biocontainers/metfrag-cli repository overview

⁠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

• Kristian Peters⁠ (IPB-Halle)

⁠Website

• https://c-ruttkies.github.io/MetFrag/⁠

⁠Git Repository

• https://github.com/c-ruttkies/MetFragRelaunched⁠

⁠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.