Abstract
Metabolite identification is an important step in non-targeted metabolomics and requires different steps. One involves the use of tandem mass spectrometry to generate fragmentation spectra of detected metabolites (LC-MS/MS), which are then compared to fragmentation spectra of known metabolites.
Here we present recent updates to xcms that enable LC-MS/MS data analysis. For experiments employing data dependent acquisition (DDA), MS2 spectra can be identified and extracted for each detected chromatographic peak or feature thus facilitating an improved compound annotation. For data independent acquisition (DIA) data such as SWATH data, xcms allows to perform chromatographic peak detection on MS2 data and reconstruct MS2 spectra for MS1 chromatographic peaks by matching MS2 chromatographic peaks to MS1 chromatographic peaks based on the correct isolation window and chromatographic peak shape correlation.