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

To demonstrate the potential of iterative strain-level identification, we compared TaxIt against classic comprehensive search strategies based on non-iterative taxonomic identification supported by either unique PSMs or the abundance similarity correction of Pipasic 44 . The final selections of the top taxa candidates for all samples and all three compared identification strategies are summarized in Table 1 . For the cowpox sample, identification results agree the most. TaxIt (Figure 2) and Pipasic (Supplementary item 1 - Figure S1 ) are both able to identify the expected Cowpox virus (Brighton Red) strain. However, unique PSMs are limited to the parent Cowpox virus species and not available at the strain level. For this reason, an incorrect identification of Bat astrovirus Hil GX bszt12 could occur based on a single unique PSM (Supplementary item 1 -Figure S1 ). The results also show that the original TaxIt counts are not an All rights reserved. No reuse allowed without permission.