Proteomics: a pragmatic perspective

Journal name:
Nature Biotechnology
Year published:
Published online


The evolution of mass spectrometry–based proteomic technologies has advanced our understanding of the complex and dynamic nature of proteomes while concurrently revealing that no 'one-size-fits-all' proteomic strategy can be used to address all biological questions. Whereas some techniques, such as those for analyzing protein complexes, have matured and are broadly applied with great success, others, such as global quantitative protein expression profiling for biomarker discovery, are still confined to a few expert laboratories. In this Perspective, we attempt to distill the wide array of conceivable proteomic approaches into a compact canon of techniques suited to asking and answering specific types of biological questions. By discussing the relationship between the complexity of a biological sample and the difficulty of implementing the appropriate analysis approach, we contrast areas of proteomics broadly usable today with those that require significant technical and conceptual development. We hope to provide nonexperts with a guide for calibrating expectations of what can realistically be learned from a proteomics experiment and for gauging the planning and execution effort. We further provide a detailed supplement explaining the most common techniques in proteomics.

At a glance


  1. Conceptual organization of proteomic experiments.
    Figure 1: Conceptual organization of proteomic experiments.

    We broadly divide the objectives of proteomics into discovery and assay experiments. The scope of these experiments can range from very narrow (few proteins) to comprehensive (all proteins). A small set of examples is shown here, along with the technology used to study them.

  2. Applications of proteomic technologies.
    Figure 2: Applications of proteomic technologies.

    For the purpose of organizing the field of proteomics, it is instructive to compare and contrast the many conceivable applications on the basis of the complexity of the biological context versus the technical difficulty of implementing the appropriate technology. Each cell in the table shows an application of proteomics that is discussed in the main text.

  3. Technologies for proteomics.
    Figure 3: Technologies for proteomics.

    This figure depicts the proteomic workflow from sample extraction to protein quantification. For each step in the workflow, the text boxes give examples of commonly used techniques, many of which may be combined in any one study. All featured techniques are discussed in detail in the Supplementary Techniques. Further details related to the terms database searching, de novo sequencing, peptide mass fingerprinting, electrospray ionization and matrix-assisted laser desorption/ionization can be found in the Supplementary Glossary. FACS, fluorescence-activated cell sorting; 1D, one-dimensional; 2D, two-dimensional.

  4. Protein identification and quantification by mass spectrometry.
    Figure 4: Protein identification and quantification by mass spectrometry.

    A typical proteomic workflow starts by extracting proteins from cells (here metabolically labeled), followed by proteome complexity reduction by fractionation techniques before MS is used to identify and quantify the proteins present in the original sample. Each element in the tubes represents a peptide, with its identically shaped elements originating from the same protein.


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  1. University of Southern California Center for Applied Molecular Medicine, Departments of Medicine and Biomedical Engineering, Los Angeles, California, USA.

    • Parag Mallick
  2. Department of Chemistry & Biochemistry, Univeristy of California, Los Angeles, Los Angeles, California, USA.

    • Parag Mallick
  3. Chair of Proteomics and Bioanalytics, Technische Universität München, Freising-Weihenstephan, Germany.

    • Bernhard Kuster
  4. Center for Integrated Protein Science Munich, Munich, Germany.

    • Bernhard Kuster

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  1. Supplementary Text and Figures (948K)

    Supplementary Glossary, Supplementary Figure 1 and Supplementary Techniques

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