SIRIUS 4.9.3 – Identification of Metabolites using single and Tandem Mass Spectrometry

Sirius 4.9.3

:: DESCRIPTION

Sirius ,(Sum formula Identification by Ranking Isotope patterns Using mass Spectrometry) a new java-based software framework for discovering a landscape of de-novo identification of metabolites using single and tandem mass spectrometry. Sirius² deduces molecular formulas of small compounds by ranking isotope patterns from mass spectra of high resolution. Sirius² further analyses the fragmentation pattern of a compound resulting in hypothetical fragmentation trees. It allows for automated and high-throughput analysis of small-compound MS data beyond elemental composition without requiring compound structures or a mass spectral database.

::DEVELOPER

Lehrstuhl Bioinformatik Jena

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

Sirius

:: MORE INFORMATION

Citation:

SIRIUS: decomposing isotope patterns for metabolite identification
Sebastian B?cker, Matthias C. Letzel, Zsuzsanna Lipták and Anton Pervukhin
Bioinformatics (2009) 25 (2): 218-224

MetExpert – Metabolite Expert System

MetExpert

:: DESCRIPTION

MetExpert is an expert system to assist users with limited expertise in informatics to interpret GCMS data for metabolite identification without querying spectral databases

::DEVELOPER

Sumner Research Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Excel

:: DOWNLOAD

MetExpert

:: MORE INFORMATION

Citation

Qiu F, Lei Z, Sumner LW.
MetExpert: An expert system to enhance gas chromatography?mass spectrometry-based metabolite identifications.
Anal Chim Acta. 2018 Dec 11;1037:316-326. doi: 10.1016/j.aca.2018.03.052. Epub 2018 Apr 6. PMID: 30292308.

PlantMAT v1.0 – Plant Metabolite Annotation Toolbox

PlantMAT v1.0

:: DESCRIPTION

PlantMAT is a computational tool combining library search and combinatorial enumeration to facilitate the structural identification of plant specialized metabolites, e.g., saponins and flavonoid glycosides.

::DEVELOPER

Sumner Research Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Excel

:: DOWNLOAD

PlantMAT

:: MORE INFORMATION

Citation

Qiu F, Fine DD, Wherritt DJ, Lei Z, Sumner LW.
PlantMAT: A Metabolomics Tool for Predicting the Specialized Metabolic Potential of a System and for Large-Scale Metabolite Identifications.
Anal Chem. 2016 Dec 6;88(23):11373-11383. doi: 10.1021/acs.analchem.6b00906. Epub 2016 Nov 23. PMID: 27934098.

MaRIboES 2.1.0 – Metabolite and Reaction Inference based on Enzyme Specificities

MaRIboES 2.1.0

:: DESCRIPTION

MaRIboES is an algorithm for metabolite and reaction inference based on enzyme specificities. MaRIboES ,has many applications, for example to complete reconstructed metabolic networks, to aid in metabolic engineering or to help identify unknown peaks in mass spectra. MaRIboES employs structural and stereochemistry similarity measures and molecular fingerprints to generalise enzymatic reactions based on data available in BRENDA.

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Matlab
C++ Compiler

:: DOWNLOAD

MaRIboES

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 15;25(22):2975-82. Epub 2009 Aug 20.
Metabolite and reaction inference based on enzyme specificities.
de Groot MJ, van Berlo RJ, van Winden WA, Verheijen PJ, Reinders MJ, de Ridder D.

MetaboMiner – Identification of Metabolites from 2D NMR spectra of Complex Biofluids

MetaboMiner

:: DESCRIPTION

MetaboMiner is a tool which can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. MetaboMiner is able to handle both 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC) data. It identifies compounds by comparing 2D spectral patterns in the NMR spectrum of the biofluid mixture with specially constructed libraries containing reference spectra of approximately 500 pure compounds.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ WIndows/ MacOsX
Java

:: DOWNLOAD

MetaboMiner

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Nov 28;9:507. doi: 10.1186/1471-2105-9-507.
MetaboMiner–semi-automated identification of metabolites from 2D NMR spectra of complex biofluids.
Xia J, Bjorndahl TC, Tang P, Wishart DS.