MaxQuantAnalysis is a tool that provides a platform for downstream analysis after execution of the MaxQuant program.

First, download MaxQuantAnalysis and ensure you have Python 3.3 or higher installed.

After that, create a new Python virtual environment using the venv module. The 'env' argument is the location where the virtual environment will be installed; you can place this in the same folder as MaxQuantAnalysis.

For Unix/Mac systems:
python3 -m venv env

For Windows:
py -m venv env

Next, you will need to activate the virtual environment by running the 'activate' file in the virtual environment folder you created in the last step.

For Unix/Mac systems:
source env/bin/activate

For Windows:
.\env\Scripts\activate

Then, install the requirements for this project using pip.

For Unix/Mac systems:
pip install -r requirements.txt

For Windows:
py -m pip install -r requirements.txt

This program uses command line arguments to determine what kind of input is being used and where the excel file to print to is saved. Available arguments include:

--direct, -d
--c18, -c
--sdc, -s
--urea, -u
--input, -i
--excel, -x

The -c/--c18 flag is not valid with the -d/--direct flag, as these are two methods of Mass Spectrometry analysis and it is not reasonable for them to be used together.

The -s/--sdc flag is not valid with the -u/--urea flag, as these are two types of experiments that should not be used together.

You should not have to worry about errors with invalid pairing of flags. If invalid flags are seen, the program will safely exit.

After the input flag, enter the location of a file named "proteinGroups.txt".

After the excel flag, enter the location of the excel file (if it does not yet exist, it will be created).

Examples:

python3 main.py --direct --urea --input ./data/direct/urea/proteinGroups.txt --excel ./data/experiment_results.xlsx
python3 main.py --c18 --sdc --input ./data/c18/sdc/proteinGroups.txt --excel ./data/experiment_results.xlsx