Immunoproteomics is the study of large sets of

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

s (

proteomics Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replicatio ...

) involved in the immune response. Examples of common applications of immunoproteomics include: * The isolation and mass spectrometric identification of MHC (major histocompatibility complex) binding peptides * Purification and identification of protein

antigen In immunology, an antigen (Ag) is a molecule, moiety, foreign particulate matter, or an allergen, such as pollen, that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune response. ...

s binding specific

antibodies An antibody (Ab) or immunoglobulin (Ig) is a large, Y-shaped protein belonging to the immunoglobulin superfamily which is used by the immune system to identify and neutralize antigens such as bacteria and viruses, including those that caus ...

(or other affinity reagents) * Comparative immunoproteomics to identify proteins and pathways modulated by a specific infectious organism, disease or toxin. The identification of proteins in immunoproteomics is carried out by techniques including gel based, microarray based, and DNA based techniques, with mass spectroscopy typically being the ultimate identification method.

Applications

Immunology

Immunoproteomics is and has been used to increase scientific understanding of both autoimmune disease pathology and progression. Using biochemical techniques,

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

and ultimately protein expression can be measured with high fidelity. With this information, the biochemical pathways causing pathology in conditions such as

multiple sclerosis Multiple sclerosis (MS) is an autoimmune disease resulting in damage to myelinthe insulating covers of nerve cellsin the brain and spinal cord. As a demyelinating disease, MS disrupts the nervous system's ability to Action potential, transmit ...

and

Crohn's disease Crohn's disease is a type of inflammatory bowel disease (IBD) that may affect any segment of the gastrointestinal tract. Symptoms often include abdominal pain, diarrhea, fever, abdominal distension, and weight loss. Complications outside of the ...

can potentially be elucidated. Serum antibody identification in particular has proven to be very useful as a diagnostic tool for a number of diseases in modern medicine, in large part due to the relatively high stability of serum antibodies. Immunoproteomic techniques are additionally used for the isolation of antibodies. By identifying and proceeding to sequence antibodies, scientists are able to identify potential protein targets of said antibodies. In doing so, it is possible to determine the antigen(s) responsible for a particular immune response. Identification and engineering of antibodies involved in autoimmune disease pathology may offer novel techniques in disease therapy.

Drug engineering

By identifying the antigens responsible for a particular immune response, it is possible to identify viable targets for novel drugs. In addition, specific antigens can further be classified based on immunoreactivity for identification of future potential

vaccine A vaccine is a biological Dosage form, preparation that provides active acquired immunity to a particular infectious disease, infectious or cancer, malignant disease. The safety and effectiveness of vaccines has been widely studied and verifi ...

preparations. In addition to the identification of vaccine candidates, immunoproteomic techniques such as western blotting can additionally be used for measuring the efficacy of a given vaccine.

Technology and instrumentation

Mass spectrometry

Mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...

can be used in the sequencing of MHC binding motifs, which can subsequently be used to predict

T cell T cells (also known as T lymphocytes) are an important part of the immune system and play a central role in the adaptive immune response. T cells can be distinguished from other lymphocytes by the presence of a T-cell receptor (TCR) on their cell ...

epitopes. The technique of peptide mass fingerprinting (PMF) can be used to check a peptide's mass spectrum against a database of protein digests which have already been documented. If the mass spectrum of the protein of interest as well as the database protein share a large amount of homology, it is likely that the protein of interest is contained within the sample.

Affinity proteomics

Affinity proteomics is a high-throughput method of studying the proteome with antibody or other affinity reagents (e.g. aptamers). Large numbers (dozens to hundreds) of immune-related cytokines and related markers can be simultaneously assayed in solution, in contrast to a solid substrate such as a microarray.

2-D gel electrophoresis and western blotting

Two-dimensional gel electrophoresis (2-D gel) techniques in culmination with western blotting has been used for many years in the identification of immune response magnitude. This can be accomplished by comparing various samples against molecular-weight size markers for qualitative analysis and against known amounts of protein standards for quantitative analysis. 2D-Gel Electrophoresis Apparatus

2-D liquid chromatography

By coupling liquid chromatography with a variety of other immunodetection techniques such as serological

proteome A proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. P ...

analysis (SERPA), it is possible to analyze the

hydrophobicity In chemistry, hydrophobicity is the chemical property of a molecule (called a hydrophobe) that is seemingly intermolecular force, repelled from a mass of water. In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to b ...

, PI, relative mass, and antibody reactivity of antibodies within a given serum.

Microarray

Microarray A microarray is a multiplex (assay), multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a Substrate (materials science), solid substrate—usu ...

analysis of various serums can be used as a means to identify changes in gene expression before, after, and during a given immune response. Immunoproteomic mice example

References

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External links

An Introduction to Protein Identification
Branches of immunology Proteomics