MetDIA: Targeted Metabolite Extraction of Multiplexed MS/MS Spectra Generated by Data-Independent Acquisition

With
recent advances in mass spectrometry, there is an increased
interest in data-independent acquisition (DIA) techniques for metabolomics.
With DIA technique, all metabolite ions are sequentially selected
and isolated using a wide window to generate multiplexed MS/MS spectra.
Therefore, DIA strategy enables a continuous and unbiased acquisition
of all metabolites and increases the data dimensionality, but presents
a challenge to data analysis due to the loss of the direct link between
precursor ion and fragment ions. However, very few DIA data processing
methods are developed for metabolomics application. Here, we developed
a new DIA data analysis approach, namely, MetDIA, for targeted extraction
of metabolites from multiplexed MS/MS spectra generated using DIA
technique. MetDIA approach considers each metabolite in the spectral
library as an analysis target. Ion chromatograms for each metabolite
(both precursor ion and fragment ions) and MS2 spectra
are readily detected, extracted, and scored for metabolite identification,
referred as metabolite-centric identification. A minimum metabolite-centric
identification score responsible for 1% false positive rate of identification
is determined as 0.8 using fully 13C labeled biological
extracts. Finally, the comparisons of our MetDIA method with data-dependent
acquisition (DDA) method demonstrated that MetDIA could significantly
detect more metabolites in biological samples, and is more accurate
and sensitive for metabolite identifications. The MetDIA program and
the metabolite spectral library is freely available on the Internet.