DeconTools

DeconTools performs automated deconvolution and deisotoping of mass spectrometry and LC-MS/MS data to detect and characterize isotopic clusters for proteomics, metabolomics, and analyses of large biomolecules such as proteins, peptides, DNA, and polymers.

Key Features:

• Automated Peak Finding: Employs a subtractive peak-finding routine and integrates the THRASH algorithm to detect isotopic clusters, using Fourier transform/Patterson methods for primary charge determination and least-squares fitting to theoretical isotopic abundance distributions to assign the most abundant isotopic peaks.
• Signal-to-Noise Calculation: Implements baseline and noise-width estimation procedures to compute signal-to-noise in spectra with high peak density.
• High-Resolution Analysis: Performs high-resolution analysis of MS and LC-MS/MS data to identify large numbers of isotopic clusters and determine accurate mass values.
• Modular Processing Classes: Provides reusable processing classes for reading raw data, routine peak finding, theoretical isotope distribution modeling, and deisotoping.
• Batch Processing and Multi-Format Support: Performs deisotoping on individual scans or entire datasets, supports batch processing across multiple datasets, and accepts multiple raw data formats.

Scientific Applications:

• Proteomics: Automated interpretation of MS and LC-MS/MS spectra for identification and quantification of peptides and proteins.
• Metabolomics and Large Biomolecule Analysis: Characterization and mass determination of metabolites and large biomolecules, including DNA and polymers, using high-resolution MS data.

Methodology:

Computational methods explicitly include THRASH, a subtractive peak-finding routine, Fourier transform/Patterson-based primary charge determination, least-squares fitting to theoretical isotopic abundance distributions, baseline and noise-width estimation for signal-to-noise calculation, deisotoping, and theoretical isotope distribution modeling applied to raw MS and LC-MS/MS data with support for batch processing.