Determination of Sodium Ion Addition Sites of Peptides by Nanoelectrospray MS/MS Sequence Docking

Sodium ion addition of 20 naturally occurring amino acids was investigated by triple quadruple tandem mass spectrometry. Results showed that most amino acids had extraordinarily weak force for non-covalent binding to sodium ion, while proline and phenylalanine easily captured sodium ion from solvents. By tandem mass spectrometry “sequence docking” method on Q-TOF2 (Waters, USA), full amino acid sequence of C-terminal peptide of acidic fibroblast growth factor was analyzed and it was confirmed that the adding site of sodium ion was proline (6Pro). Sodium ion-addition peaks in peptide mass fingerprinting (PMF) apparently decreased after adding 1% formic acid. The peptide sequence without sodium ion-addition and the sequence gap were determined using de novo technology, which was the same as the sequence of sodium ion-addition peptide.