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Search and Assign Molecular Formulas for Complex Mixtures of Small Molecules

Project description

EnviroMS

EnviroMS is a workflow for natural organic matter data processing and annotation

Current Version

1.2.2

Data input formats

  • Generic mass list in profile and centroid mode (include all delimiters types and Excel formats)

Data output formats

  • Pandas data frame (can be saved using pickle, h5, etc)
  • Text Files (.csv, tab separated .txt, etc)
  • Microsoft Excel (xlsx)
  • Automatic JSON for workflow metadata
  • Self-containing Hierarchical Data Format (.hdf5) including raw data and ime-series data-point for processed data-sets with all associated workflow metadata (JSON)

Data structure types

  • FT-ICR MS
  • LC-FT-ICR MS

Molecular formulae search and assignment

  • Automatic local (SQLite) or external (PostgreSQL) database check, generation, and search
  • Automatic molecular formulae assignments algorithm for ESI(-) MS for natural organic matter analysis
  • Automatic fine isotopic structure calculation and search for all isotopes
  • Flexible Kendrick normalization base
  • Kendrick filter using density-based clustering
  • Kendrick classification
  • Hetero atoms classification and visualization

EnviroMS Installation

  • PyPi:
pip3 install enviroms
  • From source:
pip3 install --editable .

To be able to open thermo raw files a installation of pythonnet is needed:

  • Windows:

    pip3 install pythonnet
    
  • Mac and Linux:

    brew install mono
    pip3 install pythonnet   
    

Running the workflow

enviroMS dump_json_template EnviromsFile.json
enviroMS dump_corems_json_template CoremsFile.json

Modify the EnviromsFile.json and CoremsFile.json accordingly to your dataset and workflow parameters make sure to include CoremsFile.json path inside the EnviromsFile.json: "corems_json_path": "path_to_CoremsFile.json"

enviroMS run-di path_to_MetamsFile.json

EnviroMS Docker

A docker image containing the EnviroMS command line as code entry-point

If you don't have docker installed, the easiest way is to install docker for desktop

  • Pull from Docker Registry:

    docker pull corilo/enviroms:latest
    
  • Build the image from source:

    docker build -t enviroms:latest .
    
  • Run Workflow from Container:

    $(data_dir) = dir_containing the FT-ICR MS data, EnviromsFile.json and CoremsFile.json

    docker run -v $(data_dir):/metaB/data corilo/enviroms:latest run-di /metaB/data/EnviromsFile.json    
    
  • Get the parameters templates:

    docker run -v $(data_dir):/metaB/data corilo/enviroms:latest dump_json_template /metaB/data/EnviromsFile.json    
    
    docker run -v $(data_dir):/metaB/data corilo/enviroms:latest dump_corems_json_template /metaB/data/CoremsFile.json
    

Project details


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Files for EnviroMS, version 1.2.2
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