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Hinrichs Lab - Gas chromatography coupled to mass spectrometry (GC-MS)


GC-MS is an instrumental technique by which complex mixtures of volatile, dominantly organic compounds are separated, identified and, if needed, quantified. In order to be analyzed by GC-MS, compounds must be sufficiently volatile and thermally stable. MS detection enables the determination of molecular masses of target compounds and the elucidation of their molecular structure. The latter can be deduced from the specific fragmentation patterns that organic compounds show upon bombardment with fast electrons in an MS ion source. This mode is called electron ionization (EI) under which sample molecules lose an electron resulting in a molecular ion (M+., radical cation). Due to the high amount of energy (70 eV) impacted to the molecular ion it usually fragments producing further smaller ("daughter") ions with characteristic relative abundances that provide a "fingerprint" for that molecular structure. Using searchable data bases, this information helps to identify compounds of interest and supports structural elucidation of unknown components.

In the Hinrichs Lab four GC-MS couplings exist: three regular ones and one online pyrolysis GC-MS system (see below). Two of the four GC-MS systems are additionally equipped with FIDs so that the GC effluents can be split to both detectors, the MS and the FID. This offers the simultaneous determination of concentration and molecular structure in one analytical run.

Pyrolysis GC-MS is an instrumental method that enables the characterization of the intractable and involatile macromolecular complexes found in virtually all materials in the natural environment. Instead of the direct injection of organic compounds in a solvent, a low amount (few mg) of sample material (sediment, soil, plant type etc.) or in the case of materials with a high organic carbon content such as cell biomass even less is analyzed directly. Samples are heated for a few seconds in a quartz chamber under a given atmosphere (oxic, anoxic, hydrogen or methane loaded) and eventually elevated pressure. This results in a heat mediated cleavage of chemical bonds within the macromolecular structures of interest producing a suite of low molecular weight chemical moieties. The resulting mixture of compounds is then swept onto the analytical column of the GC and MS detection is performed as described above. The final composition is indicative of the specific types of macromolecular organic matter analyzed (lignin, cellulose, peptidoglycan etc.).

For some macromolecules it is desireable to introduce a chemical reagent that, upon heating, will react with the macromolecule in a more directed manner, e.g. the preferential cleavage of ester domains, to produce a mixture of derivatized low molecular weight moieties in a process known as thermally assisted chemolysis. Typical reagents that are used include tetramethylammonium hydroxide (TMAH) and trimethylsulfonium hydroxide (TMSH).

Thermo Scientific Trace DSQ II

The Thermo Scientific Trace DSQ II is a highly sensitive, dual-stage quadrupole benchtop GC-MS instrument with a scanning mass range from m/z 1 to 1050. The Trace GC is fitted with two injectors (PTV and S/SL) and a AS3000 autosampler to facilitate high sample throughput. The system operates in electron ionization (EI) mode but does have the additional capacity for chemical ionization (CI).

Thermo Quest Trace MS

The Thermo Quest Trace MS is a sensitive, single quadrupole benchtop GC-MS instrument with a mass range from m/z 2 to 1023. It is fitted with a S/SL injector and operates in EI mode. It does have additional capacity for CI. A AS3000 autosampler is fitted to the Trace GC to facilitate high sample throughput. We have added an FID to the system to routinely switch over from MS to FID or to run both in parallel.

Agilent GC-MSD (5973)

The single quadrupole benchtop Agilent GC-MS containing a 6890 GC and a 5973 MSD is the "work-horse" instrument in our group for characterizing fractions and complex mixtures of GC-amenable organic compounds. It is operating in EI mode only and has a full scan capacity from m/z 2 to 800. It is equipped with a S/SL injector and a 7683B autosampler. Due to its robust ion source, it is routinely used to screen total lipid extracts (TLEs) or sample fractions for unknown compounds.

Agilent pyrolysis GC-MSD (5975)

The Agilent online thermal desorption-high pressure pyrolysis GC-MS instrument is a single quadrupole benchtop system containing a CDS Pyroprobe 5000 Series unit, a 7890 GC, and a 5975 MSD with a mass range from m/z 2 to 1050. The GC is fitted with a 7683B autosampler, two injectors (S/SL and on-column), and a FID. A Deans Switch enables the GC effluent to be split to the MS and FID. This system is used to analyze volatiles as well as macromolecular materials on the basis of their thermal compositional fingerprints. Pyrolysis can be performed with inert and reactive gases (hydrogen, oxygen, methane) and pressures up to 3.4 MPa.