Omnitrap MS2 and MS3 data of Herceptin

All data were acquired in a Q Exactive Plus Orbitrap MS equipped with the Omnitrap platform. Ions were produced by nanoESI using pulled borosilicate glass-coated emitters. The analysis of intact Herceptin was performed using a combination of fragmentation techniques. Mass selection of 49+ charge state at MS2 level was performed using the quadrupole mass filter of the Q Exactive Plus, while MS2 isolation of 25+ charge state and MS3 level isolation were performed in the Omnitrap platform. Orbitrap resolution was set to 240,000, CID activation time was 10 ms and Electron capture dissociation (ECD) was performed with ~0 eV electrons. All experiments were performed with intact non-reduced Herceptin in positive ion mode. Herceptin stock solution was diluted to a final concentration of 5 uM in a) 100 mM ammonium acetate for experiments with 25+ charge state and in b) 50:50:0.1 ACN:H2O:FA for experiments with 49+ charge state.