1. Pluto Knowledge Base
  2. Reference: Analysis Terms & Methods

Introduction to Proteomics

Proteomics is the large scale study of proteins and their interactions, function, composition, structure and cellular activity. These experiments capture the entire set of proteins produced or modified by your biological system of interest.

Why are proteins important?

1. Protein Expression and Function

Proteins are essential macromolecules that play diverse roles in living organisms helping cells function, serving as structural components, enzymes, signaling molecules, and more. Proteins expressed by a cell differ between cell type and the cell's environment, making this an interesting area of study. 

2. Importance of Studying Proteins

Understanding the proteome—the entire complement of proteins—provides a holistic view of cellular function. In contrast to the genome, which remains relatively constant, the proteome provides information about the cell's function and biological activity.

Techniques in Proteomics

1. Mass Spectrometry

Mass spectrometry (MS) is a high throughput technique that is commonly used to study proteins within cells.  Proteins are tagged to stably isotopes and digested to generate labeled peptides that are separated by liquid chromatography and analyzed by tandem MS which increases the accuracy of peptide fragmentation and identification. The raw output is m/z (mass to charge ratio) for each peptide fragment.

2. Protein Separation

Before MS analysis, proteins are often separated to reduce sample complexity. Techniques such as two-dimensional gel electrophoresis (2D-GE) or liquid chromatography (LC) help resolve proteins based on size, charge, and hydrophobicity.


  1. Biomarker Discovery:

    • Identifying specific proteins associated with diseases can lead to the discovery of biomarkers. These biomarkers can be used for early diagnosis, prognosis, and monitoring of diseases, including cancer, neurodegenerative disorders, and cardiovascular diseases.
  2. Disease Mechanism Elucidation:

    • Proteomics helps researchers understand the molecular mechanisms underlying diseases. By analyzing the expression levels and modifications of proteins, scientists can gain insights into the complex processes involved in various pathological conditions.
  3. Drug Target Discovery:

    • Proteomics facilitates the identification of potential drug targets by uncovering proteins involved in disease pathways. The structure/function properties of the target protein can help identify ways to modulate protein function.
  4. Pharmacoproteomics:

    • Evaluating the response of proteins to drug treatments allows for a better understanding of drug efficacy and potential side effects. Pharmacoproteomics contributes to personalized medicine by tailoring treatments based on individual protein profiles.
  5. Functional Proteomics:

    • Studying protein functions helps elucidate the roles of individual proteins and their interactions within cellular processes. This knowledge is fundamental for understanding the complexities of biological systems and how proteins interact with each other.
  6. Protein-Protein Interactions:

    • Investigating protein-protein interactions provides insights into the architecture of cellular networks. Understanding how proteins interact can reveal key players in signaling pathways and other cellular processes that may be of interest for further research.
  7. Structural Proteomics:

    • Determining the three-dimensional structures of proteins is essential for understanding their functions. Proteomics contributes to structural biology by providing information on the shapes and conformations of proteins. This is an important analysis type in finding new drug targets.
  8. Immunoproteomics:

    • Immunoproteomics focuses on the identification and characterization of immune system related proteins. This has applications in vaccine development, understanding host-pathogen interactions, and studying the immune response to diseases.
  9. Environmental Proteomics:

    • Proteomics can be applied to environmental science to study the impact of changes in the environment on organisms in a given ecosystem. It helps identify proteins involved in stress responses and adaptation to environmental changes.
  10. Agricultural Proteomics:

    • Proteomics is used in agriculture to improve crop yield, quality, and resistance to diseases. Understanding the proteome of plants and their interactions with pathogens can guide the development of more resilient crops.
  11. Food Proteomics:

    • Analyzing the proteome of food products is important for quality control, authentication, and safety assessment. Proteomics can detect allergens, contaminants, and adulterants in food.

These applications highlight the versatility of proteomics in advancing our understanding of biological systems, promoting medical advancements, and addressing challenges in diverse fields.