The descriptions and screenshots in this tutorial refer to the MaxQuant GUI around version 184.108.40.206 from August 2014.
In case you are a first time user you might be worried by the many options and parameters that one can set in the user interface. In that case we have good news for you. In almost all use cases the standard values of most parameters are fine and you only need to adjust a small number of factors. Typically there is only little information that you need to provide. Every parameter in the interface has context help which you obtain by hovering with the mouse pointer over the text string for this parameter. This wiki also has that information, and more.
You will have to tell MaxQuant where to find your raw data files and your fasta files, and which labels and digestion enymes you are using. 90% of the time that will be enough, and you can leave the rest of the bells and whistles on their default values. Of course, we are assuming you have successfully installed and started MaxQuant, and that you can find the Start button once you have finished entering the processing parameters (hint: look in the lower left corner of the GUI). Here is more detail on how to enter those four most important parameters:
After you press the “Start” button, you can monitor the progress of the analysis under the fourth tab, Performance. A popup window saying ‘Done’ will appear when MaxQuant is finished. All result files will appear in the folder ‘…\combined\txt’ as tab-delimited text files. A pdf document with a description of all columns in all tables will be written to ‘…\combined\txt\tables.pdf’.
The fifth tab is the Viewer, used to examine the results of the analysis, which will be the topic of the viewer tutorial. All columns have interactive descriptions in the Viewer program. Just move the mouse over the beginning of the column title and click on the question mark that will appear.
The sixth and final tab is Andromeda configuration. Andromeda is the peptide search engine, which needs to know what modifications, proteases, and sequence databases to take into consideration. Almost all that you will ever need are pre-configured, but you can use the buttons under this tab to add more, if your experiment requires it.
That's how easy it can be!