reconstructed ion chromatogram

A normal mass spectrometric data set consists of full mass spectra recorded sequentially in time as sample is admitted to the ion source, either from a direct-insertion probe or from a chromatograph (for example, GC/MS). The total ion current  trace is the sum of ion abundances in each mass spectrum plotted versus time. Clearly each mass spectrum will also  contain a pattern of molecular and fragment ions. Ions of  these particular masses can be specified, and the data system  can plot the scan-by-scan abundances of these specific ions  versus time, which is known as a reconstructed ion chromatogram. The reconstructed ion chromatogram can be used to identify all ions that belong together in a single mass spectrum by virtue of their coincident peaks in time (and discriminate against background ions), and can also be used to screen a GC/MS run for related classes of compounds by reconstruction of ion chromatograms for common structurally specific ions.