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Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data

Gengbo Chen¹, Scott Walmsley^2,3, Gemmy C M Cheung^4,5

¹Saw Swee Hock School of Public Health, National University of Singapore , Singapore, Singapore 117547.

Analytical Chemistry

|April 11, 2017

Summary

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MetaboDIA builds custom MS/MS spectral libraries for untargeted metabolomics. This bioinformatics workflow enhances quantification accuracy using data independent acquisition-mass spectrometry (DIA-MS) data.

Area of Science:

Metabolomics
Mass Spectrometry
Bioinformatics

Background:

Data independent acquisition-mass spectrometry (DIA-MS) is vital for untargeted metabolomics, but wide isolation windows complicate MS/MS spectra analysis.
Accurate quantification requires MS/MS spectral libraries to map precursor-fragment ions, yet existing libraries lack versatility across instrument setups.
Fragmentation patterns of small molecules can vary, necessitating customized spectral libraries for reliable analysis.

Purpose of the Study:

To develop MetaboDIA, a bioinformatics workflow for building customized MS/MS spectral libraries.
To enable MS/MS-based quantification using DIA data, complementing traditional MS1-based methods.
To allow spectral library construction directly from DIA data for large sample studies.

Main Methods:

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Developed the MetaboDIA bioinformatics workflow.
Built customized MS/MS spectral libraries using user-generated data dependent acquisition (DDA) data.
Performed MS/MS-based quantification on DIA data using the generated libraries.
Applied MetaboDIA to marine algae and clinical serum metabolomics datasets.

Main Results:

Quantification using customized MS/MS libraries yielded results comparable to MS1-based precursor ion quantification.
A DDA-based spectral library of 1829 compounds was constructed for a clinical serum metabolomics dataset.
Fragment ion quantification with DIA data and the custom library enabled sensitive differential expression analysis.

Conclusions:

MetaboDIA provides a robust method for creating tailored MS/MS spectral libraries.
The workflow enhances the accuracy and reliability of quantitative metabolomics using DIA-MS.
MetaboDIA facilitates sensitive differential expression analysis in complex biological samples.