Supplementary Figure 8: Mis-quantitation of a singlet cross-linked peptide as a consequence of overlapping signals of the light and the heavy versions.

The MS1 spectra show the signals of an example cross-linked peptide in both the forward-labeled (conformer 1+BS3/conformer II+BS3-d4) and the reverse-labeled (conformer I+BS3-d4/conformer II+BS3) analysis. The isotope peaks used for quantitation are highlighted (blue for the light version and pink for the heavy version of the peptide). The extended isotope envelope of the example peptides leads to an overlap between the signals of the light and the heavy versions. Therefore in the forward-labeled dataset, this conformer I-unique cross-linked peptide is mis-quantified as a “doublet” by the automated data process.