Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.


Table 1: Mascot scores for peptide-spectrum matches of spectra acquired under different fragmentation regimes. Values in parenthesis under the score column represent ion identity threshold score and amino acids in red color denote the differences in the matched sequence with respect to the model peptide. Only the peptides that are classed in the first place are indicated.

Table 2: Mascot matches six different sequences for peptide P1 containing (IGG) motifs and matches to only one peptide for P2 containing (LGG) motifs although same fragment ions are matched (with minor differences).

Table 3: Table shows the isomeric fragment ions for b and y ion series for the peptide P4. Red color denotes fragment ions matched only by Mascot and ions shaded in yellow are matched by PEAKS DB

Table 4: PEAKS scores for the peptide-spectrum matches of spectra obtained under different fragmentation regimes: a) CID-FT MS/MS, B) HCD-FT MS/MS and C) ETD-FT MS/MS. ALC score indicates the average score of the positional confidence of each amino acid. Amino acids in red denote the difference in amino acid with respect to the model peptide.


Figure 1: ETD-FT MS/MS spectrum of the peptide P5 showing sequence rich fragment ions. Mascot matches to the correct peptide sequence, while PEAKS DB does not match to any sequence. Fragment ions corresponding to (z3+2) to (z17+2) ions are indicated with (*), fragment ion Z16+2 is not observed.

Figure 2A: ETD- FT MS/MS spectrum of the peptide P8 (WDDDDNDDWDDDDR) showing zn+2 fragment ions (n = 3, 5 -12) and whereas the peptide P9 (WGDDDNDDWDDDDR) does not fragment to give sequence specific fragment ions (Figure 2B).

Figure 3: HCD spectrum of peptide P6 (QQFQQQQQQQR) showing the y1 fragment ion (m/z = 175.11). Both Mascot and PEAKS DB do not take into account this information and matches to a peptide with amino acids at the N-terminal inversed (QQFQQQQQQRQ)

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