Table 1.

Summary of Existing Crosslinking Software^a

Software	Website	Reference
CLPM	http://search.cpan.org/∼crabtree/BioX-CLPM-0.01/lib/BioX/CLPM/Base.pm	Tang et al.50
Crux	http://noble.gs.washington.edu/proj/crux	McIlwain et al.51
DXMSMS	http://creativemolecules.com/CM_Software.htm	Bich et al.21 and Chen et al.22
MassMatrix	http://www.massmatrix.net	Xu et al.52
CrossWork/MassAI	http://www.massai.dk/	Rasmussen et al.53
MS-Bridge (part of UCSF Prospector)	http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msbridgestandard	Clauser et al.54
PeptideMap (in PROWL)	http://prowl.rockefeller.edu/prowl/peptidemap.html	Fenyo55
Pro-Crosslink	https://c4c.uwc4c.com/express_license_technologies/pro-crosslink-version-1	Gao et al.56
ProteinXXX/GPMAW	http://www.gpmaw.com/html/downloads.html	Peri et al.57 and Nielsen et al.58
VIRTUAL-MSLAB	Available upon request at ldk@science.uva.nl	de Koning et al.59
X-Link	Available upon request	Taverner et al.60
X-Links	http://www.wsu.edu/proteomics/	Anderson et al.61
xQuest/xProphet	http://prottools.ethz.ch/orinner/public/htdocs/xquest/	Rinner et al.62
StavroX/MeroX	http://www.stavrox.com/	Gotze et al.63–64
XLPM	http://binf-app.host.ualr.edu/∼mihir/cgi-bin/xlpm.cgi	Jaiswal et al.65
X-Link Identifier	http://du-lab.org/	Du et al.66
FINDX	http://findxlinks.blogspot.de/	Soderberg et al.67
xComb	https://persephone.rxlab.umaryland.edu/xcomb.php	Panchaud et al.68
XiQ	http://xiq.rappsilberlab.org; available upon request.	Fischer et al.69

^aThe names of the programs as well as the web addresses are given.