Pathogens are known to release in their environment a large range of toxins and 
other virulence factors. Their pathogenicity relies on this arsenal of 
exoproteins and their orchestrated release upon changing environmental 
conditions. Exoproteomics aims at describing and quantifying the proteins found 
outside of the cells, thus takes advantage of the most recent methodologies of 
next-generation proteomics. This approach has been applied with great success to 
a variety of pathogens increasing the fundamental knowledge on pathogenicity. In 
this chapter, we describe how the exoproteome should be prepared and handled for 
high-throughput identification of exoproteins and their quantitation by 
label-free shotgun proteomics. We also mentioned some bioinformatics tools for 
extracting information such as toxin similarity search.