Metabolomics Data Processing Using XCMS

XCMS is one of the most used software for liquid chromatography–mass spectrometry (LC-MS) data processing and it exists both as an R package and as a cloud-based platform known as XCMS Online. In this chapter, we first overview the nature of LC-MS data to contextualize the need for data processing software. Next, we describe the algorithms used by XCMS and the role that the different user-defined parameters play in the data processing. Finally, we describe the extended capabilities of XCMS Online.