Mass spectrometry (MS) is an extremely powerful analytical tool that has become the method of choice for many researchers for addressing both immunological and molecular biological problems. With the development of a “soft” ionization technique, electrospray ionization, it is now possible to analyze non-volatile biological samples. The advantages of mass spectrometry over other methods include excellent sensitivity, rapid analysis time, high mass accuracy, the ability to analyze complex mixtures and identification of post-translational modifications.; Identification of most immunological peptides has been achieved by the combination of an immunoassay, such as T cell proliferation, with mass spectrometry. Availability and reliability of the immunoassays is a major limitation of this strategy. Therefore, two different approaches were employed for the identification of major histocompatibility complex (MHC) class I and class II peptides. The first approach utlitized a Fourier transforms mass spectrometer (FTMS) for differential analysis study of class II peptides from an autoantigen, myelin basic protein (MBP). Two new computer programs, differential analysis and nested set programs were used to assist in identifying the eighteen class II MBP peptides. The identification of these peptides will aid in understanding of both the maintenance and breakdown of tolerance mechanisms is key to understanding, preventing and potentially treating autoimmune diseases, such as multiple sclerosis. The second approach employed selected reaction monitoring scanning (SRM) using a triple quadrupole mass spectrometer to identify HLA-A3 supertype class I antigens.; Mass spectrometry also plays a significant role in the field of proteomics, such as identifying protein-protein interactions in various biological systems. An example of this type of analysis is the identification of new binding partners, Rfc2, Rfc3, and Rfc5 with a novel DNA polymerase, Trf4/Polσ. Identification of these new interactions will help to elucidate the function of the polymerase in chromosomal replication and segregation. Aberrations in these processes have been shown to be involved with the onset of tumorigenesis and the molecular events that lead to chromosomal missegregation are poorly understood. Therefore, the elucidation of the key events and proteins involved in normal chromosomal replication and segregation may lead to the identification of new drug targets for anticancer therapies.
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