Updates to xcms: simplified raw data access and enhanced MS level > 1 capabilities

The xcms Bioconductor package is one of the standard toolboxes for the preprocessing of untargeted metabolomics data. Here we present recent updates to xcms, which re-use and build upon the support for memory-efficient parallel processing capabilities in the MSnbase Bioconductor software package for proteomics and general mass spectrometry data handling.

We have improved large-scale experiment data analysis through memory- efficient parallel processing capabilities and simplify raw spectra data access throughout the whole preprocessing task. This comprises also dedicated functionality to extract ion chromatograms/traces from the original files and to perform chromatographic peak detection directly on such chromatographic data. Besides paving the road for MRM/SRM data analysis with xcms, it also allows to evaluate different peak detection settings on selected signals before applying them to the whole data set. Along these lines, we also implemented new visualization capabilities aiding in the definition and evaluation of data set- specific settings for the various preprocessing algorithms. Finally, import of MRM/SRM raw data has been added and a framework for the identification of MS2 spectra for identified chromatographic peaks was implemented.