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Python package to annotate LC-MS and DIMS data

Project description

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BEAMSpy (Birmingham mEtabolite Annotation for Mass Spectrometry) is a Python package that includes several automated and seamless computational modules that are applied to putatively annotate metabolites detected in untargeted ultra (high) performance liquid chromatography-mass spectrometry or untargeted direct infusion mass spectrometry metabolomic assays in an automated process. All reported metabolites are annotated to level 3 of the Metabolomics Standards Initiative (MSI) reporting standards (Metabolomics. 2007 Sep; 3(3): 211–221. doi: 10.1007/s11306-007-0082-2).

The package is highly flexible to suit the diversity of sample types studied and mass spectrometers applied in untargeted metabolomics studies. The user can use the standard reference files included in the package or can develop their own reference files.

Quick installation


  1. Install Miniconda.
  2. Run the following commands to install BEAMSpy.

Windows-64, Linux-64 and OSx

$ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
$ activate beamspy

Linux-64 and OSx

$ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
$ source activate beamspy


Command line interface (CLI)

$ beamspy --help

Graphical user interface (GUI)

$ beamspy start-gui

Bug reports

Please report any bugs that you find here. Or fork the repository on GitHub and create a pull request (PR). We welcome all contributions, and we will help you to make the PR if you are new to git.


Released under the GNU General Public License v3.0 (see LICENSE file)

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