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xQuest specifications


Unique identifier OMICS_02402
Name xQuest
Alternative name xProphet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License Apache License version 2.0
Computer skills Advanced
Version 2.1.1
Stability Stable
Registration required Yes
Maintained Yes


No version available


  • person_outline xQuest team


Unique identifier OMICS_02402
Name xQuest
Alternative name xProphet
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable


This tool is not maintained anymore.

Publication for xQuest

xQuest citations


RPAP3 provides a flexible scaffold for coupling HSP90 to the human R2TP co chaperone complex

Nat Commun
PMCID: 5902453
PMID: 29662061
DOI: 10.1038/s41467-018-03942-1

[…] ation.For data analysis, Xcalibur raw files were converted into the open mzXML format through MSConvert (Proteowizard) with a 32-bit precision, and the converted files were directly used as input for xQuest searches on a local installation (http://prottools.ethz.ch/orinner/public/htdocs/xquest/). The following criteria were used for the selection of cross-linked precursor MS/MS data: a mass shift […]


Structure of a human cap dependent 48S translation pre initiation complex

Nucleic Acids Res
PMCID: 5861459
PMID: 29401259
DOI: 10.1093/nar/gky054

[…] s) in buffer C (20 mM HEPES–KOH pH 8, 100 mM KCl, 5 mM MgCl2, 0.25 mM GMPPNP), dialyzed against water and lyophilized.Processing of the cross-linked complexes, LC–MS analysis and data processing with xQuest was essentially performed as described in (), with the exception that all MS data was acquired on a Thermo Orbitrap Fusion Lumos mass spectrometer connected to a Thermo Easy-nLC 1200 HPLC syste […]


Structural basis of STAT2 recognition by IRF9 reveals molecular insights into ISGF3 function

Proc Natl Acad Sci U S A
PMCID: 5789952
PMID: 29317535
DOI: 10.1073/pnas.1718426115
call_split See protocol

[…] ions were injected onto a nanoAcquity ultraperformance LC column connected to a LTQ Orbitrap Velos Pro instrument (Thermo Scientific) for LC-based MS measurements. Data processing was performed using xQuest/xProphet. Identified cross-links were mapped onto the SAXS model of the STAT2133–679/IRF9–IAD heterodimer and analyzed using Xlink analyzer (). […]


Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1

Mol Cell
PMCID: 5745148
PMID: 29220652
DOI: 10.1016/j.molcel.2017.10.017

[…] by size-exclusion chromatography, and MS analyses and cross-link assignments were carried out essentially as described previously () using an Orbitrap Elite mass spectrometer (Thermo Fisher) and the xQuest/xProphet software pipeline ().Detected cross-links were mapped onto the given structural model (ALC1fl-MC or ALC1fl-MN) and, based on distances between corresponding residues, could be divided […]


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

[…] . NOTE: When using differentially 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 adjace […]


Molecular basis of AKAP79 regulation by calmodulin

Nat Commun
PMCID: 5698441
PMID: 29162807
DOI: 10.1038/s41467-017-01715-w

[…] ted with trypsin and subsequently enriched by SEC for cross-linked peptides. LC-MS/MS analysis was carried out on an Orbitrap Elite mass spectrometer (Thermo Scientific). The data were searched using xQuest in ion-tag mode with a precursor mass tolerance of 10 p.p.m. For matching of fragment ions, tolerances of 0.2 Da for common-ions and 0.3 Da for cross-link ions were applied. Fragment ions were […]

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xQuest institution(s)
Institute of Molecular Systems Biology, ETH Zurich, Zurich, Zurich, Switzerland; Institute for Systems Biology, Seattle, WA, USA; University of Innsbruck, Innsbruck, Austria; Faculty of Science, University of Zurich, Zurich, Switzerland
xQuest funding source(s)
Supported by fellowships of the Deutsche Forschungsgemeinschaft and the Roche Research Foundation, a long-term fellowship of the European Molecular Biology Organization (EMBO), a Marie Curie fellowship of the European Commission, a grant from F. Hoffmann-La Roche Ltd (Basel, in part with Federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, under contract No. N01-HV-28179 and with funds from ETH Zurich.

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