BAFinder

BAFinder identifies unknown bile acids in LC-MS/MS datasets acquired in positive and negative electrospray ionization (ESI) modes by using MS/MS fragmentation patterns to annotate and structurally characterize bile acids.

Key Features:

• Ionization modes: Operates with LC-MS/MS data acquired in both positive and negative electrospray ionization (ESI) modes.
• Reference standards: Leverages MS/MS fragmentation patterns derived from 84 bile acid reference standards across both ionization modes.
• Expanded coverage: Includes oxidized bile acids and sugar conjugates in the annotation repertoire.
• Peak processing: Performs peak alignment and grouping of candidate features based on their respective positive or negative modes.
• Spectral matching: Searches representative MS/MS spectra against an MS/MS library using characteristic product ions and neutral losses.
• Novel identification: Facilitates recognition of bile acids not previously cataloged in the MS/MS library.
• Structural reporting: Reports number of hydroxyl groups and double bonds, conjugation status, and isomer configurations for identified bile acids.
• Confidence scoring: Assigns annotation confidence levels across four tiers.
• Validation results: Annotated 112 bile acids in human plasma (75 confirmed) and 244 bile acids in urine (111 confirmed).

Scientific Applications:

• Untargeted metabolomics bile acid identification: Identification and annotation of unknown bile acids in LC-MS/MS untargeted metabolomics datasets.
• Bile acid profiling in biofluids: Profiling bile acid composition in human plasma and urine as demonstrated by validation results.
• Database expansion: Recognition and annotation of bile acids absent from existing MS/MS libraries, including oxidized and sugar-conjugated forms.
• Structural elucidation: Determination of hydroxylation, unsaturation, conjugation status, and isomer configurations from MS/MS data.

Methodology:

Performs peak alignment and grouping by ionization mode, extracts representative MS/MS spectra, searches those spectra against an MS/MS library, and annotates using characteristic product ions and neutral losses informed by MS/MS fragmentation patterns from 84 reference standards.