Table 1.

List of Publically Available Software for Cross-link Identification, Quantitation, Visualization and/or Modeling

	Website	Cross-linkers		Identification	FDR	Quantitation		Visualization		Model	Ref
		Non-cleavable	Cleavable			LFQ	Isotope	Network	Map
xQuest/xProphet	http://proteomics.ethz.ch/cgi-bin/xquest2_cgi/index.cgi	X		X	X						[46,47]
pLink	http://pfind.ict.ac.cn/software/pLink	X		X	X						[44]
Protein Prospector	http://prospector.ucsf.edu/prospector/mshome.htm	X		X	X						[49,50]
Kojak	http://www.kojak-ms.org	X		X	X						[52]
SIM-XL	http://patternlabforproteomics.org/sim-xl	X		X	X			X	X		[51]
Xilmass	http://compomics.github.io/projects/xilmass.html	X		X	X						[54]
XLSearch	https://github.com/COL-IU/XLSearch	X		X	X						[55]
ECL2.0	http://bioinformatics.ust.hk/ecl2.html	X		X	X						[56,57]
StavroX	http://www.stavrox.com	X		X	X						[48]
MaxQuant	http://www.biochem.mpg.de/5111795/maxquant	X		X	X	X	X				[239]
xTract	http://proteomics.ethz.ch/cgi-bin/xtract_cgi/index.cgi	X				X	X				[238]
pQuant	http://pfind.ict.ac.cn/software/pQuant/index.html	X					X				[124]
mMass	http://www.mmass.org	X					X				[241]
XiQ	http://rappsilberlab.org/rappsilber-laboratory-home-page/tools	X					X				[235]
CLMSVault	https://gitlab.com/courcelm/clmsvault	X			X	X		X	X		[61]
xVis	https://xvis.genzentrum.Imu.de	X						X			[58]
MeroX	http://www.stavrox.com		X	X	X						[111]
XlinkX	https://xlinkx2beta.hecklab.com		X	X							[101]
xiNET	http://crosslinkviewer.org							X			[59]
ProXL	https://github.com/yeastrc/proxl-web-app							X	X		[60]
XlinkDB 2.0	http://xlinkdb.gs.washington.edu/xlinkdb							X	X	X	[62]
Xwalk	http://www.xwalk.org								X		[63]
XLmap	http://brucelab.gs.washington.edu/software.html								X		[65]
Xlink Analyzer	http://www.beck.embl.de/XlinkAnalyzer.html								X	X	[191]
XL-MOD	http://aria.pasteur.fr/supplementary-data/x-links									X	[169]
DynaXL	http://www.tanglab.org/resources/dynaxl									X	[170]
ROSETTA	https://www.rosettacommons.org									X	[192]
HADDOCK	https://haddock.science.uu.nl									X	[130]
IMP	https://integrativemodeling.org									X	[190]