<p>These folders are usually generated in a default directory (where the raw files are). It can however be beneficial to set the paths to these folders manually.</p>

<blockquote>
  <p>Temporary folder</p>
</blockquote>

<ul>
<li>that is obviously where temporary files go, so having an SSD or other fast drive will benefit the I/O operations. Set that path to a fast storage partition.</li>
</ul>

<blockquote>
  <p>Combined folder</p>
</blockquote>

<ul>
<li>all the output, including <code>txt</code> directory will go here. Setting it to fast storage might speed up writing the txt files. If you set it to the same path while running multiple instances of MQ it will obviously override output. </li>
</ul>

<blockquote>
  <p>Andromeda index</p>
</blockquote>

<ul>
<li>this is where index files from Andromeda search are. By default these are inside a <code>combined/search</code> folder. Since these index files can get big, once generated by MQ they can be reused. Set this path if you want to reuse previously generated index files. </li>
</ul>

CC BY-SA 4.0
2019-06-17T15:59:39.553Z
2019-06-17T15:59:39.553Z
USER_1
<p>MaxQuant is a tool for proteomics quantification. In the settings under <code>Global parameters / Folder locations</code> are three folder locations that are possible to be changed. Thought the manual does not even mention these options. Is there any benefit in changing these locations? Or can it be bad to do that? For example, if I run multiple MaxQuant instances at the same time doing different searches?</p>

<p>What is the meaning of the <code>Fixed andromeda index folder</code>, <code>Temporary folder</code> and <code>Combined folder location</code> in MaxQuant? What is it used for and when would you (not) change it?</p>

<proteomics><maxquant>
What is the purpose of 'Folder locations' in MaxQuant?
# What is the purpose of 'Folder locations' in MaxQuant?

(Asked by: username_0 on 2019-03-06)

MaxQuant is a tool for proteomics quantification. In the settings under `Global parameters / Folder locations` are three folder locations that are possible to be changed. Thought the manual does not even mention these options. Is there any benefit in changing these locations? Or can it be bad to do that? For example, if I run multiple MaxQuant instances at the same time doing different searches?

What is the meaning of the `Fixed andromeda index folder`, `Temporary folder` and `Combined folder location` in MaxQuant? What is it used for and when would you (not) change it?

**Tags:** proteomics, maxquant

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## 1 answers

### Answer by username_1 on 2019-06-17. Score: 2

These folders are usually generated in a default directory (where the raw files are). It can however be beneficial to set the paths to these folders manually.

> Temporary folder

* that is obviously where temporary files go, so having an SSD or other fast drive will benefit the I/O operations. Set that path to a fast storage partition.

> Combined folder

* all the output, including `txt` directory will go here. Setting it to fast storage might speed up writing the txt files. If you set it to the same path while running multiple instances of MQ it will obviously override output.

> Andromeda index

* this is where index files from Andromeda search are. By default these are inside a `combined/search` folder. Since these index files can get big, once generated by MQ they can be reused. Set this path if you want to reuse previously generated index files.


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