The Viewer


Cox Lab


November 15, 2023

Modern software platforms enable the analysis of shotgun proteomics data in an automated fashion resulting in high quality identification and quantification results. Additional understanding of the underlying data can be gained with the help of advanced visualization tools that allow for easy navigation through large LC-MS/MS datasets potentially consisting of terabytes of raw data. The updated MaxQuant version has a map navigation component that steers the users through mass and retention time-dependent mass spectrometric signals. It can be used to monitor a peptide feature used in label-free quantification over many LC-MS runs and visualize it with advanced 3D graphic models. An expert annotation system aids the interpretation of the MS/MS spectra used for the identification of these peptide features.

To run MaxQuant with its Viewer module, you will need .NET framework 4.5. If you use Windows you should have Windows 10 or newer.

1 Documentation outline

You can find raw files and processed data to test the Viewer (v. here.

Important note: If you load the mqpar.xml file, make sure all file paths are correct! If needed, update them using the “Change folder” option.

For additional training, consider attending our annual MaxQuant Summer School.

Also watching some MaxQuant videos on our video channel provides more insight.

For more details and better understanding of the viewer, you might be interested in reading our publication1.


Tyanova, S. et al. Visualization of LC-MS/MS proteomics data in MaxQuant. PROTEOMICS 15, 1453–1456 (2015).