The xcms software is a well established R package for the preprocessing of LC-MS-based untargeted metabolomics data. By extensively refactoring the package and re-using functionality and mass spectrometry (MS) data representation strategies from the MSnbase package for proteomics data analysis, xcms gained native MS/MS support. We recently added support for LC-MS/MS data in xcms: for data dependent acquisition (DDA) data, MS2 spectra can be identified and extracted for each detected chromatographic peak (chrom peak) or feature. For data independent acquisition (DIA) data such as SWATH data, xcms allows to perform chromatographic peak detection on MS2 data and reconstruct MS2 spectra. MS1 chrom peaks are matched to MS2 based on peak shape correlations. The recent changes in xcms, particularly the support for LC-MS/MS data analysis, facilitate an improved compound annotation for untargeted metabolomics experiments.