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Protocols

xTract specifications

Information


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

Versioning


No version available

Documentation


Maintainer


  • person_outline Ruedi Aebersold <>

Publication for xTract

xTract citations

 (82)
library_books

Systemic surfaceome profiling identifies target antigens for immune based therapy in subtypes of advanced prostate cancer

2018
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). […]

library_books

The N terminal domain of a tick evasin is critical for chemokine binding and neutralization and confers specific binding activity to other evasins

2018
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 […]

library_books

Prognostic Value of Molecular Breast Cancer Subtypes based on Her2, ESR1, PGR and Ki67 mRNA Expression in Muscle Invasive Bladder Cancer

2018
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, […]

library_books

Comparative Venomics of the Vipera ammodytes transcaucasiana and Vipera ammodytes montandoni from Turkey Provides Insights into Kinship

2018
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., […]

library_books

Exploring ECD on a Benchtop Q Exactive Orbitrap Mass Spectrometer

2017
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 […]

library_books

Top down characterization of endogenous protein complexes with native proteomics

2017
PMCID: 5726920
PMID: 29131144
DOI: 10.1038/nchembio.2515

[…] refer to average mass, when isotopic resolution was achieved the centroid average of the isotopic distribution was calculated with mmass software. high resolution ms3 spectra were deconvoluted with xtract software (thermo); in some cases artefactual peaks were removed manually. additional fragment ion analysis was performed with mmass., many of the acquired spectra proved to be challenging […]


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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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