Gas Chromatography/Mass Spectrometry-Based Metabonomics - Proteomic and Metabolomic Approaches to Biomarker Discovery - page 132

TABLE 1 Strengths and Limitations of GC/MS-Based Metabonomics

Strengths Limitations

1. High chromatographic resolution and sensitivity
Enable chromatographic resolution of endogenous
metabolites and their detection at low concentration levels
Two-dimensional GC (GC

1. Requires sample derivatization
Prolongs sample preparation, yields artifact, and damages
column

GC) further augments
chromatographic resolution and detection of metabolites

2. Excellent MS reproducibility
EI ionization produces characteristic fragmentation
patterns of analytes and aids structural identi

2. Metabolite coverage (sample bias)
Limited to analytes that are volatile, thermally stable, or
amenable to GC/MS analysis through derivatization cation of

metabolites

3. Availability of public or commercial databases facilitates
metabolite identi

3. Low throughput
Sample preparation involving drying and derivatization is
time-consuming and labor-intensive
Chromatographic analysis time is relatively long

cation
Examples include NIST, Wiley mass spectral databases,
Fiehn GC/MS metabolomics library, HMDB, and GMD

4. Derivatization extends the metabolic coverage 4. Metabolite identi cation

A major challenge if the identities of metabolites are not
available in database or pure metabolite standards are not
commercially available or synthesizable

5. Potential for drift in chromatographic and mass
spectrometer performance

samples of bladder cancer (BC) patients from
non-BC subjects based on urine odor, 39 our
group set forth to investigate the role of
GC/MS-based metabonomics in the diagnosis
of human BC. 33 As urine is in close contact
with bladder carcinoma, it was hypothesized to
be a suitable and relevant matrix for the investi-
gation. In this study, which comprises 24 BC
patients and 51 non-BC controls, OPLS-DA
revealed distinct urinary metabolic signatures
of the two groups of subjects and the model
was validated using permutation tests and
receiver operating characteristic (ROC) analysis
( Figure 2 ). Although further validation is
required using a larger study population, the
pilot study uncovered a set of marker metabo-
lites such as uridine, glycerol, senecioic acid,
and fructose responsible for differentiating BC
from non-BC subjects.
Apart from the detection of disease
biomarkers, GC/MS-based metabonomics

employed in pharmaceutical toxicological stud-
ies. The Consortium for Metabonomic Toxi-
cology (COMET), comprising scientists from
the Imperial College of London and several
pharmaceutical companies, evaluated compre-
hensively the usefulness of metabonomics in
preclinical toxicological screening. 40,41 Although
NMR was adopted as the analytical platform by
COMET, many studies have adopted GC/MS
for the evaluation of drug toxicity. 17,42,43 In
a study conducted by Ohta et al., 43 untargeted
LC/MS- and GC/MS-based metabonomics were
evaluated in Fischer 344 rats as a means to gain
further insights into the molecular pharma-
cology and toxicology of feno brate. Using the

global metabonomic approach, the investigators
sieved out a novel panel of perturbed metabo-
lites related to the pharmacology and toxi-
cology of feno brate. 43 Apart from identifying

toxicity markers and elucidating the mechanism
of toxicity, GC/MS-based metabonomics also is