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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?

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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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