What are the most important features and functions of GC-MS software for environmental analysis?

There are two types of data acquisition: SCAN and SIM. Scan will allow an analyst to monitor all compounds within a certain range of m/z ratios. An analyst typically uses SIM to select particular m/z ratios of targeted compounds. While SIM does not provide information on all compounds in a sample, it will provide an analyst better sensitivity.

In addition to SIM and SCAN, most single-quads will allow you to acquire in a dual mode, where the acquisition is split between SIM and SCAN. This gives analysts the ability to collect high-sensitivity SIM data for quantitative measurements and SCAN data to identify non-targets within samples. For triple quad systems, the same modes apply, plus various others, including MRM. This is where the first quad, Q1, runs in SIM to filter out a precursor fragment, the collision cell, or Q2, fragments the precursor to smaller fragment (known as the product) and Q3 runs in SIM to detect the fragment. This offers one of the highest sensitivity and selectivity detection capabilities for quadrupole-based mass spec.

Just to add, In a scan mode the software allows you to set quant ions such as quant 1, 2 and 3. The selection of quant ions allows better identification.

Data acquisition modes are highly dependent on the type of MS that is used. For example, older-technologies will trade off scanning ability for sensitivity (SIM), while MS/MS will be used solely for their sensitivity and the blindness to non-targets will be used almost exclusively to increase sample run times. In contrast, TOFMS systems do not have to sacrifice the ability to see unknowns for either sensitivity or speed, providing a totally different perspective to environmental analysis - the ability of seeing unexpected non-targets.

GC-MS is a powerful and quantitative technique that provides information through SCAN and SIM data acquisition modes. To acquire high-quality data, the operator needs to be aware of the boiling points of the analytes and their compatibility with the type of columns used in the instrument. The length and type of the column material play crucial roles in the separation and elution of the analytes from the column with increasing temperature and analysis time.

Routine environmental analysis is extremely dependent on software routines to maximize the productivity of the laboratory. Many laboratories use MS/MS platforms as a starting point as the data scarcity for non-targets gives the software a tremendous boost when it comes to data processing. Since the target analytes are already known, the need for advanced data processing routines is greatly reduced and the whole operation can be streamlined. In contrast, where a more general environmental analysis is required, more advanced deconvolution, alignment and comparison algorithms are required as often the data sets are far larger and more complex.

Data processing becomes more straightforward when acquired correctly. The process involves noise reduction and peak integration to determine the quantity of analytes, with MS confirming the m/z ratio, essentially serving as a fingerprint for a specific analyte. The position of the internal standard on the chromatogram validates the quality of the data.

Too often analysts blindly trust their software to provide the correct analyte identification. MS/MS users often have an edge here as their method validation protocols should automatically remove doubt in the identification process. For more generalized environmental analyses, the data interpretation becomes much more complex and library matches are not sufficient. Where standards cannot be used to establish the retention times of analytes, using a software platform that can reject automated analyte identifications due to incorrect retention indices will greatly assist the laboratory and increase sample throughput.