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MaxQuant goes Linux

Nature Methods volume 15, page 401 (2018)Cite this article

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To the Editor: We report a Linux version of MaxQuant1 (http://www.biochem.mpg.de/5111795/maxquant), our popular software platform for the analysis of shotgun proteomics data.

One of our main intentions in developing MaxQuant was to ‘take the pain out of’ quantifying large collections of protein profiles2. However, unlike, for instance, the Trans-Proteomic Pipeline3, the original version of MaxQuant could be run only on Microsoft Windows, and thus its use was restricted in high-performance computing environments, which very rarely use Windows as an operating system. When we began developing MaxQuant, Windows was the only operating system supported by vendor-provided raw data access libraries. Therefore, we wrote MaxQuant in the C# programming language on top of the Windows-only .NET framework. Windows support for cloud platforms is more expensive, and the operating system is harder to use and less scalable compared with Linux.

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Fig. 1: Benchmarking MaxQuant on Linux and Windows.

References

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  2. Azvolinsky, A., DeFrancesco, L., Waltz, E. & Webb, S. Nat. Biotechnol. 34, 256–261 (2016).

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Acknowledgements

This project has received funding from the European Union’s Horizon 2020 research and innovation program (grant agreement no. 686547 to J.C., J.R. and S.Y.) and from the FP7 (grant GA ERC-2012-SyG_318987–ToPAG to S.T. and F.S.).

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Authors and Affiliations

  1. Computational Systems Biochemistry, Max Planck Institute for Biochemistry, Martinsried, Germany

    Pavel Sinitcyn, Shivani Tiwary, Jan Rudolph, Petra Gutenbrunner, Christoph Wichmann, Şule Yılmaz, Hamid Hamzeiy, Favio Salinas & Jürgen Cox

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  1. Pavel Sinitcyn
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  2. Shivani Tiwary
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  3. Jan Rudolph
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  4. Petra Gutenbrunner
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  5. Christoph Wichmann
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  6. Şule Yılmaz
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  7. Hamid Hamzeiy
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  8. Favio Salinas
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  9. Jürgen Cox
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Contributions

P.S., S.T., J.R., P.G., C.W., S.Y., H.H., F.S. and J.C. developed the software. P.S. conducted the performance analysis. J.C. wrote the manuscript.

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Correspondence to Jürgen Cox.

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The authors declare no competing interests.

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Sinitcyn, P., Tiwary, S., Rudolph, J. et al. MaxQuant goes Linux. Nat Methods 15, 401 (2018). https://doi.org/10.1038/s41592-018-0018-y

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