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Ramaker RC, Gordon ER, Cooper SJ. R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R. Bioinformatics. 2018;34(10):1789-1791doi: 10.1093/bioinformatics/btx825.
Ramaker, R. C., Gordon, E. R., & Cooper, S. J. (2018). R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R. Bioinformatics (Oxford, England), 34(10), 1789-1791. https://doi.org/10.1093/bioinformatics/btx825
Ramaker, Ryne C, et al. "R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R." Bioinformatics (Oxford, England) vol. 34,10 (2018): 1789-1791. doi: https://doi.org/10.1093/bioinformatics/btx825
Ramaker RC, Gordon ER, Cooper SJ. R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R. Bioinformatics. 2018 May 15;34(10):1789-1791. doi: 10.1093/bioinformatics/btx825. PMID: 29280991; PMCID: PMC6248453.
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Bioinformatics. 2018 May 15;34(10):1789-1791. doi: 10.1093/bioinformatics/btx825.

R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R.

Bioinformatics (Oxford, England)

Ryne C Ramaker, Emily R Gordon, Sara J Cooper

Affiliations

  1. HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
  2. Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.

PMID: 29280991 PMCID: PMC6248453 DOI: 10.1093/bioinformatics/btx825

Abstract

SUMMARY: Comprehensive 2D gas chromatography-mass spectrometry is a powerful method for analyzing complex mixtures of volatile compounds, but produces a large amount of raw data that requires downstream processing to align signals of interest (peaks) across multiple samples and match peak characteristics to reference standard libraries prior to downstream statistical analysis. Very few existing tools address this aspect of analysis and those that do have shortfalls in usability or performance. We have developed an R package that implements retention time and mass spectra similarity threshold-free alignments, seamlessly integrates retention time standards for universally reproducible alignments, performs common ion filtering and provides compatibility with multiple peak quantification methods. We demonstrate that our package's performance compares favorably to existing tools on a controlled mix of metabolite standards separated under variable chromatography conditions and data generated from cell lines.

AVAILABILITY AND IMPLEMENTATION: R2DGC can be downloaded at https://github.com/rramaker/R2DGC or installed via the Comprehensive R Archive Network (CRAN).

CONTACT: [email protected].

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

References

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  2. Anal Chem. 2011 Apr 15;83(8):3058-67 - PubMed
  3. BMC Bioinformatics. 2012 Feb 08;13:27 - PubMed
  4. Nat Rev Drug Discov. 2016 Jul;15(7):473-84 - PubMed

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