Simplification of Fragmentation Patterns

Most of the research performed in this field is based on tryptic peptides. As discussed earlier, such peptides contain basic amino acid residues on their C-terminus, which causes formation of the high intensity C-terminal ion series, mostly y-ions. In such peptides the N-terminal ions have lower intensity and do not provide important sequence information. Introduction of a highly basic group, such as dimethylalkyl-ammonium acetyl (DMAA) or tra(2,4,6-trimcthoxyphcnyl)phosphonium acetate into 

Such modifications can be very helpful when the fragmentation efficiency of a peptide is poor or the number of sequence-specific peptides is limited. 

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