Introduction

GC-MS provides a versatile analytical technique for the analysis of chemical substances involved in virtually all sectors in economic and social development: trade, mineral exploitation, medicine, food, water and environment, to highlight just a few. It has the capacity to play a pivotal role in providing both qualitative and quantitative scientific data that will aid and catalyse development so that sustainable policies can be formulated and their implementation monitored. Provision of quality water is a major challenge in the developing world and so is the challenge of providing quality analytical data which will be directly addressed through an increase in the capacity in analytical chemistry. This will, as a result, create and sustain chemical monitoring and the management of activities. This is achievable by the provision of hardware (laboratories and equipment) but also in parallel, the training of scientifically qualified and practically trained human resources. Many countries are unfortunately poor in both aspects and GC-MS instruments are still scarce in these laboratories!

For example, in Africa activities are diverse, including transportation, mining, manufacturing, food and agriculture, drugs and pharmaceuticals, tourism and wildlife. The identification of materials for the processing industries impacts on the custom duty revenues. Similarly, any suspected drugs of abuse, for example cocaine need to be identified. This leads to forensic laboratory capacity for which MS data will lead to success in the prosecution of offenders. The same facility will find applications in the detection of both human and wildlife chemical poisoning, for the identification of chemicals used, which ultimately leads to policy adjustments/formulation to reduce the possibility of chemical misuse. The agricultural sector uses chemicals for pest control, including animal pest and disease control. GC-MS should be the technique of choice for the identification of organic chemicals which are volatile at the instrument operating temperatures.

For the safety of food, destined for both the local and export market, regular surveillance of chemical residues is very important. The pharmaceutical industrial sector is growing rapidly in Africa. Although the main equipment used in their laboratories are UV-visible and infrared spectrophotometers alongside liquid chromatographs, some pharmacopeia protocols require GC analysis. The industry would benefit from access to GC-MS, particularly with headspace sampling for conducting analysis, for example, of residual solvents in raw materials. GC-MS is an important tool for the testing of materials, maintenance of standards and specifications of products.

The areas of pollution and environmental contamination of air, water and soil would benefit significantly from GC-MS analysis. Recently the occurrence of cancer related mortalities in the region has greatly increased. The relevant laboratories in the areas of the world with the mandate for environmental pollution analysis do not have GC-MS and LC-MS capabilities. The identification of organic pollutants in the environment within Africa currently remains a significant challenge.

Crude oil has recently been discovered within the African region and commercial drilling and exploitation are ongoing or expected to commence soon. This will result in increased potential environmental pollution and the development of related industries creating further potential issues. GCMS is a vital tool to the petroleum and petrochemicals industries.

Provision of instrumentation without the consideration of maintenance, spare parts, consumables, power stabilisers and back-up solutions, only results in instruments in institutional laboratories gathering dust, constantly devaluing and being of no benefit to anybody. Instruments will continue to be unavailable to benefit the region if there is no well thought-out plan for procurement and importation, installation and qualification, servicing and maintenance and finally decommissioning. Locally available and institutional staff with a reasonable skill level in GC-MS maintenance must be available for the instrument to have the expected impact on society. GC-MS training workshops and other training for scientists and technical staff will go a long way to address this issue.

Gas chromatography is an analytical separation technique, used to separate and detect chemical components in a sample mixture, which are usually organic compounds and gases, otherwise known as analytes, with molecular weights below 1250 u. A column is used to perform the separation, with the mobile phase being a gas, while the stationary phase may be a solid or a liquid coated on the inside of the column or held (immobilised) on a solid support packed into the column. The sample components need to be in the gas phase during the chromatographic separation process, as components will preferentially elute through the column at a rate determined by their affinity for the stationary phase. The requirements for analytes to be analysable using GC are that they:

• Must be volatile enough to be vaporised and move through the GC at operational temperatures below 480 °C, although most common GCs do not operate above 350 °C. Some analytes can be modified to form volatile derivatives that are GC amenable.

• Be thermally stable and not decompose at the temperature required to vaporise the sample.

• Should not undergo reactions with the stationary or mobile phases or be broken down by any flow-path components during the analysis.

• Should give a signal with the detection system and be visible above the limit of detection of the method at the lowest concentration required.

• Interact reversibly with the stationary phase and not be irreversibly adsorbed in the system.

The role of chromatography is to separate the components of a complex mixture while the detection system gives a signal as each of the components elute from the column. In cases in which the above mentioned conditions cannot be satisfied, then gas chromatographic analysis will not be the best analytical technique. Other techniques include liquid chromatography, spectrophotometric, isotopic, nuclear and electroanalytical analyses.

Problem analytes include those that are thermally labile, have a high molecular weight, are present at trace levels or are active in the system, being irreversibly adsorbed or broken down thermally or catalytically. Some of these analytes may still be analysed using GC, however more care is needed when choosing, optimising and maintaining the analytical system. For example, thermally labile analytes could be introduced using a cold injection technique. Explosives are analysed by optimising the method with temperatures as low as possible for each parameter and ensuring the system is as clean as possible to prevent activity.

Available detection systems for GC include selective and non-selective detectors, of which there are many! Non-selective detectors respond to specific bulk properties of the molecules, for example thermal conductivity. Selective detectors respond to specific properties unique to a class of molecules, such as specific elements, bonds, functional groups, electron capture capability, the combustion of organic molecules to give specific radiation or ions with a mass to charge ratio. All detectors have varying sensitivities and dynamic ranges. Universal detectors are good for observing most organic compounds in a sample, whereas selective detectors can reduce matrix interferences and improve detection limits.

Mass spectrometry is an analytical technique that can be used to identify unknown analytes, quantify known analytes and determine the structural and chemical properties of molecules, usually organic. The mass selective detector (mass spectrometer) gives the mass to charge ratio of ions produced by the molecules eluting from the GC column. This means that the two systems need to be coupled or interfaced so that each can operate under optimal conditions of pressure and temperature. The mass spectrometer operates under reduced pressure (vacuum) while GC separation takes place under pressures higher than atmospheric pressure. The mass spectrometer is comparatively more expensive to acquire than the flame ionisation (FID), thermal conductivity (TCD) or electron capture (ECD) detectors. However, the mass spectrometer has the advantage of unequivocal identification of the molecules as they elute from the column. In some cases, the molecular ion is not detected because it fragments as soon as it is formed. The fragmentation pattern of a compound is unique, like a fingerprint. It may be used for identification of the analyte through mass spectral interpretation and a library of mass spectra can be built. The availability of library spectra is a useful tool in qualitative analysis for the fast identification of analytes through library searching. Only a fraction of the molecules that enter the ion source in the mass spectrometer are converted into ions. Compared to selective detectors, for example ECD, only the most modern MS instruments can now approach the lower detection limits for some analytes. It is also important to note that the MS does not distinguish between many isomers and therefore the retention time of the analyte on the GC column, if the isomers have been separated chromatographically, is important for identification.

This book is not a book on mass spectrometry, there are plenty of those out there which you may like to reference. Nor is it a book on GC, sample prep or analytical statistics – there are plenty of these out there too. This is a book written around the concept of the “How do I…?” question, taking the reader from the start of their analysis to the final conclusion. The start of any method is the sample, thinking about how it is collected, transported to the laboratory and stored, ready for analysis. Then, the analysis itself including how to prepare the sample, how to introduce the sample onto the GC column, how to separate the components and how to detect those components. The final step is data analysis, how to find out what the components are, how much of each component is present and report the findings with confidence. Underlying all of this is the GC-MS instrument itself which needs maintenance and troubleshooting to keep it fully operational and to keep giving the correct answers. So how do I select the best techniques for my application? How do I develop and optimise my method so that it is robust and gives the correct answers? How do I look after my instrument?

This book has been written by authors with a significant amount of experience of performing and teaching GC-MS all over the world, including in Africa, and who understand the challenges that analysts face when it comes to solving problems using analytical science. It should be a useful guide for anyone who is called upon to solve problems via the application of GC-MS in any country. It will help the reader to develop their GC-MS knowledge in a practical way and not just learn how the techniques work but how to get their instrument working with high quality, robust methods and keep it working.