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= Immunoproteomics Sandbox =

Immunoproteomics is the study of large sets of proteins (proteomics) involved in the immune response.

Examples of common applications of immunoproteomics include: An important aspect to proteomics in general is that mass spectrometry is typically the method which is ultimately used or protein identification.
 * the isolation and mass spectrometric identification of MHC (major histocompatibility complex) binding peptides
 * purification and identification of protein antigens binding specific antibodies (or other affinity reagents), and
 * comparative immunoproteomics to identify proteins and pathways modulated by a specific infectious organism, disease or toxin.

In addition to mass spectrometry, gel based, microarray based, and DNA based techniques, are also commonly used for identifying protein expression.

Immunology
Immunoproteomics is and has been used to increase scientific understanding of both autoimmune disease pathology and progression. Using biochemical techniques, gene and ultimately protein expression can be measured with high fidelity. With this information, the biochemical pathways causing pathology in conditions such as Multiple Sclerosis, Crohn's disease, etc. 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.

Mass Spectrometry
Mass spectrometry can be used in the sequencing of MHC binding motifs, which can subsequently be used to predict T 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 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.

Western Blotting
Western blotting techniques have been used for many years in the identification of immune response magnitude.