The assignment of the fragment ions derived from the linearized peptides should be included in the scoring methods and algorithms of software dedicated to the identification of type 2 peptides improve the confidence of the results and to rescue some dubious assignments such as the depicted in Figure . In the MS/MS spectrum of the 2+ precursor ion (Figure ) the two-most intense signals detected at m/z 1110.55, 1+ and m/z 1557.69, 1+ were assigned to linker fragment ions ([ 192 T-K 200 ]+71) + and (( 1 Z-K 16 )+98) + , respectively. Both signals were more intense that the y5α (m/z 589.28, 1+), a fragmentation of a very labile peptide bond at the N-terminal end of proline .