Response to Reviewer #1

Figure S1. Scan function used for the charge increase from a singly protonated peptide to a doubly protonated peptide. Please note that cooling steps after analyte injection and two mutual storage steps are not drawn in the scan function.

Aux. RF OR SK ~ ~ IQ1 Deflector Nano-ESI Q0 Q1 Q2 Q3 Nano-ESI Nano-ESI Detector IQ2 IQ3 EX

+1300 V -10 V -12 V +50 V cation injection -16 V (analyte) -20 V

+16 V rf barrier +15 V anion injection +12 V -1000 V +10 V rf barrier (1st reagent) rf barrier +15 V +15 V +12 V +10 V mutual storage 0 V (1st reaction) +1300 V cation injection -10 V rf barrier -12 V -15 V (2nd reagent) -16 V 0 V rf barrier rf barrier mutual storage -10 V -12 V (2nd reaction) -15 V -15 V +50 V 0 V 0 V +2~4 V Ion detection -10 V -12 V (MASE) -15 V Figure S2. Scan function used for the sequential proton-transfer charge inversion and electron-transfer dissociation of a phosphopeptide. Please note that cooling steps after analyte injection and two mutual storage steps are not drawn in the scan function.

Aux. RF OR SK ~ ~ IQ1 Deflector APCI Q0 Q1 Q2 Q3 Nano-ESI Nano-ESI Detector IQ2 IQ3 EX +20 V +16 V +12 V anion injection -1000 V +10 V -50 V (analyte) +1300 V cation injection -10 V rf barrier -12 V -15 V (1st reagent) -16 V mutual storage 0 V rf barrier st -10 V -12 V rf barrier (1 reaction) -15 V -15 V rf barrier +16 V +15 V +12 V anion injection +10 V nd -2500 V (2 reagent) rf barrier rf barrier +15 V +15 V +12 V +10 V mutual storage 0 V +50 V (2nd reaction) +15 V +12 V +2~4 V Ion detection 0 V +10 V 0 V (MASE) Figure S3. Scan function used for the ubiquitin identification using the sequential electron-transfer and proton-transfer ion/ion reactions. Please note that cooling steps after analyte injection and two mutual storage steps are not drawn in the scan function.

Aux. RF OR SK ~ ~ IQ1 Deflector APCI Q0 Q1 Q2 Q3 Nano-ESI Nano-ESI Detector IQ2 IQ3 EX

+1300 V cation injection -10 V -12 V +50 V (analyte) -16 V -20 V

+16 V rf barrier +12 V +15 V +10 V -2500 V rf barrier anion injection rf barrier (1st reagent) +15 V +15 V +12 V +10 V mutual storage 0 V (1st reaction) rf barrier +16 V +15 V +12 V -1100 V +10 V anion injection rf barrier (2nd reagent) rf barrier +15 V +15 V +12 V +10 V mutual storage 0 V +50 V nd (2 reaction) +15 V +12 V +2~4 V Ion detection 0 V +10 V 0 V (MASE)