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Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology

Nature Immunology volume 15, pages 112–117 (2014)Cite this article

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Proteomics based on high-resolution mass spectrometry has become a powerful tool for the analysis of protein abundance, modifications and interactions. Here we describe technical aspects of proteomics workflows, instrumentation as well as computational considerations to obtain high-quality proteomics data.

Proteins are the functionally most diverse class of biological molecules and facilitate all cellular processes. Traditionally, proteins of interest are characterized via targeted approaches using antibodies or genetically encoded tags and techniques such as immunoblotting, enzyme-linked immunosorbent assay (ELISA), microscopy or fluorescence activated cell sorting (FACS). However, each of these only opens up a small window into a multilayered and highly interconnected network of functionally and physically interacting proteins in the cellular context.

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Figure 1: Cellular and immunological processes that can be studied using proteomics tools.
Figure 2: Shotgun proteomics workflow.
Figure 3: Strategies for quantification of peptides from MS1 spectra.
Figure 4: Computational data analysis.

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Authors and Affiliations

  1. Felix Meissner and Matthias Mann are in the Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,

    Felix Meissner & Matthias Mann

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  1. Felix Meissner
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  2. Matthias Mann
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Correspondence to Felix Meissner or Matthias Mann.

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Meissner, F., Mann, M. Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology. Nat Immunol 15, 112–117 (2014). https://doi.org/10.1038/ni.2781

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