Supplementary Figure 7: Examples of correctly and incorrectly isolated signals.

(a) An example of a correctly isolated chromatographic signal of a peptide. The elution peak is correctly isolated; the isotope distribution of the isolated signals is in good agreement (with the “idotp” close to 1) with the expected pattern calculated based on the sequence of the target peptide; the measured signals of isotope peaks are in good matches with the calculated m/z of isotope peaks of the target peptide. (b) One error on peptide signal picking is incorrectly isolated elution peak of the target peptide. (c) Skyline might pick wrong signals for a target peptide, the error can be indicated by poor agreement on isotope distribution between the expected and the measured pattern, showing as low “idotp”. (d) The mistakenly selected signal may share the same charge as the target peptide which might resulted in an “idotp” value close to one. Such signal picking error would only be revealed when compare isotope peaks of the isolated signal in the MS1 spectra with the m/z of expected isotope peaks of the target peptide.