MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. MaxQuant is freely available and can be downloaded from this site. The download includes the search engine andromeda, which is integrated into MaxQuant as well as the viewer application for inspection of raw data and identification and quantification results. For statistical analysis of MaxQuant output, we offer the Perseus framework.
To run MaxQuant, you will need .NET framework 4.5 as well as the MSFileReader for Thermo data and/or SQLite for Bruker data (you can find a manual here). If you use Windows you should have Vista or newer. Like most Windows software, MaxQuant can also be run on a Mac. There is currently no support for linux, but it is on the horizon.
This documentation is organized as a wiki, so if you find anything that is wrong or hard to understand, in most cases you can fix it yourself. The wiki can be browsed by using the links below or by searching with the box in the upper right. Anyone is allowed to read the wiki, but to make changes you will have to register and login using the button in the upper right. (The registration mechanism is currently not working properly and probably cannot be fixed before the beginning of November (2015). If you do not need to edit the wiki right now, please try to register again in a few weeks.)
Cox, J. and Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol, 2008, 26, pp 1367-72.
Note that the paper has a large supplement containing in-depth descriptions of algorithms.
Cox, J and Mann, M., Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap. J Am Soc Mass Spectrom., 2009, 20, pp 1477-85.
Cox, J., Michalski, A., and Mann, M., Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors. J Am Soc Mass Spectrom., 2011, 22, pp 1373–1380.
Schaab C., Geiger T., Stoehr G., Cox J., and Mann M. Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database. Mol Cell Proteomics, 2012, 11, M111.014068.
Cox J., Hein M. Y., Luber C. A., Paron I., Nagaraj N., and Mann M., Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ. Mol Cell Proteomics, 2014, 13, pp 2513–2526.
Tyanova, S., Temu, T., Carlson, A., Sinitcyn, P., Mann, M. and Cox, J., Visualization of LC-MS/MS proteomics data in MaxQuant, Proteomics, 2015, 15, pp 1453–1456