The positive charge on proteins in electrospray ionization mass spectrometry is the result of

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The positive charge on proteins in electrospray ionization mass spectrometry is the result of the protonation of positively charged amino acid side chains, such as Arg and Lys. Asp and Glu have negatively charged side chains and will not contribute to the positive charge. The pH of the solution can affect the extent of protonation, but it is not responsible for the positive charge itself. Protons or electrons fired at the protein would not necessarily cause protonation and are not typically used in electrospray ionization.

The Positive Charge on Proteins in Electrospray Ionization Mass Spectrometry