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In this page, we present the disulfide bonds determined by MS2DB++ and 8 other different methods for our dataset. These methods are: MS2DB+, SVM, CSP, MassMatrix, DISULFIND, PreCys, DiANNA, and DISLOCATE. While MS2DB+ and MassMatrix are MS-based methods (disulfide bond determination occurs via MS/MS data analysis), all other six methods are sequence-based methods; thus, the disulfide bonds are determined based on predictive techniques using protein sequence data.

MS2DB++ determined the disulfide linkages by applying the Shafer rule (one of the information-fusion approaches developed by us based on Dempster-Shafer theory (DST)) using the disulfide connectivity provided by the following methods: MS2DB+, SVM, and CSP.

As it can be seen in the table below, MS2DB++ outperformed all other methods, finding 16 out of the 17 disulfide bonds listed on UniProt as the known disulfide connectivity for the 7 molecules analyzed. The only S-S bond missed by MS2DB++ was not found by any of the other methods either (C91-341 for the molecule FTIII).

For the dataset analyzed, MS2DB++ achieved the following performance measures: sensitivity: 0.929, specificity: 0.992, accuracy: 0.985, and Mathews correlation coefficient: 0.911.

Comparison between 9 different methods for disulfide bond connectivity determination
Proteins Known Bonds MS2DB++ MS2DB+ SVM CSP MassMatrix DISULFIND PreCys DiANNA DISLOCATE
ST8SiaIV 142-292 bondfound bondfound bondfound bondfound bondfound bondnotfound bondnotfound bondfound bondnotfound
156-356 bondfound bondfound bondfound bondfound bondfound bondnotfound bondnotfound bondnotfound bondnotfound
Beta-LG 82-176 bondfound bondfound bondnotfound bondnotfound bondfound bondnotfound bondnotfound bondfound bondfound
122-135 bondfound bondnotfound bondfound bondfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound
FucT VII 68-76 bondfound bondfound bondfound bondfound bondfound bondnotfound bondfound bondnotfound bondnotfound
211-214 bondfound bondfound bondfound bondfound bondfound bondnotfound bondfound bondnotfound bondnotfound
318-321 bondfound bondfound bondfound bondfound bondfound bondnotfound bondfound bondnotfound bondnotfound
B1,4GalT 134-176 bondfound bondfound bondnotfound bondfound bondfound bondnotfound bondnotfound bondnotfound bondnotfound
247-266 bondfound bondfound bondnotfound bondfound bondfound bondnotfound bondnotfound bondnotfound bondnotfound
C2GnT-I 59-413 bondfound bondfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound
100-172 bondfound bondnotfound bondfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound
151-199 bondfound bondfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound
372-381 bondfound bondfound bondfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound
Lysozyme 24-145 bondfound bondfound bondfound bondnotfound bondnotfound bondfound bondnotfound bondfound bondnotfound
48-133 bondfound bondfound bondnotfound bondnotfound bondfound bondfound bondnotfound bondfound bondnotfound
FTIII 81-338 bondfound bondfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound
91-341 bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound bondnotfound