ImShot

ImShot integrates MALDI-IMS and LC-MS (shotgun proteomics) data to assign IMS-detected peptide masses to parent proteins, improving peptide identification and enabling functional enrichment analysis.

Key Features:

• IMS–LC-MS integration: Integrates MALDI-IMS and shotgun proteomics (LC-MS) measurements from serial tissue sections to correlate spatial ion signals with proteomic identifications.
• Deisotoping and search-space refinement: Performs deisotoping of IMS spectra followed by a two-group comparison approach to refine the search space for IMS masses.
• Scoring system for annotation ambiguity: Applies a scoring system to resolve ambiguous peptide annotations and identify the most probable parent protein for each detected IMS peptide.
• Modular LC-MS analysis: Handles LC-MS data independently and generates enrichment analyses and plots for downstream interpretation.
• Functional visualization: Produces visualizations of enriched Gene Ontology terms and cellular pathways linked to LC-MS-derived protein identifications.

Scientific Applications:

• Peptide identification in MALDI-IMS: Assigns peptide masses detected by MALDI-IMS to parent proteins using combined spatial and LC-MS evidence.
• Resolving ambiguous annotations: Disambiguates competing peptide assignments to increase confidence in peptide-to-protein mapping.
• Comparative spatial proteomics: Applies two-group comparisons to detect and refine group-specific IMS mass differences.
• Functional interpretation: Links IMS-detected peptides to proteomic enrichment results for Gene Ontology and pathway-level interpretation.

Methodology:

Integrates IMS and LC-MS measurements from serial sections, performs deisotoping of IMS spectra, applies a two-group comparison to refine the IMS search space, uses a scoring system to resolve peptide annotation ambiguities and assign probable parent proteins, and analyzes LC-MS data to produce enrichment analyses and visualizations of Gene Ontology terms and cellular pathways.