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Comparison of GC-MS and GC×GC-MS in the analysis of human serum samples for biomarker discovery.

Publication ,  Journal Article
Winnike, JH; Wei, X; Knagge, KJ; Colman, SD; Gregory, SG; Zhang, X
Published in: J Proteome Res
April 3, 2015

We compared the performance of gas chromatography time-of-flight mass spectrometry (GC-MS) and comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) for metabolite biomarker discovery. Metabolite extracts from 109 human serum samples were analyzed on both platforms with a pooled serum sample analyzed after every 9 biological samples for the purpose of quality control (QC). The experimental data derived from the pooled QC samples showed that the GC×GC-MS platform detected about three times as many peaks as the GC-MS platform at a signal-to-noise ratio SNR ≥ 50, and three times the number of metabolites were identified by mass spectrum matching with a spectral similarity score Rsim ≥ 600. Twenty-three metabolites had statistically significant abundance changes between the patient samples and the control samples in the GC-MS data set while 34 metabolites in the GC×GC-MS data set showed statistically significant differences. Among these two groups of metabolite biomarkers, nine metabolites were detected in both the GC-MS and GC×GC-MS data sets with the same direction and similar magnitude of abundance changes between the control and patient sample groups. Manual verification indicated that the difference in the number of the biomarkers discovered using these two platforms was mainly due to the limited resolution of chromatographic peaks by the GC-MS platform, which can result in severe peak overlap making subsequent spectrum deconvolution for metabolite identification and quantification difficult.

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Published In

J Proteome Res

DOI

EISSN

1535-3907

Publication Date

April 3, 2015

Volume

14

Issue

4

Start / End Page

1810 / 1817

Location

United States

Related Subject Headings

  • Signal-To-Noise Ratio
  • Serum
  • Humans
  • Gas Chromatography-Mass Spectrometry
  • Chromatography, Gas
  • Biomarkers
  • Biochemistry & Molecular Biology
  • 34 Chemical sciences
  • 31 Biological sciences
  • 06 Biological Sciences
 

Citation

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MLA
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Winnike, J. H., Wei, X., Knagge, K. J., Colman, S. D., Gregory, S. G., & Zhang, X. (2015). Comparison of GC-MS and GC×GC-MS in the analysis of human serum samples for biomarker discovery. J Proteome Res, 14(4), 1810–1817. https://doi.org/10.1021/pr5011923
Winnike, Jason H., Xiaoli Wei, Kevin J. Knagge, Steven D. Colman, Simon G. Gregory, and Xiang Zhang. “Comparison of GC-MS and GC×GC-MS in the analysis of human serum samples for biomarker discovery.J Proteome Res 14, no. 4 (April 3, 2015): 1810–17. https://doi.org/10.1021/pr5011923.
Winnike JH, Wei X, Knagge KJ, Colman SD, Gregory SG, Zhang X. Comparison of GC-MS and GC×GC-MS in the analysis of human serum samples for biomarker discovery. J Proteome Res. 2015 Apr 3;14(4):1810–7.
Winnike, Jason H., et al. “Comparison of GC-MS and GC×GC-MS in the analysis of human serum samples for biomarker discovery.J Proteome Res, vol. 14, no. 4, Apr. 2015, pp. 1810–17. Pubmed, doi:10.1021/pr5011923.
Winnike JH, Wei X, Knagge KJ, Colman SD, Gregory SG, Zhang X. Comparison of GC-MS and GC×GC-MS in the analysis of human serum samples for biomarker discovery. J Proteome Res. 2015 Apr 3;14(4):1810–1817.
Journal cover image

Published In

J Proteome Res

DOI

EISSN

1535-3907

Publication Date

April 3, 2015

Volume

14

Issue

4

Start / End Page

1810 / 1817

Location

United States

Related Subject Headings

  • Signal-To-Noise Ratio
  • Serum
  • Humans
  • Gas Chromatography-Mass Spectrometry
  • Chromatography, Gas
  • Biomarkers
  • Biochemistry & Molecular Biology
  • 34 Chemical sciences
  • 31 Biological sciences
  • 06 Biological Sciences