Figure 3

Four types of overlaps between chemically different peptides. The red stars represent the monoisotopic peaks of triplex isotopic clusters of a target peptide. (a) Two isotopic clusters are overlapped, but no isotopic peak is shared. (b) An MS scan in the elution area of ‘HPIKHQGLPQEVLNENLLR’ of which expected ratio is 3:1:1. The red lines represent its theoretical isotopic distribution. Since an isotopic cluster with a different charge value is overlapped with the light-labeled isotopic cluster, the LSQ value becomes significantly high, so we discard this MS scan during the quantification of the target peptide. (c) An MS scan in the elution area of ‘TVGGKEDVIWELLNHAQEHFGK’ of which expected ratio is 3:1:10. An isotopic cluster with the same charge and a higher mass is overlapped with the medium-labeled isotopic cluster. Since the fifth peak increases the LSQ value, only the first to the fourth peaks are used to quantify. (d) An MS scan in the elution area of ‘GITWGEETLMEYLENPK’ of which expected ratio is 3:3:1. An isotopic cluster with the same charge and 1 Da smaller mass is overlapped with the heavy-labeled isotopic cluster. Since it is difficult to separate these overlapping isotopic clusters accurately, we discard this MS scan during the quantification.