Proteomic analysis using high performance liquid chromatography and matrix assisted laser desorption ionization fourier transform mass spectrometry
Parks, Bryan Albert
MetadataShow full item record
Proteomic analyses have become of increasing importance to systems biology due to the ability to examine proteins on a global scale that have been produced from the genes present in the system. Presently, studies typically use two-dimensional gel electrophoresis (2-DE) combined with mass spectrometry to identify proteins extracted from cells. As the field of proteomics has grown, developments have focused on the analysis of proteins not visualized by 2-DE. Of particular interest are shotgun proteomic methods, for which the proteome undergoes batch digestion with a specific protease, and the resulting peptides are analyzed to determine the original protein components. High performance liquid chromatography (HPLC) is an essential tool due to the speed of separation in addition to the ability to interface directly with mass spectrometry (MS). Although lower resolution MS technologies are often used to examine complex mixtures, Fourier-transform mass spectrometry (FTMS) is the only analyzer capable of making mass measurements with errors of 1-5 ppm. In this dissertation, matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) have been used to explore the proteome of the methanogenic archaea Methanococcus maripaludis. As a by-product of their life cycle, M. maripaludis produces methane which could be used as an alternate resource. 15General and targeted proteomic studies have been made using N labeling in combination with gene-knockout experiments to understand membrane proteins that are believed to be pivotal in methane production of this archaea.