If you have questions you can't find the answer to in the documentation, try asking in the Google group with the topic closest to your problem:
All of the packages in the MaxQuant family use the Github repository "CoxLab Bug Reporting" for bug reporting. Before you create an issue, please first try the latest version of our software, following the download link on the home page. Perhaps we have already fixed the problem.
To use Github, you need to create your personal account.