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Spectrum Deconvolution of LC-MS Data
Spectral deconvolution differentiates analyte signals from contaminants or instrumental noise, and reduces data dimensionality to benefit downstream statistical analysis.
Version 5.2 - published on 17 Jun 2010
This tool is closed source.
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Abstract
The purpose of spectral deconvolution is to differentiate signals arising from the real analyte as opposed to signals arising from contaminants or instrumental noise, and to reduce data dimensionality which will benefit downstream statistical analysis. This tool extracts peak information from thousands of raw mass spectra and reports the peak information in a simple peak table.
This tool is part of the Proteome Discovery Pipeline, a data analysis pipeline for mass spectrometry based differential proteomics. The deconvolution code was developed at Bindley Bioscience Center at Purdue University, and is based on GISTool, a software package with chemical noise filtering, charge state fitting, and de-isotoping for the analysis of complex peptide samples. Overlapping peptide signals in mass spectra are deconvoluted by correlating the observed spectrum with modeled peptide isotopic peak profiles. Isotopic peak profiles for peptides are generated in silico from a protein database producing reference model distributions. The GISTool algorithm has been modified to enable the analysis of metabolomics data generated from a LC-MS analytical platform.
The latest version of the Deconvolution Tool reflects major improvements such as the capability of analyzing data generated from low resolution MS instruments. It provides for data deconvolution of overlapping mass spectral peaks, identifies doublets, and calculates the ratio of the doublets.
LC-MS Datasets for the Deconvolution Tool: Input and Output Users can access the cceHUB shared data repository to search for LC-MS datasets to input into the Deconvolution Tool. Search criteria include instruments (e.g., LS-MSD TOF, XCT PLUS), data formats (e.g., mzXML, mzData, CDF), and stored data collections. Users can also access datasets stored in their own cceHUB home folders. See How to Use WebDAV for information on setting up WebDAV to "drag and drop" your datasets into your home folder at cceHUB. Files in your home folder can be input into the Deconvolution Tool by selecting the option to choose your dataset from your own collection. The Spectrum Deconvolution Tool generates one deconvoluted output file for each input LC-MS file. The output file can then be loaded as input to the Peak Alignment Tool, the next step in the cceHUB Discovery Pipeline. See the supporting documents Getting Started for more information.
LC-MS Datasets for the Deconvolution Tool: Input and Output Users can access the cceHUB shared data repository to search for LC-MS datasets to input into the Deconvolution Tool. Search criteria include instruments (e.g., LS-MSD TOF, XCT PLUS), data formats (e.g., mzXML, mzData, CDF), and stored data collections. Users can also access datasets stored in their own cceHUB home folders. See How to Use WebDAV for information on setting up WebDAV to "drag and drop" your datasets into your home folder at cceHUB. Files in your home folder can be input into the Deconvolution Tool by selecting the option to choose your dataset from your own collection. The Spectrum Deconvolution Tool generates one deconvoluted output file for each input LC-MS file. The output file can then be loaded as input to the Peak Alignment Tool, the next step in the cceHUB Discovery Pipeline. See the supporting documents Getting Started for more information.
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