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xQuest specifications

Information


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

Versioning


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Maintainer


  • person_outline xQuest team <>

Information


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

Maintainer


This tool is not maintained anymore.

Publication for xQuest

xQuest in pipeline

2017
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

 (56)
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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