A short history of XCMS

XCMS is an open-source, platform-independent R-package that was developed to perform untargeted metabolite profiling with LC/MS. XCMS reads and processes LC/MS data stored in netcdf , mzXML, mzData and mzML files. It provides method for peak picking, non-linear retention time alignment, visualization, relative quantization and statistics. XCMS is capable of simultaneously preprocessing, analyzing, and visualizing the raw data from hundreds of samples.  The original XCMS paper published in 2006 was cited more than 270 times (Google Scholar, 11/12/2010).
Colin Smith initially developed XCMS in 2004.  In 2008 Steffen Neumann and Ralf Tautenhahn joined the development team and later in 2009 Paul Benton. Today, XCMS contains two methods for LC/MS feature detection and a method for peak detection in single high-res spectra (FTICR, MALDI, DIMS). Two different non-linear retention time correction methods are available, and  two methods to group  LC/MS features.   A separate method is implemented to align single high-res spectra using a moving-window technique. Mass spectra, TICs, EICs and EIC overlays, 3D LC/MS surface plots and boxplots can be generated by XCMS.  Methods to read and preprocess MS/MS data are available. XCMS can make use of multicore processors, as well as MPI or SNOW clusters to speed up the data processing.  XCMS is now widely used for untargeted metabolomics, metabolic profiling and  biomarker discovery.

 Spring    2004: Added methods for reading and displaying raw data from NetCDF files (Colin)
Summer    2004: Developed methods for kernel density peak grouping and LOESS retention time alignment (Colin)
Fall      2004: Developed matched filter peak picker, EIC generation (Colin)
March     2005: Checked into Bioconductor SVN repository (Colin)
December  2005: mzXML, mzData import added (Colin)
April     2007: centWave peak detection added (Ralf)
November  2007: Reading of MS/MS spectra added (Steffen)
January   2008: single spectra alignment method added (Steffen)
July      2008: Multiprocessor peak picking added via MPI (Ralf)
March     2009: OBI-Warp retention time alignment added (Steffen, Ralf)
April     2009: group nearest alignment method added (Steffen, Ralf)
June      2010: gap filler/stitch method added (Paul)
September 2010: 64 bit support added (Steffen, Ralf)