DeconTools
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PNNL-Comp-Mass-Spec
Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.
DeconTools
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.
Installation
Download the 64-bit DeconTools installer from https://github.com/PNNL-Comp-Mass-Spec/DeconTools/releases \
- Alternatively, download
DeconTools_x64.zip, which has the executables (DeconConsole.exe and DeconToolsAutoProcessV1.exe) and required DLLs
Requirements
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 https://proteowizard.sourceforge.io/
- You typically will need the 64-bit version.
Using DeconTools
DeconTools has both a GUI version (DeconToolsAutoProcessor) and a command-line version (DeconConsole).
DeconConsole Syntax
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.
Example usage:
DeconConsole.exe QCDataset.raw SampleParameterFile.xml
Results files
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) |
Contacts
Written by Gordon Slysz for the Department of Energy (PNNL, Richland, WA)
E-mail: [email protected] or [email protected]
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics
License
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.
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PNNL-Comp-Mass-Spec
Metadata
Used to deisotope mass spectra and to detect features from mass spectrometry data using observed isotopic signatures.