SpectroGene

SpectroGene performs top-down proteogenomic analysis to improve bacterial genome annotation by identifying proteoforms and unannotated genes from intact-protein tandem mass spectrometry data.

Key Features:

• Top-Down Proteogenomics Approach: Utilizes intact protein analysis via top-down tandem mass spectrometry rather than peptide-centric bottom-up methods.
• Six-Frame Genome Translation: Searches spectra against the six-frame translation of a genome to enable proteogenomic discovery.
• Discovery of Unannotated Genes: Identifies previously unannotated genes within bacterial genomes by detecting protein evidence not present in existing annotations.
• Comprehensive Proteoform Identification: Aims to identify nearly all proteoforms in a sample, matching or exceeding identifications from searches against annotated proteomes.
• Addresses Bottom-Up Limitations: Targets challenges unmet by conventional bottom-up mass spectrometry through intact-protein analysis.

Scientific Applications:

• Refinement of Bacterial Genome Annotation: Provides protein-level evidence to correct or extend existing bacterial genome annotations.
• Proteogenomic Studies: Supports studies requiring precise mapping between genome sequences and expressed proteoforms.
• Proteoform Diversity Characterization: Enables comprehensive characterization of proteoform diversity within bacterial proteomes.
• Biological Insight and Therapeutic Research: Contributes protein-level discoveries that can inform biological mechanisms and potential therapeutic strategies.

Methodology:

Performs intact-protein top-down tandem mass spectrometry analysis with searches against six-frame translated genome sequences and comparisons to annotated proteomes by analyzing complete protein spectra.