The typical workflow of metabolomics studies is shown in the figure. First, samples are collected from tissue, plasma, urine, saliva, cells, etc. Next, metabolites are extracted often with the addition of internal standards and derivatization. During sample analysis, metabolites are quantified (
liquid chromatography or
gas chromatography coupled with
MS and/or
NMR spectroscopy). The raw output data can be used for metabolite feature extraction and further processed before statistical analysis (such as
principal component analysis, PCA). Many bioinformatic tools and software are available to identify associations with disease states and outcomes, determine significant correlations, and characterize metabolic signatures with existing biological knowledge.
Separation methods Initially, analytes in a metabolomic sample comprise a highly complex mixture. This complex mixture can be simplified prior to detection by separating some analytes from others. Separation achieves various goals: analytes which cannot be resolved by the detector may be separated in this step; in MS analysis,
ion suppression is reduced; the retention time of the analyte serves as information regarding its identity. This separation step is not mandatory and is often omitted in NMR and "shotgun" based approaches such as
shotgun lipidomics.
Gas chromatography (GC), especially when interfaced with mass spectrometry (
GC-MS), is a widely used separation technique for metabolomic analysis. GC offers very high chromatographic resolution, and can be used in conjunction with a
flame ionization detector (GC/FID) or a mass spectrometer (GC-MS). The method is especially useful for identification and quantification of small and volatile molecules. However, a practical limitation of GC is the requirement of chemical derivatization for many biomolecules as only volatile chemicals can be analysed without derivatization. In cases where greater resolving power is required, two-dimensional chromatography (
GCxGC) can be applied.
High performance liquid chromatography (HPLC) has emerged as the most common separation technique for metabolomic analysis. With the advent of
electrospray ionization, HPLC was coupled to MS. In contrast with
GC, HPLC has lower chromatographic resolution, but requires no derivatization for polar molecules, and separates molecules in the liquid phase. Additionally HPLC has the advantage that a much wider range of analytes can be measured with a higher sensitivity than GC methods.
Capillary electrophoresis (CE) has a higher theoretical separation efficiency than HPLC (although requiring much more time per separation), and is suitable for use with a wider range of metabolite classes than is GC. As for all electrophoretic techniques, it is most appropriate for charged analytes. In direct-infusion mass spectrometry (DI-MS), sample is directly introduced into the spectrometer and separation steps are skipped. DI-MS can be employed to perform single cell metabolic analysis of human cells.
Detection methods Mass spectrometry (MS) is used to identify and quantify metabolites after optional separation by
GC,
HPLC, or
CE.
GC-MS was the first hyphenated technique to be developed. Identification leverages the distinct patterns in which analytes fragment. These patterns can be thought of as a mass spectral fingerprint. Libraries exist that allow identification of a metabolite according to this
fragmentation pattern . MS is both sensitive and can be very specific. There are also a number of techniques which use MS as a stand-alone technology: the sample is infused directly into the mass spectrometer with no prior separation, and the MS provides sufficient selectivity to both separate and to detect metabolites. For analysis by mass spectrometry, the analytes must be imparted with a charge and transferred to the gas phase.
Electron ionization (EI) is the most common ionization technique applied to GC separations as it is amenable to low pressures. EI also produces fragmentation of the analyte, both providing structural information while increasing the complexity of the data and possibly obscuring the molecular ion.
Atmospheric-pressure chemical ionization (APCI) is an atmospheric pressure technique that can be applied to all the above separation techniques. APCI is a gas phase ionization method, which provides slightly more aggressive ionization than ESI which is suitable for less polar compounds.
Electrospray ionization (ESI) is the most common ionization technique applied in LC/MS/MS especially with triple quadrupole mass spectrometers where multiple reaction monitoring (MRM) or untargeted MRM can be performed. This soft ionization is most successful for polar molecules with ionizable functional groups. Another commonly used soft ionization technique is
secondary electrospray ionization (SESI). In the 2000s, surface-based mass analysis has seen a resurgence, with new MS technologies focused on increasing sensitivity, minimizing background, and reducing sample preparation. The ability to analyze metabolites directly from biofluids and tissues continues to challenge current MS technology, largely because of the limits imposed by the complexity of these samples, which contain thousands to tens of thousands of metabolites. Among the technologies being developed to address this challenge is Nanostructure-Initiator MS (NIMS), a desorption/ ionization approach that does not require the application of matrix and thereby facilitates small-molecule (i.e., metabolite) identification.
MALDI is also used; however, the application of a MALDI matrix can add significant background at that complicates analysis of the low-mass range (i.e., metabolites). In addition, the size of the resulting matrix crystals limits the spatial resolution that can be achieved in tissue imaging. Because of these limitations, several other matrix-free desorption/ionization approaches have been applied to the analysis of biofluids and tissues.
Secondary ion mass spectrometry (SIMS) was one of the first matrix-free desorption/ionization approaches used to analyze metabolites from biological samples. SIMS uses a high-energy primary ion beam to desorb and generate secondary ions from a surface. The primary advantage of SIMS is its high spatial resolution (as small as 50 nm), a powerful characteristic for tissue imaging with MS. However, SIMS has yet to be readily applied to the analysis of biofluids and tissues because of its limited sensitivity at and analyte fragmentation generated by the high-energy primary ion beam.
Desorption electrospray ionization (DESI) is a matrix-free technique for analyzing biological samples that uses a charged solvent spray to desorb ions from a surface. Advantages of DESI are that no special surface is required and the analysis is performed at ambient pressure with full access to the sample during acquisition. A limitation of DESI is spatial resolution because "focusing" the charged solvent spray is difficult. However, a recent development termed
laser ablation ESI (LAESI) is a promising approach to circumvent this limitation. Most recently, ion trap techniques such as
orbitrap mass spectrometry are also applied to metabolomics research.
Nuclear magnetic resonance (NMR) spectroscopy is the only detection technique which does not rely on separation of the analytes, and the sample can thus be recovered for further analyses. All kinds of small molecule metabolites can be measured simultaneously - in this sense, NMR is close to being a universal detector. The main advantages of NMR are high analytical reproducibility and simplicity of sample preparation. Practically, however, it is relatively insensitive compared to mass spectrometry-based techniques. Although NMR and MS are the most widely used modern-day techniques for detection, there are other methods in use. These include
Fourier-transform ion cyclotron resonance,
ion-mobility spectrometry, electrochemical detection (coupled to HPLC),
Raman spectroscopy and radiolabel (when combined with thin-layer chromatography). == Statistical methods ==