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maxquant:manual:beginner

First steps with MaxQuant

The descriptions and screenshots in this tutorial refer to the MaxQuant GUI around version 1.4.3.14 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:

  1. Raw data: Along the top of the GUI are six tabs. The first of these is Raw files. Select that tab, then click “Load” to open a browser where you can select the file containing your raw data. You can select any number of files. You can also select all the raw data files in a single folder by using the “Load folder” button. In the screen shot, two files have been loaded. (If you still have questions, there is a page that goes into details about the Raw Files tab.)
  2. Labels: The second tab is Group-specific parameters. You need to go there to specify your labels. The “Type” will usually be “Standard” (obviously), and the “Multiplicity” will be 1 for label-free quantification, 2 if you have light and heavy labels, and 3 if you have light, medium, and heavy. Any number of labels can be checked in the lists. In this example, the light sample is unlabeled and the heavy sample has been labeled with Arg10 and Lys8. (You can't see them both without scrolling.)
  3. Enzymes: Also under the Group-specific parameters tab, you should enter the “Enzyme” (one or more) with which you have digested your proteins. They can be moved from the list at the left and back with the arrow buttons, and the order changed with the “t” (to top), “u” (up one place), “d” (down one place), and “b” (to bottom) buttons. In this example, we used Trypsin/P.
  4. FASTA: Finally you will need to go to the third tab, “Global parameters” to specify where to find the “Fasta files” (one or more) you want to use. The “Add file” button will open a file browser.

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!


The info below the line is from an earlier version of the wiki. It is probably not particularly useful and will be deleted soon.

  1. Start with the Raw Files tab to specify the raw data files that you want to process with MaxQuant. (Assume for now that all your data will be processed with the same parameters. Otherwise you would have to Set parameter groups.) You have two options:
    • Load - Here you can load one or more individual raw data files for processing by MaxQuant.
    • Load folder - Use this option if you have many raw data files in one folder and want to lload them all.
  2. Move on to the Group-specific parameters tab. The General button should be pre-selected. If it is not, click on it. Unless your data analysis involves Label-free quantification, that is usually the only button you will need under this tab. Start by selecting the Type of your LC-MS runs from the drop-down list. We will assume here that you are doing a Standard analysis with MS1 labels. (You would also choose “Standard” for label-free quantification. “Reporter ion” refers to runs with MS2 level labels.)
  3. Which additional parameters you must set here depends on the type chosen. For “Standard”, you need to specify the Multiplicity. Multiplicity = 1 stands for label free. Currently, multiplicity up to 3 is implemented (but we will soon have more). Then, in case of MS1 level labeling specify the labels that were used in each channel. If the Type is ‘Reporter ion’, please specify the isobaric labels accordingly. There are pre-select buttons for four common isobaric label configurations.
  4. Still assuming a “Standard” analysis, you will now specifiy the Labels you used, one or more for each of light and heavy or light, medium, and heavy.
  5. Optionally, add suitable Variable modifications, that is, modifications that might or might not be present in any given peptide. “Acetyl (Protein N-term)” and “Oxidation (M)” are pre-chosen because they are so hard to avoid, and that is the most common choice, but you could add phospho(STY), for example, if your samples are enriched in phosphopeptides.
  6. Specify next the Digestion mode that was used for digestion of proteins to peptides. Most commonly this will be “Specific”, and the Enzyme will be “Trypsin/P”, but you can select a different enzyme or even more than one from the list. (The default values for “Max. missed cleavages” and “Match” type seldom need to be changed.)
  7. Move on now to the Global parameters tab. Specify the Fasta files with the protein sequences for the Andromeda search by using the “Add file” button and the file browser it opens.
  8. Optionally use ‘Match between runs’, ‘iBAQIntensity Based Absolute Quantification’ or ‘Label-free quantification’.
  9. Press start. You can monitor the progress on the ‘Performance’ page. 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. The results can also be browsed with the program ‘Viewer.exe’. 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. A pdf document with a description of all columns in all tables will be written to ‘…\combined\txt\tables.pdf’.
maxquant/manual/beginner.txt · Last modified: 2016/03/04 15:06 by art