Douglas M. Molina, Alex Loukas, Angela Trieu, Phil L. Felgner, and Donald P. McManus Abstract The host serological profile to a parasitic infection, such as schistosomiasis, can be used to define potential vaccine and diagnostic targets. Determining the host antibody response using traditional approaches is hindered by the large number of putative antigens in any parasite proteome. Parasite protein microarrays offer the potential for a high-throughput host antibody screen to simplify this task. In order to construct the array, parasite proteins are selected from available genomic sequence and protein databases using bio- informatic tools. Selected open reading frames are PCR amplified, incorporated into a vector for cell-free protein expression, and printed robotically onto glass slides. The protein microarrays can be probed with antisera from infected/immune animals or humans and the antibody reactivity measured with fluorophore labeled antibodies on a confocal laser microarray scanner to identify potential targets for diagnosis or thera- peutic or prophylactic intervention. Key words Schistosomiasis, Protein microarray, Parasite, Antibody/serum screening, Vaccine and diagnostic discovery 1 Introduction The serological profile of a parasitic disease, such as schistosomiasis, is the result of the interaction between the host’s immune system and exposed parasite antigens. The recognition by and affinity of host antibodies for specific components of the parasite proteome indicates which antigens are accessible to the host immune response. When correlated with disease immunity or severity, these data can provide important information for vaccine and diagnostic target selection. Conventionally, antibody specificity and reactivity against native or recombinant antigens are measured using tech- niques such as ELISA or two-dimensional protein gels but these methods are difficult to adapt for high-throughput screens [1, 2]. Clearly, a protein microarray comprising hundreds to thousands of antigens which can be probed with antisera and individual antigen