A new strategy for MS/MS data acquisition applying multiple data dependent experiments on Orbitrap mass spectrometers in non-targeted metabolomic applications

The annotation and identification of metabolites is a current bottleneck in non-targeted metabolomics studies. Although accurate measurement of m/z is applied routinely in UPLC–MS applications to putatively annotate metabolites, the acquisition of MS/MS or MSn data is required to deduce structural information, further reducing the chemical search-space and providing greater confidence in metabolite annotation by comparison to mass spectral databases. Here we propose an innovative new strategy for data dependent acquisition (DDA) for on-line MS/MS data acquisition in parallel to full-scan metabolite profiling on LTQ-Orbitrap mass spectrometers. We recommend the application of different and integrated DDA MS/MS experiments to increase the coverage of unique metabolites for which MS/MS data were acquired. We demonstrate, for the first time, that the integrated application of both CID and higher-energy collisional dissociation ion activation methods, multiple different activation energies and narrow precursor ion m/z ranges of 100 or 300 for acquisition of MS/MS spectra provide complementary information and increases the number of unique metabolites for which MS/MS data is acquired. The strategies herein provide a different approach for data acquisition to increase the number of unique MS/MS mass spectra acquired for metabolite annotation purposes in non-targeted metabolomics studies. MS/MS data are available on request from the corresponding author.