EnviroMS 1.0.0

Search and Assign Molecular Formulas for Complex Mixtures of Small Molecules

EnviroMS

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

Current Version

1.0.0

Data input formats

• CoreMS self-containing Hierarchical Data Format (.hdf5)

Data output formats

• Pandas data frame (can be saved using pickle, h5, etc)
• Text Files (.csv, tab separated .txt, etc)
• Microsoft Excel (xlsx)
• 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 metadata stored as json attributes

Data structure types

• FT-ICR MS
• LC-FT-ICR MS

Available features

Signal Processing

• Baseline detection, subtraction, smoothing
• Manual and automatic noise threshold calculation
• First and second derivatives peak picking methods
• Peak Area Calculation
• EIC Chromatogram deconvolution(TODO)

Calibration

• Ledford
• Linear
• Quadratic

Compound Identification

• Automatic local (SQLite) or external (PostgreSQL) database check, generation, and search
• Automatic molecular match algorithm

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   
  

Usage

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-gcms-workflow path_to_MetamsFile.json

EnviroMS Docker

A docker image containing the EnviroMS command line as the 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 gcms data, EnviromsFile.json and CoremsFile.json

  docker run -v $(data_dir):/metaB/data corilo/enviroms:latest run-gcms-workflow /metaB/data/EnviromsFile.json    
  

• Getting 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