MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics.

ABSTRACT: The global SARS-CoV-2 pandemic emphasized the need for accurate pathogen diagnostics. While genomics is the gold standard, integrating mass spectrometry-based proteomics offers additional benefits. However, current proteomic and genomic reference databases are often biased toward specific taxa, such as pathogenic strains or model organisms, and proteomic databases are less comprehensive. These biases and gaps can lead to inaccurate identifications. To address these issues, we introduce MultiStageSearch, a multistep database search method that combines proteome and genome databases for taxonomic analysis. Initially, a generalist proteome database is used to infer potential species. Then, MultiStageSearch generates a specialized proteogenomic database for precise identification. This databas

SUBMITTER: Pipart J 

PROVIDER: S-EPMC12150323 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature