DtaRefinery statistics

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Citations per year

Number of citations per year for the bioinformatics software tool DtaRefinery
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Tool usage distribution map

This map represents all the scientific publications referring to DtaRefinery per scientific context
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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


No version available

Maintainer


  • person_outline Richard Smith

Publication for DtaRefinery

DtaRefinery citations

 (5)
library_books

Predicting Species Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach

2017
Front Microbiol
PMCID: 5468372
PMID: 28659875
DOI: 10.3389/fmicb.2017.01020

[…] mmon 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 (), includi […]

library_books

Position dependent termination and widespread obligatory frameshifting in Euplotes translation

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

[…] ss 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, we re […]

library_books

Multi omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica

2016
BMC Genomics
PMCID: 4766638
PMID: 26911370
DOI: 10.1186/s12864-016-2471-2

[…] 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 (+79 […]

library_books

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non coding genes

2016
eLife
PMCID: 5053804
PMID: 27623010
DOI: 10.7554/eLife.15614.024

[…] 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 included […]

library_books

Proteomic Analysis of the Organ of Corti Using Nanoscale Liquid Chromatography Coupled with Tandem Mass Spectrometry

2012
Int J Mol Sci
PMCID: 3430228
PMID: 22942697
DOI: 10.3390/ijms13078171

[…] 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 for B […]


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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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