Table 1.
Site localization algorithms
| Name | Class of algorithm | Core algorithm | Activation methods supported | Notes and availability | Interface | Prerequisites and/or dependencies | Report alternate sitesa | References |
|---|---|---|---|---|---|---|---|---|
| Ascore | PBL | Cumulative binomial probability | CID | First to implement site-determining ions http://ascore.med.harvard.edu/ (Free)> |
Commandline | Requires a pepXML containing PSM information and corresponding MS/MS in individual.dta formatted files | No | [80] |
| SloMo/TuboSloMo | PBL | Cumulative Poisson distribution | CID, ETD | Was the first PBL available for ETD-derived data http://massspec.bham.ac.uk/slomo/ (Free) |
Commandline | Requires a pepXML containing PSM information and corresponding MS/MS in individual.dta formatted files | Yes (Top-2) |
[81] |
| PhosphoRS | PBL | Cumulative binomial probability | CID, ETD, HCD | Has been built and tested on CID-, ETD-, and HCD-MS/MS Version 1.0 http://cores.imp.ac.at/protein-chemistry/downliscoverer; Version 3.1 can be downloaded for ProteomeDiscoverer software |
Commandline (v1.0) Vendor (v3.1) |
Version 1.0 requires a custom XML format containing both PSM information and corresponding MS/MS. No specific search engine is preferred, as long as the necessary PSM details can be extracted | Yes (All) | [82] |
| LuciPhor | PBL | Log odds | CID, HCD | First algorithm to implement FLR estimate http://luciphor.sourceforge.net/ (Free) |
Commandline | Uses Transproteomic-pipeline (TPP) supported search engines (Mascot, X!Tandem, and SEQUEST/COMET), processed via xinteract to pepXML file. Available under Linux OS | Yes (Top-2) |
[86] |
| MaxQuant PTM score | PBL | Exact binomial probability | All | Also includes site occupancy when quantification information is available, scored based on equation used in Olsen et al. [8] paper http://www.maxquant.org/downloads.htm |
GUI | None | Yes (All) | [8] |
| Mascot Delta | SED | Score difference between first- and second-ranked isomers | All | http://www.matrixscience.com/server.html | Commandline | Mascot.dat files are required. Many groups have written code (including Mascot) to process.dat files | Yes (All) | [58] |
| ProteinProspector (SLIP) | SED | Score difference between first- and second-ranked isomers | All | http://prospector.ucsf.edu/prospector/mshome.htm | Webserver | Requires (free) registration on ProteinProspector webserver | Yes (all) | [83] |
| PhosphoScore | Node cost delta between best and second-best candidates | Directed acyclic graph using intensity and mass deviations to weight nodes | CID | https://github.com/evansenter/ucsb/tree/master/school/CS167/main_project/code/PhosphoScore | GUI or commandline | Specific to SEQUEST search engine and explicitly requires.OUT (SEQUEST results) and.dta (peaklists) | No | [104] |
| PhosphoScan | PBL | Cumulative binomial probability | CID | Available upon request to authors | GUI | Standalone (GUI) tool | Yes | [105] |
| D-Score | SED | Difference between top- and second-ranked site isomers (posterior error probability (PEP)) | All | Standardized localization metric enabling comparison with other search engines. Proof-of-principle paper suggesting the applicability of universal deltas with PEP. No “tool” is currently available | NA | Computation of posterior error probabilities for first- and second-ranked hits required for delta PEP | Yes (all) | [84] |
| PhosSA | DP (delta between first and second best site candidates) | Dynamic programming using sum intensity of matched site-determining ions to find best site candidates | CID, HCD | http://helixweb.nih.gov/ESBL/PhosSA/ | GUI | Compatible with SEQUEST, Mascot search engines and ProteomeDiscoverer | Yes (status assigned to all candidate peptides) | [106] |
GUIs: graphical user interfaces.
a)
At least second candidate sites are also provided. In principle, all candidate sites are reported by most PBL tools, usually up to and including a maximum of two sites per peptide.