Comparison of GC-MS and GC×GC-MS
in the Analysis
of Human Serum Samples for Biomarker Discovery
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Abstract
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 <i>R</i><sub>sim</sub> ≥ 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