To cite the XCMS package in publications use:

Philippine Louail, Carl Brunius, Mar Garcia-Aloy, William Kumler, Norman Storz, Jan Stanstrup, Hendrik Treutler, Pablo Vangeenderhuysen, Michael Witting, Steffen Neumann, and Johannes Rainer: xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem Analytical Chemistry, (2025),<doi:10.1021/acs.analchem.5c04338>

Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.: XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)

Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)

H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)

Some functions (e.g. group.mzClust, findPeaks.MSW() or retcor.obiwarp() use 3rd party algorithms, see manpages and related packages for respective citations.

Corresponding BibTeX entries:

  @Article{,
    author = {Philippine Louail and Carl Brunius and Mar Garcia-Aloy
      and William Kumler and Norman Storz and Jan Stanstrup and Hendrik
      Treutler and Pablo Vangeenderhuysen and Michael Witting and
      Steffen Neumann and Johannes Rainer},
    title = {xcms in Peak Form: Now Anchoring a Complete Metabolomics
      Data Preprocessing and Analysis Software Ecosystem},
    journal = {Analytical Chemistry},
    year = {2025},
    doi = {10.1021/acs.analchem.5c04338},
    url = {https://doi.org/10.1021/acs.analchem.5c04338},
  }

  @Article{,
    author = {{Smith} and {C.A.} and {Want} and {E.J.} and {O'Maille}
      and {G.} and {Abagyan,R.} and {Siuzdak} and {G.}},
    title = {XCMS: Processing mass spectrometry data for metabolite
      profiling using nonlinear peak alignment, matching and
      identification},
    journal = {Analytical Chemistry},
    year = {2006},
    volume = {78},
    pages = {779--787},
  }

  @Article{,
    author = {Ralf Tautenhahn and Christoph Boettcher and Steffen
      Neumann},
    title = {Highly sensitive feature detection for high resolution
      LC/MS},
    journal = {BMC Bioinformatics},
    year = {2008},
    volume = {9},
    pages = {504},
  }

  @Article{,
    author = {H. Paul Benton and Elizabeth J. Want and Timothy M. D.
      Ebbels},
    title = {Correction of mass calibration gaps in liquid
      chromatography-mass spectrometry metabolomics data},
    journal = {BIOINFORMATICS},
    year = {2010},
    volume = {26},
    pages = {2488},
  }