DeconTools protocols

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DeconTools specifications

Information


Unique identifier OMICS_02417
Name DeconTools
Alternative name Decon2LS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for DeconTools

DeconTools in pipelines

 (4)
2017
PMCID: 5305211
PMID: 28109157
DOI: 10.7554/eLife.21477.036

[…] spray voltage, 1.5 kv; no sheath and auxiliary gas flow; heated capillary temperature, 250°c; ion selection threshold, 33.000 counts., each thermo binary raw file was converted to a dta file using decon2ls () or to an mgf file using proteome discoverer 1.4 (thermo) and -as needed- recalibrated with the post-search recalibrator node. crosslinks were mapped by crossfinder (; ). typical error […]

2016
PMCID: 4951065
PMID: 27434306
DOI: 10.1371/journal.pone.0155839

[…] providing a look-up database of mass and elution time values for peptides identified in the prospective samples. high resolution ms scans from the same technical replicates were deisotoped using decon2ls [] to provide neutral mass and elution time values for all isotopic features in the technical replicates. isotopic features were combined across ms scans to provide lc-ms elution features […]

2014
PMCID: 3981673
PMID: 24717448
DOI: 10.1371/journal.pone.0089366

[…] (2) xcorr ≥2.2 for charge state +2, and (3) 3.75 for charge state +3, using 3.0 and 1.0 da for parent and fragment ion tolerances, respectively. high resolution lc-ms features were deconvoluted by decon2ls (version 1.0.2, using default parameters) and aligned to the mass and time tag database using viper (version 3.45 using default parameters) using the theoretical mass and observed normalized […]

2011
PMCID: 3216512
PMID: 22355544
DOI: 10.1038/srep00025

[…] generated ms/ms spectra) scores of ≥ 1.9, 2.2, or 3.5, respectively, were added to the existing s. amazonensis sb2b amt tag database., orbitrap™ spectra were deisotoped using the software tool decon2ls and the tool viper was used to identify mass and elution time features within mass measurement accuracy and elution time accuracy cut-offs of 5 ppm and 1%, respectively. abundances […]


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DeconTools in publications

 (29)
PMCID: 5923415
PMID: 29662015
DOI: 10.3390/md16040128

[…] of kso sample was shown in a. the results confirmed that the major repeating unit of the isolated ks was the disulfated disaccharide, (-3gal6sβ1→4glcnac6sβ1-). the raw data was deconvoluted using decontools, and then the output of decontools was processed by glycresoft to generate matching structures and to provide relative quantitative information []. a total of 31 oligosaccharides […]

PMCID: 5330483
PMID: 28245256
DOI: 10.1371/journal.pone.0172486

[…] detected in the individual samples were matched against the entries in the amt tag database using the prism data analysis system [], which is a series of software tools developed in-house (e.g. decon2ls [] and viper []) and freely available at omics.pnl.gov/software. individual steps in this data processing approach are reviewed in []. the peptides identified from this matching process […]

PMCID: 5305211
PMID: 28109157
DOI: 10.7554/eLife.21477.036

[…] spray voltage, 1.5 kv; no sheath and auxiliary gas flow; heated capillary temperature, 250°c; ion selection threshold, 33.000 counts., each thermo binary raw file was converted to a dta file using decon2ls () or to an mgf file using proteome discoverer 1.4 (thermo) and -as needed- recalibrated with the post-search recalibrator node. crosslinks were mapped by crossfinder (; ). typical error […]

PMCID: 4408067
PMID: 25905710
DOI: 10.1371/journal.pone.0123188

[…] and negative esi modes., data were acquired under the control of thermo xcalibur software (thermo scientific) and high resolution ms scans in raw data files were subjected to deisotoping using decon2ls []. lc-ms features were identified and then chromatographically aligned across all replicates for each sample using multialign [], and detected lipids were identified manually. all lipid […]

PMCID: 4378558
PMID: 25523396
DOI: 10.1186/1471-2164-15-1140

[…] two functions (figure ). compared with m-score, l-score increases the auc from 0.696 to 0.825 for the st test envelope matches and from 0.678 to 0.816 for the ec hcd test envelope matches.figure 5, decon2ls [], a reimplementation of thrash [], reports a list of ranked envelope matches from a top-down mass spectrum. to test l-score coupled with decon2ls, l-score was utilized to re-rank […]


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DeconTools institution(s)
Pacific Northwest National Laboratory, Richland, WA, USA

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