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: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
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.