DeconTools is a software package used for detecting features in MS data by using the isotopic signatures of expected components. The tool uses different algorithms for different parts of the deconvolution process: noise reduction, peak detection, prediction of theoretical isotopic envelope and scoring functions that quantitate the quality of signature observed in the data.
Download the DeconTools installer from https://github.com/PNNL-Comp-Mass-Spec/DeconTools/releases
Preferably use the 64-bit installer: DeconTools_Installer_x64.exe
DeconTools can read the following file formats. However, some of the file formats require that you install the vendor-supplied data browsing software so that DeconTools has access to the necessary DLLs.
- mzXML files (Requires 64-bit ProteoWizard installation)
- mzML files (Requires 64-bit ProteoWizard installation)
- mz5 files (Requires 64-bit ProteoWizard installation)
- Thermo .Raw files (uses ThermoFisher.CommonCore.RawFileReader.dll)
- Agilent .Wiff files (requires Analyst)
- Agilent .D folders (requires Chemstation)
- Micromass files (requires MassLynx)
- Bruker acqu files
- IMS .UIMF files
Download ProteoWizard from http://proteowizard.sourceforge.net/ You typically will need the 64-bit version.
DeconTools has both a GUI version (DeconToolsAutoProcessor) and a command-line version (DeconConsole).
DeconConsole.exe DataFilePath ParameterFilePath [OutputDirectoryPath]
The first argument is the data file to process (typically .Raw or .mzML)
The second argument is the DeconTools parameter file.
- Example parameter files are available at https://github.com/PNNL-Comp-Mass-Spec/DeconTools/tree/master/Parameter_Files
The third argument is optional. If not defined, the output files are created in the same directory as the input files.
DeconConsole.exe QCDataset.raw SampleParameterFile.xml
For each dataset processed, DeconTools creates a pair of .CSV (comma-separated value) files containing information on the spectra in the input files and the deisotoped data found.
The _scans.csv file contains information about each mass spectrum (aka scan); columns are:
| Column | Description |
|---|---|
| scan_num | The scan number, aka spectrum number |
| scan_time | The number of minutes from the start of the analysis |
| type | 1 for MS spectra, 2 for MS/MS spectra |
| bpi | The Base Peak Intensity value |
| bpi_mz | The m/z of the Base Peak ion |
| tic | The Total Ion Current value |
| num_peaks | The number of data points in the spectrum above the background noise level |
| num_deisotoped | The number of peaks that were successfully deisotoped |
| info | For Thermo Raw files, the scan header |
The _isos.csv file contains the deisotoped data; columns are:
| Column | Description |
|---|---|
| scan_num | The spectrum number containing the data point |
| charge | The charge determined via the deisotoping process |
| abundance | The data point's abundance |
| mz | The Mass-to-Charge Ratio for the data point |
| fit | The Isotopic fit value: the least square error between the theoretical data and the experimental data. Values closer to 0 are better. Values larger than ~0.15 are typically low quality results. |
| average_mw | The Average Mass determined |
| monoisotopic_mw | The Monoisotopic Mass determined |
| mostabundant_mw | The mass of the most abundant ion in the isotopic distribution |
| fwhm | Full width at half maximum |
| signal_noise | Signal to noise ratio |
| mono_abundance | For 16O/18O processing, the abundance of the 16O peak |
| mono_plus2_abundance | For 16O/18O processing, the abundance of the peak 2 Da away from the 16O peak |
| flag | Specialized column for ion mobility (IMS) data |
| interference_score | Measures the likelihood that another isotopic distribution is overlapping with the given distribution (0 means no interference) |
Written by Gordon Slysz for the Department of Energy (PNNL, Richland, WA)
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://omics.pnl.gov or https://panomics.pnl.gov/
Licensed under the Apache License, Version 2.0; you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.