Table 2.
Strengths and weaknesses of analytical tools used in metabolomics studies
| Technique | Strengths | Weaknesses |
|---|---|---|
| NMR | • Nondestructive technique | • Low sensitivity (only metabolites with relatively high concentration [micrograms] can be detected) |
| • Versatility for analyzing metabolites in biofluids, tissues, or in vivo | ||
| • Reproducibility and repeatability | • Overlap in peaks and high chemical degeneracy (different metabolites have resonances in the same spectral region) | |
| • More relative quantification | • Identifies mainly polar compounds | |
| • Applicable to intact biomaterial | • Usually large sample size | |
| GC-MS | • High-resolution capacity | • High molecular weight analytes |
| • High spectral resolution | • Derivatization required | |
| • Very sensitive | • Fragmentation in MS | |
| • High mass accuracy to detect compounds | • Requires technical skill | |
| • Reproducible retention time | • Extensive sample preparation steps | |
| • Highly developed compound libraries | • Poor quantification | |
| • Small sample size (50 μl) | • Possible variation due to sample preparation | |
| • High separation efficiency | • Compound degradation (high temperature) | |
| • Ideal for thermostable and volatile and nonpolar metabolites | • Problem with ionization | |
| LC-MS | • Short separation time | • Vaporization errors |
| • High resolution | • More instrumental variables than in NMR and LC-MS | |
| • Ideal for nonvolatile compounds | • High solvent consumption and lower separation power | |
| • Very sensitive (picogram quantities) | • Lower reproducibility (within and across laboratories) | |
| • Reasonable robustness | • Ionization of metabolites | |
| • Selectivity | • Selectivity | |
| • High mass accuracy to detect compounds | • Poor quantification | |
| • Simple sample preparation | • Lower reproducibility for retention time with different system | |
| • Detects a wider range of metabolites than GC-MS | • Destructive to sample | |
| • Analysis of more polar compounds without derivatization | • High instrumental cost | |
| DI-MS/MS | • High throughput | • Matrix effects |
| • Minimal sample preparation | • Lack of differentiation between isomers | |
| • Rapid analysis (1–3 min) | • Lack of accuracy of selection of ions | |
| • Good reproducibility | • Competitive ionization | |
| • Highly sensitive | ||
| • Simpler data analysis than LC-MS and GC-MS | ||
| • Considerable structural information |
Definition of abbreviations: DI-MS/MS = direct infusion tandem mass spectroscopy; GC-MS = gas chromatography-mass spectrometry; LC-MS = liquid chromatography-mass spectroscopy; NMR = nuclear magnetic resonance.