From genomics to proteomics (Review article

What is proteomics and how does it relate to genomics

Proteomics is the study of the function of all expressed proteins, including their isoforms, modifications, interactions, and structural descriptions. It complements genomics, which provides the blueprint of possible gene products that are the focus of proteomics studies.

What are some of the challenges faced in proteomics

Challenges in proteomics include limited and variable sample material, sample degradation, vast dynamic range in protein abundance, numerous post-translational modifications, tissue and developmental specificity, and disease and drug perturbations.

What role does mass spectrometry play in proteomics

Mass spectrometry is a primary driving force in proteomics due to its ability to identify small amounts of protein from complex mixtures. It has shifted the balance from traditional protein separation methods to direct mass spectrometric analysis, increasing sensitivity, robustness, and data handling.

What are protein arrays and how are they used in proteomics

Protein arrays are platforms that allow rapid interrogation of protein activity on a proteomic scale. They can be based on recombinant proteins or reagents that interact specifically with proteins, such as antibodies, peptides, and small molecules. They are used to study protein interactions, modifications, and enzymatic activities.

What is structural proteomics and why is it important

Structural proteomics aims to systematically understand the structural basis for protein interactions and function. It involves techniques like X-ray crystallography, NMR, electron microscopy, and electron tomography to visualize proteins and their complexes at various scales, providing insights into cellular behavior.

How does informatics contribute to proteomics

Informatics is crucial for managing the vast data generated in proteomics. It involves sample documentation, implementation of standards, proper annotation of gene function, and development of software for data exchange and analysis. Informatics helps integrate proteomic data with other genome-wide data sets.

What are the clinical applications of proteomics

Proteomics has significant implications for clinical diagnosis and drug discovery. It enables the detection of protein profiles associated with disease states, identification of new drug targets, and understanding of biological networks. Proteomics can revolutionize protein-based diagnostics and therapeutic monitoring.

What is the significance of orthogonal omics in proteomics

Orthogonal omics refers to the integration of proteomic data with other genome-wide data sets, such as transcriptomics and phenomics. This cross-validation approach allows for robust biological insights and the generation of non-obvious hypotheses that would not arise from individual approaches.

What future developments are anticipated in proteomics

Future developments in proteomics include improvements in mass spectrometry sensitivity and throughput, advancements in sample preparation and microfluidics, and the creation of visualization tools for data integration. Proteomics is expected to converge with other technologies to provide a comprehensive description of cellular properties.

Why is open access important in proteomics research

Open access to proteomic data is essential for fostering collaboration and participation across the biomedical research community. It ensures that raw data, including protein structures, modifications, and interactions, are publicly available, facilitating research in both academic and industrial sectors.

What role does HUPO play in proteomics

The Human Proteome Organisation (HUPO) aims to coordinate large-scale proteomics efforts, avoid duplication, and provide a rationale for funding. HUPO has set goals such as defining the plasma proteome, generating antibodies to all human proteins, and developing new technologies and informatics infrastructure.

How can proteomics impact drug discovery

Proteomics can accelerate drug discovery by identifying new disease-specific targets, particularly those on the cell surface, and by providing a rational basis for target suitability through an understanding of biological networks. It also has the potential to resurrect failed drugs by uncovering their mechanisms of acti