What is the purpose of 'Folder locations' in MaxQuant?
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.