An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples

Mathias Kuhring; Joerg Doellinger; Andreas Nitsche; Thilo Muth; Bernhard Y. Renard

ranular taxonomic relation cannot be ascertained from the NCBI taxonomy, we expect the Beaudette strains to feature a considerably closer relationship as compared to other Infectious bronchitis virus strains. Therefore, we consider the draw between Beaudette strains as sufficiently appropriate strain identification. For the unique-PSMs-based strategy, we observed a poor availability of unique PSMs at the strain level. While the exploitation of purely unique features is a common theme for species-level identification, the low amount of unique PSMs in strains is insufficient for strain-level inference. However, the frequency of All rights reserved. No reuse allowed without permission.