Fig. 5
Average MS/MS fragmentation spectra of the SVG and SEE peptides. Replicate CID fragmentation spectra and 300 ppm theoretical ion tables of the SVG (a, b) and SEE (c, d) analyte peptides derived from eVLP lot ‘A’. a, b Represent the y-series assignments at the 1:2 (1) and 1:32 (5) dilution samples respectively (see dilution scheme in Fig. 4a). Prominent y-series sequence ions are indicated. The SVG series contains 10 consecutive y-series ions resulting in a MASCOT Ions Score of 69 and an Expect score of 6.7 × 10−6 at dilution ‘1’ with the ‘5’ dilution Ions Score at 57 with an Expect Score of 8.8 × 10−5. The SEE peptide contains 7 y-series ions in both the ‘1’ and ‘5’ dilutions with Ions Scores of 55 and 41 with Expect Scores of 8.2 × 10−5 and 0.0021 respectively. With the exception of the SEE ‘5’ dilution, peptide assignments from every dilution run were of sufficient quality to obtain non-ambiguous sequence identifications