XCMS

XCMS is an R package for metabolite profiling using liquid chromatography/mass spectrometry (LC-MS) data. XCMS can preprocess data for high-throughput, untargeted analyte profiling. A web-based version is available at Xcms web.

Topic

Metabolomics

Detail

  • Operation: Chromatogram visualisation;Label-free quantification;Validation;Filtering;Chromatographic alignment;Peak detection;Mass spectrum visualisation

  • Software interface: Command-line user interface

  • Language: R, C, C++

  • License: GNU GPL 2

  • Cost: Free

  • Version name: 3.16.1

  • Credit: -

  • Input: Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files.

  • Output: -

  • Contact: sneumann at ipb-halle.de

  • Collection: -

  • Maturity: Mature

Publications

  • XCMS Online: a web-based platform to process untargeted metabolomic data.
  • Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G. XCMS Online: a web-based platform to process untargeted metabolomic data. Anal Chem. 2012 Jun 5;84(11):5035-9. doi: 10.1021/ac300698c. Epub 2012 May 10. PMID: 22533540; PMCID: PMC3703953.
  • https://doi.org/10.1021/ac300698c
  • PMID: 22533540
  • PMC: PMC3703953
  • Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data
  • Benton HP, Want EJ, Ebbels TM. Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data. Bioinformatics. 2010 Oct 1;26(19):2488-9. doi: 10.1093/bioinformatics/btq441. Epub 2010 Jul 29. PMID: 20671148.
  • https://doi.org/10.1093/bioinformatics/btq441
  • PMID: 20671148
  • PMC: -
  • Highly sensitive feature detection for high resolution LC/MS
  • Tautenhahn R, Böttcher C, Neumann S. Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics. 2008 Nov 28;9:504. doi: 10.1186/1471-2105-9-504. PMID: 19040729; PMCID: PMC2639432.
  • https://doi.org/10.1186/1471-2105-9-504
  • PMID: 19040729
  • PMC: PMC2639432

Download and documentation

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