Protein identification by spectral networks analysis -- Bandeira et al. 104 (15): 6140 Data Supplement - HTML Page - index.htslp -- Proceedings of the National Academy of Sciences

Bandiera et al. 10.1073/pnas.0701130104.

Supporting Information

Files in this Data Supplement:

SI Figure 4
SI Table 2
SI Appendix A
SI Appendix B
SI Appendix C
SI Appendix D

SI Figure 4

Fig. 4. Improvements in signal-to-noise ratio and separation of b/y-ion ladders. The scored MS/MS spectrum for peptide SEELVAEAH (from the IKKb dataset) has both b and y ions, along with several noise peaks (Top). By using the spectral alignment of a pair of spectra (e.g., with KSEELVAEAH), many of the y ions and noise peaks that do not reside on the selected diagonal are eliminated. Although paired spectra provide very good separation of b/y-ion ladders, they may sometimes be too selective (e.g., causing the loss of the b₁, b₂, b₆, and b₈ ions) (Middle). By incorporating more paired spectra to form a spectral star, all noise peaks are removed and all missing b ions are adequately recovered (Bottom).