GPMsDB-tk

GPMsDB-tk provides a genomically predicted protein mass database and matching workflow to identify bacterial and archaeal isolates from Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) by predicting protein masses from nearly 200,000 publicly available genomes.

Key Features:

• Database scope: Built from predicted protein masses derived from nearly 200,000 publicly available genomes.
• Predicted-mass matching: Matches MALDI-TOF MS spectra to predicted protein masses rather than relying solely on reference spectral libraries.
• Taxonomic resolution: Enables taxonomic identification of bacteria and archaea at species level and below from measured spectra.
• High accuracy: Demonstrated correct identification of over 90% of measured spectra at species level and below.
• Metagenome integration: Supports incorporation of metagenome-assembled genomes to expand identification of uncultured strains and complex-sample isolates (e.g., mouse feces).
• Broad-spectrum identification: Extends identification capacity to diverse and uncultured microbial isolates not well represented in traditional spectral libraries.

Scientific Applications:

• Metagenomics and environmental microbiology: Identification of uncultured strains and community profiling from metagenomic samples and complex matrices.
• Clinical diagnostics: Species-level microbial identification from MALDI-TOF MS spectra for diagnostic workflows.
• Food safety testing: Detection and taxonomic assignment of bacteria and archaea relevant to food safety monitoring.
• Biotechnology research: Characterization of microbial isolates and discovery of novel strains using predicted-mass matching.

Methodology:

Predict protein masses from genomic sequences, compile them into a large-scale database derived from nearly 200,000 publicly available genomes (including metagenome-assembled genomes), and match MALDI-TOF MS spectra to the predicted masses for taxonomic identification.