5 Conclusions
We have shown that proteogenomic analysis is beneficial in the assessment of the virulence of P. larvae . The concept that we present is that diversity/variations in successful identifications from draft genome assemblies may be a factor underlying differences among strains. However, such an analysis is not appropriate for all types of samples. The method is useful in that proteogenomic search is performed on a high-quality MS/MS dataset of the exoprotein fraction of different type strains. That dataset, although composed of different genotypes, serves in the first step as one source of data, and interstrain differences in the proteome are not considered; however, the success of the decoy database components is considered. In the next step, the differences in identifications are used for the identification of expression differences among the type strains. Finally, the unique differences in the identification success of databases and protein markers that were mined from proteome differences are connected. This study provided novel markers that could be further studied. Our findings support the idea that many differently virulent strains can exist and may not be limited to the current ERIC I–V genotypes. Various P. larvae strains have specificities that make them unique and different from ERICs. Finally, we stress the importance of sharing high-quality proteomics data, making them available for multiple reanalyses, since we also reused previously reported MS/MS data. Secondary data evaluation using an alternative approach and/or updated databases may provide alternative interpretations and identify novel markers.