compareMS2

compareMS2 compares sets of tandem mass spectra to compute pairwise spectral distances and derive distance matrices for clustering, species and tissue identification, and molecular phylogenetic reconstruction.

Key Features:

• Annotation-free pairwise comparison: Performs pairwise comparisons of tandem mass spectra without requiring annotated spectra, enabling use of all acquired data.
• Dot-product distance metric: Computes spectra dot products and derives a distance metric by analyzing dot-product distributions and inverting shared-peptide fractions.
• Molecular phylogenetics: Reconstructs phylogenetic trees from pairwise spectral distances derived from enzymatically digested proteins.
• Application to tryptic digests: Has been applied to tryptic digests from primate species to reconstruct phylogenetic relationships.
• Species and mixture identification: Calculates distances between sets of spectra for species identification and mixture characterization in food and feed.
• Multiple comparison metrics: Includes a newly introduced metric for spectral comparison in addition to existing metrics.
• File format support: Accepts Mascot Generic Format (MGF) inputs and exports distance matrices and common image formats.
• Proteomics–phylogenetics integration: Integrates proteomic spectral data with molecular phylogenetic techniques to contextualize protein evolution and inter‑species comparisons.

Scientific Applications:

• Phylogenetic analysis: Reconstructs phylogenetic trees to infer evolutionary relationships from proteomic data.
• Species and tissue identification: Identifies species or tissues from tandem mass spectra for authentication and quality control.
• Sample clustering: Clusters samples based on spectral similarity for comparative analyses.
• Mixture characterization: Characterizes and deconvolves sample mixtures in contexts such as food and feed analysis.
• Quality control: Supports quality control and authentication of biological and processed samples using proteomic profiles.

Methodology:

Performs pairwise comparisons of tandem mass spectra by computing spectra dot products, analyzes dot-product distributions to estimate shared-peptide fractions and inverts these into a distance metric, and processes Mascot Generic Format (MGF) input to produce distance matrices and image outputs.