GC-MS detects target compounds by comparing the retention time and relative intensities of ion fragments in unknown samples to those obtained for reference compounds. The collected data are reduced to dedicated windows consisting of selected time slices and mass-to-charge (m/z) ions corresponding to the expected retention times and mass spectral fragments for each target compound. Interfering peaks and background noise can complicate GC-MS data reading because screening methods are designed to detect entire classes of compounds and are not optimized for individual compounds. Furthermore, a single ion fragment may not be unique and might be shared by compounds. These issues limit the use of automated software programs for GC-MS data reading and require that experienced data readers carefully evaluate all data. In contrast, LC-MS/MS and GC-MS/MS measure the relative abundance of precursor/product ion pairs (transitions). Because the likelihood of a target compound and an interfering substance having the same precursor/product ion pairs is relatively small, the data usually are easier to interpret compared to GC-MS data and can be more easily evaluated by computer software.
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