Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species.

ABSTRACT: In bottom-up proteomics, selecting an appropriate protein amino acid sequence database is vital for reliable peptide identification. However, this approach excludes species with unsequenced genomes, limiting the comprehensiveness. This is a major challenge in current microbiota proteomics, a rapidly developing field, which involves simultaneously assigning proteins to species in a sample and analyzing them using databases of protein amino acid sequences with known genomes. We aimed to develop a method to extend the database species diversity by generating protein amino acid sequences of unknown species using phylogenetic relationships among known species. To evaluate this approach, we generated the Helicobacter pylori F16 strain sequence based on the phylogenetic relationships of 29

SUBMITTER: Miura N 

PROVIDER: S-EPMC12167054 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature