Informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography and high-resolution mass spectrometry (GCxGC-HRMS)

Stephen E. Reichenbach, Xue Tian, Qingping Tao, Edward B. Ledford, Zhanpin Wu, Oliver Fiehn

Research output: Contribution to journalArticle

57 Scopus citations

Abstract

Abstract: This paper describes informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography (GCxGC) and high-resolution mass spectrometry (HRMS). GCxGC-HRMS analysis produces large data sets that are rich with information, but highly complex. The size of the data and volume of information requires automated processing for comprehensive cross-sample analysis, but the complexity poses a challenge for developing robust methods. The approach developed here analyzes GCxGC-HRMS data from multiple samples to extract a feature template that comprehensively captures the pattern of peaks detected in the retention-times plane. Then, for each sample chromatogram, the template is geometrically transformed to align with the detected peak pattern and generate a set of feature measurements for cross-sample analyses such as sample classification and biomarker discovery. The approach avoids the intractable problem of comprehensive peak matching by using a few reliable peaks for alignment and peak-based retention-plane windows to define comprehensive features that can be reliably matched for cross-sample analysis. The informatics are demonstrated with a set of 18 samples from breast-cancer tumors, each from different individuals, six each for Grades 1-3. The features allow classification that matches grading by a cancer pathologist with 78% success in leave-one-out cross-validation experiments. The HRMS signatures of the features of interest can be examined for determining elemental compositions and identifying compounds.

Original languageEnglish (US)
Pages (from-to)1279-1288
Number of pages10
JournalTalanta
Volume83
Issue number4
DOIs
StatePublished - 2011

Keywords

  • Biomarker discovery
  • Cheminformatics
  • Comprehensive two-dimensional gas chromatography
  • High-resolution mass spectrometry
  • Metabolomics
  • Sample classification

ASJC Scopus subject areas

  • Chemistry(all)

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