Command line interface of MetFrag.
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README.md

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MetFrag-CLI

Version: 0.2

Short Description

Command Line Interface for MetFrag.

Description

MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.

Key features

  • Annotation of fragments

Functionality

  • Annotation / MS

Approaches

  • Metabolomics

Instrument Data Types

  • LC-MS/MS

Tool Authors

  • Christoph Ruttkies (IPB-Halle)

Container Contributors

Website

Git Repository

Installation

For local individual installation:

docker pull docker-registry.phenomenal-h2020.eu/phnmnl/metfrag-cli

Usage Instructions

For direct docker usage:

docker run --volume=$PWD:/mnt:rw -i -t docker-registry.phenomenal-h2020.eu/phnmnl/metfrag-cli java -jar /usr/local/bin/MetFragCLI.jar PeakListPath=/mnt/Training-048.txt MetFragDatabaseType=PubChem IonizedPrecursorMass=345.0874 DatabaseSearchRelativeMassDeviation=5 FragmentPeakMatchAbsoluteMassDeviation=0.001 FragmentPeakMatchRelativeMassDeviation=5 PrecursorIonMode=-1 IsPositiveIonMode=FALSE MetFragScoreTypes=FragmenterScore MetFragScoreWeights=1.0 MetFragCandidateWriter=CSV SampleName=Training-048 ResultsPath=/mnt MaximumTreeDepth=1 MetFragPreProcessingCandidateFilter=UnconnectedCompoundFilter 

Publications

  • Ruttkies C, Schymanski EL, Wolf S, Hollender J, Neumann S. MetFrag relaunched: incorporating strategies beyond in silico fragmentation. Journal of Cheminformatics. 2016;8:3. doi:10.1186/s13321-016-0115-9.