Figure 2

Common nomenclature. Each portion or summary of an MS run is referred to by a different name. A spectrum contains all points with a single RT value. The sum of signals across all spectra is called the total ion spectrum (TIS). A slice of data containing a contiguous m/z range extending across all RT is called an extracted ion chromatogram (XIC). While the total ion chromatogram (TIC) is the sum of all signals across all m/z, the base peak chromatogram (BPC) is the set containing the most intense signal for each RT across all m/z. An isotope trace is the signal produced by a single ion of a single analyte (i.e., a peptide or a lipid) at a particular charge state. An isotopic envelope trace is the group of isotopic traces produced by a single analyte at a particular charge state. Note that certain terms like peak, feature, and chromatogram, are overloaded in the literature and as such are exceedingly unclear.