To cite the XCMS package in publications use:

  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)

A BibTeX entry for LaTeX users is

  @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},
  }

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

A BibTeX entry for LaTeX users is

  @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},
  }

  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)

A BibTeX entry for LaTeX users is

  @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},
  }

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