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The advent of the post genomics era coupled with advances in proteomics presents unprecedented opportunities for expedited discovery of microbial targets for subsequent development of novel modalities for management of infectious diseases. Here, we review a new application of proteomics called Proteomics-based Expression Library Screening (PELS). This functional proteomics tool permits rapid definition of comprehensive microbial immunoproteomes (microbial proteins expressed in vivo that elicit and interact with the host humoral immune response), a subset of which have excellent potential as diagnostic, drug and vaccine targets. PELS is a platform technology that is applicable to any sequenced pathogen. It offers several advantages over existing methods for global identification of immunogenic microbial proteins, and is both a rapid alternative and an adjunct to emerging protein antigen array/chip technologies.