xTract protocols

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xTract specifications


Unique identifier OMICS_18721
Name xTract
Software type Package/Module
Interface Command line interface
Restrictions to use None
Programming languages Perl
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes


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  • person_outline Ruedi Aebersold <>

Publication for xTract

xTract in pipelines

PMCID: 5647560
PMID: 28938074
DOI: 10.1021/acs.analchem.7b01581

[…] as two separate spectra, one at higher energy in the collision cell for fragments from sites 6–79, and one at lower energy for fragments from sites 114–130. data analysis was performed with xtract (thermo scientific) or mmass software, and graphical fragment maps were created with prosight lite. all intensity values used for the determination of weighted-average charges were normalized […]

PMCID: 5140025
PMID: 27976756
DOI: 10.21956/wellcomeopenres.10667.r17585

[…] meaning that cross-link analysis is not routinely possible. maxquant was recently adopted for quantifying cross-links being a first exception here. also, walzthoeni et al. developed software xtract to be used in conjunction with their identification pipeline for automated quantitation of cross-linking data . previously performed proof-of-principle work relied on an elementary […]

PMCID: 4165458
PMID: 25162384
DOI: 10.1021/ac502790j

[…] “sweet heart for hcd” approach could succeed., c* corresponds to carbamidomethyl cys; cys(o) indicates the oxidation of alkyl cys. the first column represents automated deconvolution values using xtract, a feature of thermo’s xcalibur software. the correct value determined for the man6 and man7 dimer indicates that it can compensate for the missing monoisotopic peak., assumed formylation […]

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xTract in publications

PMCID: 5949005
PMID: 29686080
DOI: 10.1073/pnas.1802354115

[…] as described (). peptides were fractionated by multidimensional chromatography followed by tandem mass spectrometric analysis on a ltq-orbitrap mass spectrometer (thermo fisher scientific). raw-xtract (version 1.8) was used to extract peak list information from xcalibur-generated raw files. database searching of the ms/ms spectra was performed by using the prolucid algorithm (version 1.0). […]

PMCID: 5912465
PMID: 29487134
DOI: 10.1074/jbc.RA117.000487

[…] (80, 100, 150, and/or 180 v) of hcd. all precursor and fragment ions were acquired using a mass resolution of 60,000 with an average of 3 microscans and a signal-to-noise threshold of 3. the xtract algorithm from xcalibur 3.0 software (thermo fisher scientific) was used to determine the decharged masses of the observed ions, which were then inserted into prosight lite […]

PMCID: 5834659
PMID: 29477637
DOI: 10.1016/j.tranon.2018.02.001

[…] case of less malignant tissue on the section macro-dissection of malignant tissue was performed. rna isolation was conducted according to a fully automated, high-throughput extraction workflow on an xtract xl liquid-handling robot (stratifyer molecular pathology gmbh, cologne, germany). the extraction solutions and chemicals are commercially available in germany as part of the xtrakt ffpe kit, […]

PMCID: 5793110
PMID: 29301241
DOI: 10.3390/toxins10010023

[…] were inspected with the xcalibur qual browser (thermo xcalibur 2.2 sp1.48, thermo fisher scientific, waltham, ma, usa) and deconvolution of isotopically resolved spectra was carried out by using the xtract algorithm of xcalibur qual browser. the protein assignment was done by comparison to the retention time of the hplc run and corresponding lc-ms/ms information from sds-page trypsin digests., […]

PMCID: 5799867
PMID: 29249155
DOI: 10.1021/acs.jproteome.7b00622

[…] the supporting information., for tandem spectra of sp, fragments were manually analyzed for b, c, y, and z ion types. for intact protein analyses, extracted mass spectra were deconvoluted using auto xtract in protein deconvolution 4.0 (thermo fisher scientific, bremen, germany). deconvolution settings were s/n threshold: 1, fit factor: 80%, and remainder threshold: 25%. deconvoluted results […]

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xTract institution(s)
Department of Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland; Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany; Department of Biology and Genetics, Stanford University, Stanford, CA, USA; PhD Program in Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland; PhD Program in Systems Biology, University of Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
xTract funding source(s)
Supported by the European Union 7th Framework project PROSPECTS (Proteomics Specification in Time and Space; grant HEALTH-F4-2008-201648), the European Research Council (ERC) advanced grant “Proteomics v.3.0” (grant 233226), ERC advanced grant “Proteomics 4D—the proteome in context” (grant 670821) and ETH Zurich.

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