In silico analysis software tools | Mass spectrometry based untargeted glycomics
The successful interpretation of mass spectrometry data often depends on the comparison of the detected signals with theoretical features of a putative molecule: Isoelectric point, retention time, sequence digestion, decoy database generation, consider post-translational modifications, molecular formula prediction, FASTA sequence databases reader, isotopic distribution.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Allows to manage and analyse Liquid chromatography coupled to mass spectrometry (LC-MS) data. OpenMS is a programming library and tool collection integrated into full-featured workflow systems, such as KNIME, Galaxy and WS-PGRADE, to facilitate bioinformatics research in the field of MS on all levels. The software provides pre-built and ready-to-use tools for analysis of both proteomics and non-targeted metabolomics data.
Provides a platform able to read various binary mass spectrometry data files such as Agilent, Bruker, Thermo or mzXML. Mascot Distiller supplies a graphic user interface that detects peaks by trying to adjust the best isotopic distribution to the experimental data. The generated lists can be handled, saved or directly uploaded to a Mascot server for database searching. The functionalities can be enriched by adding multiple toolboxes.
An efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, DeconTools is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs.
A program for generating isotope profiles. MS-Isotope allows up to six, potentially overlapping, profiles to be displayed on the same graph. The profiles can be specified as peptide sequences, elemental composition or averagine masses. The charges and intensities of the profiles must also be specified. The program can be used to simulate quantification data or entire MS/MSMS spectra. The program can simulate multiple overlapping profiles with different charge states.