Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow

Data
independent acquisition-mass spectrometry (DIA-MS) coupled
with liquid chromatography is a promising approach for rapid, automatic
sampling of MS/MS data in untargeted metabolomics. However, wide isolation
windows in DIA-MS generate MS/MS spectra containing a mixed population
of fragment ions together with their precursor ions. This precursor-fragment
ion map in a comprehensive MS/MS spectral library is crucial for relative
quantification of fragment ions uniquely representative of each precursor
ion. However, existing reference libraries are not sufficient for
this purpose since the fragmentation patterns of small molecules can
vary in different instrument setups. Here we developed a bioinformatics
workflow called MetaboDIA to build customized MS/MS spectral libraries
using a user’s own data dependent acquisition (DDA) data and
to perform MS/MS-based quantification with DIA data, thus complementing
conventional MS1-based quantification. MetaboDIA also allows users
to build a spectral library directly from DIA data in studies of a
large sample size. Using a marine algae data set, we show that quantification
of fragment ions extracted with a customized MS/MS library can provide
as reliable quantitative data as the direct quantification of precursor
ions based on MS1 data. To test its applicability in complex samples,
we applied MetaboDIA to a clinical serum metabolomics data set, where
we built a DDA-based spectral library containing consensus spectra
for 1829 compounds. We performed fragment ion quantification using
DIA data using this library, yielding sensitive differential expression
analysis.