MaxQuant

MaxQuant is a 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.

1 Documentation outline

• Download and installation
• First steps in MaxQuant
• Viewer
• Andromeda
• Output Tables
• Google groups
• maxquant Bug reporting
• Glossary

For additional training, consider attending the annual MaxQuant Summer School. Also watching some MaxQuant videos provides more insight.

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2 Bibliography

For a deep-dive into the technique and progress behind MaxQuant, many papers of varying degrees of details were published over the last decades. For further reading, you can look at a small list of the more important corner stones of the MaxQuant development history.¹ (Note that the paper has a large supplement containing in-depth descriptions of algorithms),²,³,⁴,⁵,⁶ (Note that this paper explains how to run MaxQuant in detail.),⁷

References

1.

Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology 26, 1367–1372 (2008).

2.

Cox, J., Michalski, A. & Mann, M. Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors. Journal of the American Society for Mass Spectrometry 22, 1373–1380 (2011).

3.

Schaab, C., Geiger, T., Stoehr, G., Cox, J. & Mann, M. Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database. Molecular & Cellular Proteomics 11, M111.014068 (2012).

4.

Cox, J. et al. Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ. Molecular & Cellular Proteomics 13, 2513–2526 (2014).

5.

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

6.

Tyanova, S., Temu, T. & Cox, J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nature Protocols 11, 2301–2319 (2016).

7.

Sinitcyn, P. et al. MaxQuant goes Linux. Nature Methods 15, 401–401 (2018).