A gel-free proteomic-based method for the characterization of Bordetella pertussis clinical isolates

► We describe a direct gel-free enzymatic method for B. pertussis proteomes. ► We describe an antibody-affinity capture method for B. pertussis proteomes. ► Information is useful for possible B. pertussis strain differentiation. ► Information is useful for possible improved B. pertussis diagnostics and vaccine. ► Methods described are applicable to characterization of other microbial proteomes.