XlinkX statistics

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Citations per year

Number of citations per year for the bioinformatics software tool XlinkX

Tool usage distribution map

This map represents all the scientific publications referring to XlinkX per scientific context
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Associated diseases

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XlinkX specifications


Unique identifier OMICS_30025
Name XlinkX
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens




No version available


  • person_outline Albert Heck

Publication for XlinkX

XlinkX citations


The interactome of intact mitochondria by cross linking mass spectrometry provides evidence for coexisting respiratory supercomplexes*

PMCID: 5795388
PMID: 29222160
DOI: 10.1074/mcp.RA117.000470

[…] ing the native protein structures and interactions by cross-linking with the lysine-reactive DSSO, the reaction was quenched and the cross-linked proteins were analyzed using our previously described XlinkX v2.0 workflow (). Based on mitochondrial preparations from two separate hearts, imposing a 2% false discovery rate, we obtained 3,322 unique Lys-Lys connections, covering 359 mitochondrial prot […]


Combining Chemical Cross linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi subunit Protein Assemblies

PMCID: 5755487
PMID: 29286378
DOI: 10.3791/56747

[…] erentially labeled cross-linkers, the mass increase caused by the linker needs to be configured. There is also other commonly used software for cross-link identification, e.g., xQuest, MassMatrix, or XlinkX.Evaluate the database search results by the quality of fragmentation spectra. Acceptable spectra of cross-links should show ion series of both peptides (at least 4 adjacent ions) at a reasonabl […]


Facilitating identification of minimal protein binding domains by cross linking mass spectrometry

Sci Rep
PMCID: 5647383
PMID: 29044157
DOI: 10.1038/s41598-017-13663-y
call_split See protocol

[…] Raw data files were converted to *.mgf files using Proteome Discoverer 1.4 software (Thermo Fisher Scientific) with deconvolution option provided by add-on node MS2-Spectrum Processor (IMP, Vienna). XlinkX v2.0 algorithm was used for cross-link identification. The following settings were used: MS ion mass tolerance: 10 ppm; MS2 ion mass tolerance: 20 ppm; MS3 ion mass tolerance, 0.6 Da; fixed mod […]


Optimized fragmentation schemes and data analysis strategies for proteome wide cross link identification

Nat Commun
PMCID: 5454533
PMID: 28524877
DOI: 10.1038/ncomms15473

[…] All cross-links are reported in the . XlinkX v2.0 is publically available via http://xlinkx2beta.hecklab.com/. The data that support the findings of this study are available from the corresponding author upon request. […]


The diverse and expanding role of mass spectrometry in structural and molecular biology

PMCID: 5167345
PMID: 27797822
DOI: 10.15252/embj.201694818

[…] phy and MS setups in combination with software tools tailor‐made for the respective cross‐linker. To simplify such advanced in vivo cross‐linking experiments, we recently introduced the search engine XlinkX, the algorithm of which is compatible with any MS‐cleavable cross‐linker and with standard Orbitrap MS‐based data acquisition workflows. In a proof of concept study, XlinkX was able to identify […]

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XlinkX institution(s)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands; Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands

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