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 residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...

s (

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

) involved in the

immune response An immune response is a reaction which occurs within an organism for the purpose of defending against foreign invaders. These invaders include a wide variety of different microorganisms including viruses, bacteria, parasites, and fungi which coul ...

. 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 or molecular structure or any foreign particulate matter or a pollen grain that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune respon ...

s binding specific

antibodies An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of ...

(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 An autoimmune disease is a condition arising from an abnormal immune response to a functioning body part. At least 80 types of autoimmune diseases have been identified, with some evidence suggesting that there may be more than 100 types. Nearly a ...

pathology and progression. Using biochemical techniques,

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

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 (cerebral) sclerosis (MS), also known as encephalomyelitis disseminata or disseminated sclerosis, is the most common demyelinating disease, in which the insulating covers of nerve cells in the brain and spinal cord are damaged. This ...

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 (which may be bloody if inflammation is severe), fever, abdominal distensi ...

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 preparation that provides active acquired immunity to a particular infectious or malignant disease. The safety and effectiveness of vaccines has been widely studied and verified.

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 u ...

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

T cell A T cell is a type of lymphocyte. T cells are one of the important white blood cells 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 r ...

epitope An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The epitope is the specific piece of the antigen to which an antibody binds. The p ...

s. The technique of

peptide mass fingerprinting Peptide mass fingerprinting (PMF) (also known as protein fingerprinting) is an analytical technique for protein identification in which the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately ...

(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 Two-dimensional gel electrophoresis, abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins. Mixtures of proteins are separated by two properties in two dimensions on 2D gels. 2-DE was first ...

(2-D gel) techniques in culmination with

western blot The western blot (sometimes called the protein immunoblot), or western blotting, is a widely used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract. Besides detect ...

ting 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 In chemical analysis, chromatography is a laboratory technique for the separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it through a system (a ...

with a variety of other immunodetection techniques such as serological

proteome The 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. ...

analysis (SERPA), it is possible to analyze the

hydrophobicity In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, t ...

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

Microarray

Microarray A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silicon ...

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