DtaRefinery
The DtaRefinery program improves mass measurement errors for parent ions of tandem MS/MS data by modeling systematic errors based on putative peptide identifications. This information is used to subtract out errors from parent ion protonated masses. The software reads concatenated dta files, which can be obtained either by concatenating individual dta files from extract_msn output or by running DeconMSn with the -XCDTA option. It is recomended to use DeconMSn as a preprocessing tool since it not only picks the right monoisotopic mass for parent ions, but also provides additional information that can be used for statistical analysis (specifically, ion intensity, total ion current, and AGC accumulation times).
As an output, DtaRefinery produces a concatenated dta file, but with corrected protonated parent ion mass values. Optionally it can output a mass error distribution histogram with the estimates of mean and standard deviation of parent ion mass measurements, along with scatterplots showing original and final dependencies of mass measurement errors on parameters like scan number, m/z, ion intensity and total ion current.
Modeling of the systematic mass measurement error is based on robust non-parametric regression analysis of dependecy of error residuals on multiple parameters, including scan number, m/z, ion intensity, and total ion current.
After installing, please see the Readme.txt file for additional details on using DtaRefinery. Note that several example data files will be included in the examples folder.
The journal article describing DTARefinery is:
| Download Software Tool | Download Source Code |
| Version | v1.2 | Requirements | Use of the source code requires Python |
| Date Updated | February 16, 2010 | File Size (Software Tool) | 32 MB (ZIP) |
| Registration Required | No | File size (Source Code) | 345 KB (ZIP) |
| Developers | Vlad Petyuk | ||
| Comments | See the Readme for additional program details | ||
DTA Refinery Features
DTARefinery GUI
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The DtaRefinery user interface allows you to customize the data processing options and process _dta.txt files |
Mass Error Histograms
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Mass error histogram, before and after mass correction by the DtaRefinery application |
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Mass errors, as a function of ion intensity, before and after mass correction by the DtaRefinery application |
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Mass errors, as a function of m/z, before and after mass correction by the DtaRefinery application |
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Mass errors, as a function of scan number (i.e., elution time), before and after mass correction by the DtaRefinery application |
Acknowledgment
All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:
Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.