Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-07-14T12:30:40.783Z
Answers.Text: Kohl, the link is broken. Could you update it please?
Answers.UserDisplayName: Gian Arauz
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-13T22:21:57.477Z
Answers.LastActivityDate: 2018-07-13T22:21:57.477Z
Answers.UserDisplayName: Kohl Kinning
Answers.Body: <p>You can now install MaxQuant simply with Conda:</p>
  <pre><code>conda install -c bioconda maxquant
  </code></pre>
  <p>and to run MaxQuant type:</p>
  <pre><code>maxquant mqpar.xml
  </code></pre>
  <p><a href="https://bioconda.github.io/recipes/maxquant/README.html" rel="nofollow noreferrer">Reference</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-21T17:57:52.857Z
Answers.LastActivityDate: 2022-05-18T00:58:20.340Z
Answers.LastEditDate: 2022-05-18T00:58:20.340Z
Answers.UserDisplayName: Soerendip
Body: <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>
  
Tags: <mass-spectrometry>
Title: How to run MaxQuant in command line mode?
ThreadText: # How to run MaxQuant in command line mode?
  
  (Asked by: username_0 on 2018-07-13)
  
  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](http://www.coxdocs.org/doku.php?id=maxquant:common:download_and_installation) 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.
  
  **Tags:** mass-spectrometry
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2018-07-13. Score: 2 | Accepted answer
  
  Give
  
  ```
  mono MaxQuantCmd.exe [OPTIONS]
  
  ```
  
  a try.
  
  [University of Oslo](https://www.uio.no/english/services/it/research/hpc/abel/help/software/maxquant.html) description of how to use the tool in their infrastructure.
  
  > **Comments:**
  > **username_2**: username_1, the link is broken. Could you update it please?  
  
  ---
  
  ### Answer by username_0 on 2020-07-21. Score: 0
  
  You can now install MaxQuant simply with Conda:
  
  ```
  conda install -c bioconda maxquant
  
  ```
  
  and to run MaxQuant type:
  
  ```
  maxquant mqpar.xml
  
  ```
  
  [Reference](https://bioconda.github.io/recipes/maxquant/README.html)
  
  
  ---
  
  