MetaboKit

MetaboKit performs comprehensive compound identification and relative quantification for mass spectrometry-based untargeted metabolomics using DDA and DIA data.

Key Features:

• Customized Spectral Library Construction: Constructs experiment-specific spectral libraries by integrating compound identities from reference spectral libraries with adducts, dimers, in-source fragments (ISFs), MS/MS fragmentation spectra, and retention time data specific to the chromatography system.
• Targeted Peak Integration: Performs targeted peak integration for precursor ions in DDA analyses and for both precursor and product ions in DIA analyses.
• Stringent Identification Algorithm: Requires matches by both MS and MS/MS data to increase specificity and reduce false positives.
• In-Source Fragment Screening: Implements an MS/MS-based screening process for ISFs to reduce unverifiable identifications.
• Quantification Module: Produces peak area values at MS1 and MS2 levels that correlate with known concentrations in DIA analyses and enable quantification when precursor ion chromatograms are noisy.

Scientific Applications:

• Lipid profiling in Cdk1Liv-/- mouse livers: Identified a broad spectrum of lipid species and their ISFs and enabled quantitative reconstruction of the fatty liver phenotype in Cdk1Liv-/- mouse livers.
• Differential abundance in DIA studies: Provided consistent fold change estimates using MS1- and MS2-level peak area data and enabled quantitative comparisons for compounds with noisy precursor ion chromatograms using MS2-level data.

Methodology:

Constructs customized spectral libraries by integrating reference spectral library identities with adducts, dimers, ISFs, MS/MS fragmentation spectra, and retention time; performs targeted peak integration for precursor ions (DDA) and precursor/product ions (DIA); applies a stringent identification algorithm requiring MS and MS/MS matches; conducts MS/MS-based ISF screening; computes peak area values at MS1 and MS2 for quantification.