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  • Protocol Update
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The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

Abstract

MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis. Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms. Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques. This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda. This protocol update describes an adaptation of an existing protocol that substantially modifies the technique. Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs). The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail. Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs. The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores. The software is written in C# and is freely available at http://www.maxquant.org.

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Figure 1: Overview of the computational workflow.
Figure 2: Labeling and quantification modes.
Figure 4: 10plex TMT quantification results for peptide feature-level quantification of spiked-in peptides in a 10Plex TMT experiment from Keshishian et al.38.
Figure 3: The graphical user interface for group-specific labeling parameters.
Figure 5: 'Match between runs' algorithm.

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Acknowledgements

This project received funding from the European Union's Horizon 2020 Research and Innovation Programme under grant agreement no. 686547 (to J.C.).

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T.T. analyzed the data. All authors wrote and edited the manuscript.

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Correspondence to Juergen Cox.

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The authors declare no competing financial interests.

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Tyanova, S., Temu, T. & Cox, J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 11, 2301–2319 (2016). https://doi.org/10.1038/nprot.2016.136

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