<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>

CC BY-SA 4.0
2022-07-14T12:30:40.783Z
Kohl, the link is broken. Could you update it please?
Gian Arauz
CC BY-SA 4.0
2018-07-13T22:21:57.477Z
2018-07-13T22:21:57.477Z
Kohl Kinning
<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>

CC BY-SA 4.0
2020-07-21T17:57:52.857Z
2022-05-18T00:58:20.340Z
2022-05-18T00:58:20.340Z
Soerendip
<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>

<mass-spectrometry>
How to run MaxQuant in command line mode?
# 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 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

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## 2 answers

### Answer by username_1 on 2018-07-13. Score: 2 | Accepted answer

Give 
mono MaxQuantCmd.exe [OPTIONS]

a try.
University of Oslo description of how to use the tool in their infrastructure.

> **Comments:**
> **username_2**: Kohl, 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


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