GAVIN

- Deprecated

Version: 1.07

Description

GC-MS Assignment Validator and Integrator (GAVIN) is designed to compliment AMDIS (it cannot be used alone), which used alone has a high false positive rate and generates many missing values. GAVIN produces a cleaned peak table with the results from different samples integrated. The multiple AMDIS output files (.elu and .fin) are combined to produce a peak table of metabolites identified in at least one spectrum. A use defined threshold of samples a feature must be present in to be considered a metabolite is used. A quantification ion (QI) and 2 validation ions (VI) are extracted from the compound with the lowest mean retention time. The QI can be integrated over the integration region, which can also have its parameters altered. There is the option to remove a peak from all samples. The software is available in the supplementary material.

Functionality

• Other Tools

Instrument Data Type

• MS/GC-MS

Approaches

• Metabolomics/Targeted

Computer Skills

Advanced

Software Type

• MATLAB Script

Interface

• Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

MATLAB, Perl

Dependencies

N/A

Input Formats - Open

AMDIS.elu, netCDF

Input Formats - Proprietary

N/A

Published

2011

Last Updated

2011

License

Paper

http://www.ncbi.nlm.nih.gov/pubmed/21575589

PMID

21575589