When preparing your extracts for analysis, it is important to know which instrument to use and why you should be using that specific one. Of course, we know that each EPA method dictates which analysis instrument must be used within each method, however, we will be determining why that option was chosen in the first place in this blog post!


    Let’s start with the characteristics of the kinds of compounds that are analyzed by gas chromatography/mass spectrometry (GC-MS). By gas chromatography, the analytes need to be converted into the gaseous state in order to be carried by the heated carrier gas. This means that the compounds analyzed by GC-MS must have a relatively low boiling point, so they can be put into their gaseous state easily. The intent is to use enough heat to convert the compounds into the gaseous phase, but not so much heat that the compounds degrade from the level of heat applied to them.


    Now, we are moving onto the characteristics of liquid chromatography/mass spectrometry (LC-MS). The nature of the chromatography is in the name just as gas chromatography. The nice aspect of LC-MS is that the analytes are already in a liquid after concentration, so heat is not required during the chromatography. However, the liquid needs to be converted into a gas in order to be analyzed by the mass spectrometer. When analyzing by GC-MS, compounds are already in the gaseous phase when they exit the column and enter the source of the mass spectrometer, where they are ionized before detection (by electron ionization (EI) or the more gentle chemical ionization (CI)). On the other hand, LC-MS needs to convert the liquid leaving the column into the gaseous phase, and the analytes into ions before entering the mass spectrometer for analysis to be effective. This is achieved using atmospheric pressure ionization (API). API techniques are used for a wide range of compounds, polar and non-polar, volatile and non-volatile, and large or small. For larger molecules like peptides, and compounds that are already ionized in the liquid phase, electrospray ionization (ESI) is used. A high voltage is applied, and aided by a nebulizing gas, creates a spray. Next, the ions move onto the desolvation step which pulls away all the uncharged material and shrinks the charged droplets. As they continue to shrink, the droplets eventually move into the gaseous phase ending with the final step, ionization. In APCI (atmospheric pressure chemical ionization) nebulization occurs in a very hot chamber and the heat evaporates the droplets to a point where they turn into the gas phase. A corona discharge is used to ionize the analyte molecules (similar to chemical ionization in GC-MS). This is generally used for smaller, neutral molecules, both polar and non-polar.

    Compare and Contrast

    The only downfall with GC-MS is that some compounds are subject to thermal decomposition, so the chromatography may not be very appealing or helpful in analysis. Gas chromatography is a much harsher means for analyzing compounds, but it is effective for analysis. As we know, we can only analyze compounds a certain way based on the EPA method we are following, but LC-MS can be used for a wide range of compounds with many different characteristics.

    The sample preparation side of GC-MS and LC-MS also differs greatly. GC-MS requires your compounds to be in a non-polar solvent, where LC-MS requires your compounds in polar solvents. When extracting water samples, it is clear that if there is some residual water within a sample going onto the LC-MS that it is okay. LC-MS is a water-friendly analysis technique due to the fact that water-miscible solvents are used by the instrument (carrier solvents) throughout the time the extract goes through the LC-MS. However, an additional step must be done before concentration when putting extracts onto the GC-MS. The GC-MS does not like water at all! It destroys the column and could really ruin your day…that is why the extract drying step is so important when using GC-MS for analysis. There is always some residual water in any water extract, but if you are running the extract to analyze by GC-MS then it is very important to make sure that you use sodium sulfate or our DryDisk® to dry your sample extracts. Depending on the EPA method you are following, sodium sulfate may be a requirement that your lab must stick to. However, if the EPA method you are following does not have any guidelines indicating that you must use sodium sulfate to dry your extracts, then I recommend the DryDisk® because they are much easier to use than sodium sulfate because there is no baking or special disposal needed!

    For more information on the DryDisk® system for high throughput extract drying, follow the link below!

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