Binner

Binner annotates and clusters degenerate features in untargeted electrospray ionization (ESI)-LC-MS metabolomics data to improve compound annotation, data reduction, and pattern exploration.

Key Features:

• Implementation: Java-based application that processes numerical feature tables exported from preprocessing software such as XCMS or MZmine.
• Feature clustering: Groups closely eluting, highly correlated metabolite features into clusters representing related ion species.
• Pairwise correlations and mass differences: Computes pairwise correlations and mass differences among clustered features to reveal relationships such as adducts and neutral losses.
• Putative annotations: Generates putative annotations linking features to isotopes, adducts, and in-source fragments to aid interpretation.
• Degenerate feature elimination: Detects and removes degenerate signals arising from isotopes, adducts, and in-source fragments common in untargeted ESI-LC-MS data.
• Adduct and neutral loss cataloging: Catalogs complex adducts and neutral losses to facilitate data reduction and exploration of ionization-generated patterns.

Scientific Applications:

• Compound annotation improvement: Enhances accuracy of compound identification by prioritizing correctly annotated principal ions and reducing incorrectly annotated features.
• Platform applicability: Applicable to untargeted analyses performed with reversed-phase LC-MS and hydrophilic interaction chromatography (HILIC).
• Benchmarking and validation: Validated on human plasma datasets where it increased the number and accuracy of annotations compared with three similar tools.
• Data reduction and pattern discovery: Facilitates recognition of molecular interactions and previously unrecognized adduct/neutral-loss patterns in complex datasets.

Methodology:

Processes numerical feature tables from XCMS or MZmine, clusters closely eluting highly correlated features, computes pairwise correlations and mass differences, generates putative annotations, detects and eliminates degenerate features (isotopes, adducts, in-source fragments), and catalogs adducts and neutral losses.