Table 2 Pros, cons and sample types of the main metabolomic technologies for the analysis of cancer metabolism
From: To metabolomics and beyond: a technological portfolio to investigate cancer metabolism
Method | Pros | Cons | Sample types |
|---|---|---|---|
Gas chromatography-Mass spectrometry (GC-MS) | • High sensitivity for volatile metabolites • High-resolution separation • Analysis of different groups of metabolites simultaneously • Large linear range | • Long sample preparation (derivatization step for non-volatile metabolites) • Thermolabile compounds cannot be analysed • Slow dynamic range speed • Slow analysis | • Cultured cells • Supernatant • Biofluids • Tissues • Organoids |
Liquid chromatography-Mass spectrometry (LC-MS) | • Simple and fast sample preparation (derivatization not usually required) • Wide coverage of metabolites • Thermolabile compounds can be analysed • High sensitivity • Soft ionization | • Ion suppression • Expensive • Slow analysis | • Cultured cells • Supernatant • Biofluids • Tissues • Organoids |
Capillary electrophoresis-Mass spectrometry (CE-MS) | • Low sample volume • High resolution • Rapid analysis • No derivatization required | • Affected by salt • Low stability compared to GM- and LC-MS • Poor reproducibility and sensitivity | • Cultured cells • Supernatant • Biofluids • Tissues • Organoids |
Direct infusion-Mass spectrometry (DI-MS) | • High-throughput • Simple data processing | • Do not distinguish the isomers | • Supernatant • Biofluids |
Matrix-assisted laser desorption ionization-Mass spectrometry (MALDI-MS) | • Low sample volume • Fast analysis • High tolerance towards salts • Suitable for high MW metabolites • Non-destructive | • Low reproducibility • Hard identification due to complex matrix | • Cultured cells • Supernatant • Biofluids • Tissues • Organoids |
Mass spectrometry imaging (MSI) | • In situ detection • Preserve histological integrity | • High resolution is time-consuming • No functional profile | • Cultured cells • Tissues • Organoids |
Direct real-time analysis (DART) | • No sample processing • Direct analysis | • Not suitable for polar compounds | • Supernatant • Biofluids |
Nuclear magnetic resonance (NMR) | • No separation • Structural information • High reproducibility • Fast sample preparation • Non-destructive | • Low sensitivity • Expensive instrument • Some chemical classes are not detected | • Cultured cells • Supernatant • Biofluids • Tissues • Organoids |
Metabolic flux analysis (MFA) | • Quantitative analysis and information on metabolites fate | • Isotope tracing is expensive • Compartment specific flux | • Cultured cells • Tissues • Organoids |
Extracellular flux analysis (EFA) | • Real time measurement • High feasibility • Relatively cheap | • Bulk analysis • Only relative and indirect measurement • Cell purification is required | • Cultured cells • Organoids |
Single-cell RNA-sequencing (scRNAseq) | • Low cell number • High-resolution • Unbiased gene expression analysis • Metabolic phenotype at mRNA level | • Expensive • Temporal discordance between mRNA and protein/functional effect • Do not consider post-transcriptional and post-translational mechanisms | • Cultured cells • Tissues • Organoids |
Single-cell metabolomics (SCM) | • Low cell number • High resolution • High-throughput | • Challenge of combining single cells sorting and metabolism quenching • Need of high sensitivity and throughput analytical platform | • Cultured cells • Tissues • Organoids |
Single-cell energetic metabolism by profiling translation inhibition (SCENITH) | • Functional analysis coupled to large phenotype • Fast and simple sample preparation and analysis | • Only relative and indirect measurement • Not suitable for cells with undetectable level of protein synthesis | • Cultured cells • Tissues • Organoids |
Cytometry by Time-of-flight (CyTOF) | • High-dimensional • High-throughput • Metabolic phenotype at protein level | • Not suitable for weakly expressed markers • Requires advanced biostatistics and bioinformatics | • Cultured cells • Tissues • Organoids |
Met-flow | • Fast and single-cell analysis • Metabolic phenotype at protein level | • Measurements are indirect • No functional profile | • Cultured cells • Tissues • Organoids |
In situ dehydrogenase activity assay | • Single-cell analysis in native microenvironment • Functional profile | • Measurement at saturated substrate concentrations | • Cultured cells • Tissues • Organoids |
Genetic screening | • Precise gene targeting (few off-targets) • Robust signal derived by permanent gene disruption | • Complicated to perform • For some types of studies, it is not good having a permanent gene disruption | • Cultured cells • Organoids |
