text: user3061: MaxQuant is a software package for mass spectroscopy and proteomics. There is a windows version and a linux version. To run on linux you have to use a program that is called mono. I think, it is developed by Microsoft, which I find quite nice from them. I installed mono on Linux and started MaxQuant. 
  mono MaxQuant.exe
  
  The documentation claims it is for running MaxQuant in commandline mode, though a GUI is started anyway. How can I start the program in commandline mode to perform batch analysis? I think, there is not enough information given on the web-page. 
  
  user181: Give 
  mono MaxQuantCmd.exe [OPTIONS]
  
  a try.
  University of Oslo description of how to use the tool in their infrastructure.
  
original_text: 3061: <p>MaxQuant is a software package for mass spectroscopy and proteomics. There is a windows version and a linux version. To run on linux you have to use a program that is called <code>mono</code>. I think, it is developed by Microsoft, which I find quite nice from them. I installed mono on Linux and started MaxQuant. </p>
  
  <pre><code>mono MaxQuant.exe
  </code></pre>
  
  <p>The <a href="http://www.coxdocs.org/doku.php?id=maxquant:common:download_and_installation" rel="noreferrer">documentation</a> claims it is for running MaxQuant in commandline mode, though a GUI is started anyway. How can I start the program in commandline mode to perform batch analysis? I think, there is not enough information given on the web-page. </p>
   181: <p>Give </p>
  
  <pre><code>mono MaxQuantCmd.exe [OPTIONS]
  </code></pre>
  
  <p>a try.</p>
  
  <p><a href="https://www.uio.no/english/services/it/research/hpc/abel/help/software/maxquant.html" rel="nofollow noreferrer">University of Oslo</a> description of how to use the tool in their infrastructure.</p>
  