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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


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


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Publication for xQuest

xQuest in pipeline

PMCID: 5527848
PMID: 28743795
DOI: 10.15252/msb.20167412

[…] of protein co‐elution was performed by pearson correlation of protein abundance profiles. lc‐ms data were processed using the maxquant (cox & mann, )., the cross‐linking datasets searched with xquest: isotope‐coded disuccinimidyl suberate (dss; creative molecules) was used to perform cross‐linking reactions as described previously (walzthoeni et al, ). cross‐linked peptides were enriched […]

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xQuest in publications

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

[…] 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 […]

PMCID: 5861459
PMID: 29401259
DOI: 10.1093/nar/gky054

[…] 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 […]

PMCID: 5789952
PMID: 29317535
DOI: 10.1073/pnas.1718426115

[…] 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 ()., proteins were extensively dialyzed against itc […]

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 […]

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 […]

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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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