Table 3. List of Common Algorithms for Cross-Link Data Analysis.
| support
for |
|||||
|---|---|---|---|---|---|
| name | MS-cleavable XL | user-definable XL | proteome wide | quantitative XL data | web site |
| DXMSMS Match95 | yes | yes | yes | no | creativemolecules.com/CM_Software.htm |
| Formaldehyde XL Analyzer96 | FA only | yes | no | biolchem.huji.ac.il/nirka/software.html | |
| Kojak97 | no | yes | no | no | kojak-ms.org/ |
| MassAI (CrossWork)98 | no | yes | no | no | massai.dk/ |
| MassSpec Studio99 | no | yes | yes | no | msstudio.ca/crosslinking/ |
| MaxLinker33 | yes | yes | yes | no | yulab.org/resources/MaxLinker/ |
| MeroX (incl StavroX)82,100 | yes | yes | yes | no | stavrox.com |
| MetaMorpheusXL101 | yes | yes | yes | yes | github.com/smith-chem-wisc/MetaMorpheus |
| pLink232 | no | yes | yes | yes | pfind.ict.ac.cn/software/pLink/ |
| Protein Prospector102 | no | yes | no | no | prospector.ucsf.edu/prospector/mshome.htm |
| SIM-XL103,104 | no | yes | yes | yes | patternlabforproteomics.org/sim-xl/ |
| Xi Search22,105,106 | yes | yes | yes | no | rappsilberlab.org/software/xisearch/ |
| Xilmass107 | no | yes | no | no | github.com/compomics/xilmass |
| XlinkX80,85 | yes | yes | yes | no | hecklab.com/software/xlinkx/ |
| Xolik108 | no | yes | no | no | bioinformatics.ust.hk/Xolik.html |
| xQuest/xProphet74,109 | no | yes | no | yes | proteomics.ethz.ch/cgi-bin/xquest2_cgi/index.cgi |
| ECL2110 | no | yes | yes | no | bioinformatics.ust.hk/ecl2.html |
| Xlink-Identifier111 | no | yes | no | no | du-lab.org/ |