Table 1.
Software tools for MS-based disulfide bond identification
| Software | MS function required | Type of data analyzed | Advantages (A) and limitations (L) | References |
|---|---|---|---|---|
| SearchXLinks | MALDI source | MS1 | L: Works only for very simple samples | Wefing et al. (2006) |
| MassMatrix | CID or HCD | CID or HCD MS2 | A: Complex forms of disulfide bonds are taken into consideration; L: Only for low-complexity samples digested using specific proteases |
Xu et al. (2007) |
| DBond | CID or HCD | CID or HCD MS2 | A: Disulfide-specific fragment ions are considered; L: No automatic FDR control, only for low-complexity samples |
Choi et al. (2009) |
| MS2DB+ | CID or HCD | CID or HCD MS2 | L: No FDR control | Murad and Singh (2013) |
| MixDB | CID or HCD | CID or HCD MS2 | A: Automatic FDR control, can handle large protein databases; L: Not easy to use, not tested with real-world samples |
Wang et al. (2014) |
| RADAR | HCD | HCD MS2 | A: Specific dimethyl labeling at peptide N-terminus improves accuracy of identification; L: Requires labeling after digestion; No FDR control |
Huang et al. (2014) |
| PepFinder | EThcD or high-resolution ETD | HCD MS2 | L: One reduced and one non-reduced samples need to be analyzed side by side, works only for low-complexity samples | From Thermo Scientific |
| SlinkS | EThcD and high-resolution ETD | ETD or EThcD MS2 | A: ETD and EThcD complement each other; L: Requires a unique ion pattern, efficiency of ETD varies depending on the peptides |
Liu et al. (2014) |
| pLink-SS | HCD or high-resolution ETD | HCD MS2 | A: Automatic workflow with FDR estimation, disulfide-specific ions and internal ions are considered, works for complex samples; L: highly complex forms such as three peptides inter-linked through two disulfide bonds cannot be identified |
Lu et al. (2015) |