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DtaRefinery specifications

Information


Unique identifier OMICS_09657
Name DtaRefinery
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Version 1.2.0.1
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Richard Smith <>

Publication for DtaRefinery

DtaRefinery in pipelines

 (3)
2017
PMCID: 5468372
PMID: 28659875
DOI: 10.3389/fmicb.2017.01020

[…] contaminant protein sequences (human keratin, bovine trypsin, and serum albumin precursor) to detect residual peptides derived from processing. ms/ms spectra were preprocessed using deconmsn and dtarefinery tools to deconvolute, deisotope, and remove systematic error in mass measurement accuracy (; ). the ms-gf+ search algorithm was used to match ms/ms spectra to peptide sequences (), […]

2016
PMCID: 5295771
PMID: 27870834
DOI: 10.1038/nsmb.3330

[…] spectrometry (lc-ms/ms) was performed using a 100 min lc gradient. the details on the gradient and mass spectrometer settings can be found elsewhere. the data were pre-processed with deconmsn and dtarefinery tools, and analyzed using ms-gf+. the raw, peak lists and ms/ms identification files were deposited at pride (dx.doi.org/10.6019/pxd004333). amongst the all peptide identifications, […]

2012
PMCID: 3430228
PMID: 22942697
DOI: 10.3390/ijms13078171

[…] heated capillary was maintained at 175 °c, while the spray voltage was kept at 2.2 kv., raw ms/ms files were processed with deconmsn (version 2.2.2.2, pacific northwest national laboratory (pnl)), dtarefinery (version 1.1, pnl) and dtatexttomgf (version 1.2.3952, pnl) to produce mgf files. sequence assignment was performed using omssa ms/ms search engine [] (version 2.1.9, national center […]


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DtaRefinery in publications

 (3)
PMCID: 4766638
PMID: 26911370
DOI: 10.1186/s12864-016-2471-2

[…] going back to starting conditions. the column was equilibrated for 52 min before the next sample was loaded onto the column., raw tandem mass spectra from the mass spectrometer were processed using dtarefinery [] coupled to msgfplus [] and searched against a collection of y. lipolytica proteins obtained from uniprot. briefly, a parent mass tolerance of +/− 20 ppm, dynamically phosphorylated […]

PMCID: 5053804
PMID: 27623010
DOI: 10.7554/eLife.15614.024

[…] gradient was used for the separation, which started with 100% a and gradually increased to 60% b over 100 min., the acquired ms/ms spectra datasets were preprocessed with deconmsn [18304935] and dtarefinery [20019053] software followed by spectra interpretation using msgfplus [25358478] software by matching against custom protein fasta file build based on rna-seq data. the fasta file […]

PMCID: 3430228
PMID: 22942697
DOI: 10.3390/ijms13078171

[…] heated capillary was maintained at 175 °c, while the spray voltage was kept at 2.2 kv., raw ms/ms files were processed with deconmsn (version 2.2.2.2, pacific northwest national laboratory (pnl)), dtarefinery (version 1.1, pnl) and dtatexttomgf (version 1.2.3952, pnl) to produce mgf files. sequence assignment was performed using omssa ms/ms search engine [] (version 2.1.9, national center […]


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DtaRefinery institution(s)
The Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
DtaRefinery funding source(s)
This work was supported, in whole or in part, by National Institutes of Health Grant RR18522 from the National Center for Research Resources.

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