MetaboMiner

Version: 1

Website

http://wishart.biology.ualberta.ca/metabominer/

Description

This performs semi-automated metabolite quantification of 2D TOCSY and HSQC spectra. It contains reference libraries split by biofluid: CSF, plasma and urine, as well as a biofluid library and a total library. There are 223 TOCSY spectra (from BMRB and MRMD) and 502 HSQC spectra (from HMDB). A number of peak processing methods are included: streak removal and symmetry editing. Streaks (usually residual solvent signals) are found and removed by finding groups of peaks at common locations and removing them. Symmetrical editing is for TOCSY spectra, as TOCSY peak signals form a symmetrical square pattern along the diagonal line, and thus off diagonal peaks without symmetry can be considered as artifacts. A metabolite is identified if it satisfies the minimum signature requirement - the minimum peak set that can uniquely identify a compound from all others in the library. The false positive rate is reduced by having a minimum number of matched peaks and a minimum fraction of peaks. There are two compound identification techniques: minimal signature method (MS) and percentage match method (PM).

Functionality

• Annotation/NMR

Instrument Data Type

• NMR/2D TOCSY NMR
• NMR/2D HSQC NMR

Approaches

Computer Skills

Advanced

Software Type

Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

Java

Dependencies

≥ JRE 5.0

Input Formats - Open

List of peaks with optional amplitudes

Input Formats - Proprietary

N/A

Published

2008

Last Updated

2008

License

Paper

https://www.ncbi.nlm.nih.gov/pubmed/19040747

PMID

19040747