The XCMS package (including XCMS²) reads and processes LC/MS data stored in NetCDF (AIA/ANDI), mzXML, and mzData files. It includes numerous options for visualizing and interacting with that data. In addition, it includes functionality for peak picking, non-linear retention time alignment, and relative quantitation. It is capable of simultaneously preprocessing, analyzing, and visualizing the raw data from hundreds of samples.

XCMS is distributed by bioconductor and can be downloaded here: Current XCMS Version. The latest cutting edge XCMS can be obtained here: Devel XCMS

XCMS can also be downloaded directly in your R session by copying and pasteing the following code into your R sessionsource("http://bioconductor.org/biocLite.R") biocLite("xcms")