Supplement-to-Reiter-et-al.-2022a

Metabolites

Metabolic footprinting of microbial systems based on comprehensive in-silico predictions of MS/MS revelant data

Alexander Reiter^1,2 (ORCID: 0000-0003-3499-2901),
Jian Asgari^1,2
Wolfgang Wiechert^1,3 (ORCID: 0000-0001-8501-0694),
Marco Oldiges^1,2 (ORCID: 0000-0003-0704-5597)

¹ Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich 52425, Germany
² RWTH Aachen University, Institute of Biotechnology, Aachen 52062, Germany
³ RWTH Aachen University, Computational Systems Biotechnology, Aachen 52062, Germany

Corresponding author: Prof. Dr. Marco Oldiges, mail: [email protected], phone: +49 2461 61-3951. fax: +49 2461 61-3870

Description

Supplement code for database creation (database), method creation (development) and evaluation (scan).
Example files are provided in the database folder.

General procedure:

• Create the necessary database files with database code
• Create the analysis method (project) for the organism with development code
• Transfer the methods created to your instrument
• Create a plate layout for your samples and run batch creation
• Integrate your data with the corresponding vendor software
• Use development and experiment files for data evaluation scan code

Database

Automated creation of a database based on KEGG, Pubchem and ChEMBL:

• Organisms
• Pathways
• Metabolites
• CFM-ID MS/MS Predictions

Development

Automated method development:

• Organism specific analysis methods
• Analysis batch creation

Scan

Automated data evaluation:

• Preprocessing
• Univariate analysis
• Multivariate analysis
• Cluster analysis

Requirements

Software:

• Anaconda, Python = 3.9
• Git

Channels:

• defaults
• conda-forge

Dependencies:

• adjusttext=0.7.3.1
• jupyterlab=3.2.1
• notebook=6.4.5
• numpy=1.21.3
• scipy=1.7.1
• pandas=1.3.4
• xlrd=2.0.1
• openpyxl=3.0.9
• joblib=1.1.0
• matplotlib=3.4.3
• seaborn=0.11.2
• ipython=7.29.0
• python=3.9.7
• pathlib=1.0.1
• statsmodels=0.13.0
• biopython=1.79
• pubchempy=1.0.4
• requests=2.26.0
• selenium=3.141.0
• scikit-learn=1.0.1

Anaconda

1. Install Python Environment manager with Python 3.9 (Anaconda with Anaconda Navigator).
2. Create new environment.
3. Add channels for packages.
4. Add python packages based on dependencies above.

Using the supplement code from the repository

1. In a shell, navigate to the folder where you want the repository to be located.
2. Open a terminal / shell and clone the repository via git clone {repo adress}.
3. Select the new environment in Anaconda Navigator.
4. Open terminal.
5. With cd {absolute path}, navigate to the location where the project example folder is now found.
6. Open jupyter lab window with jupyter lab.
7. The methods in this package are made to be used with the jupyter notebooks provided in the example folder.

Additional licences

pyChemometrics

BSD 3-Clause License

Copyright (c) 2017, Gonçalo dos Santos Correia All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

• Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.