High throughput proteomic studies using fourier transform ion cyclotron resonance mass spectrometry

With the advent of soft ionization techniques, namely matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI), mass spectrometry has emerged as the method of choice for proteomic analysis. Traditionally, two-dimensional gel electrophoresis (2D-GE) followed by mass spectrometry has been utilized to identify proteins. Due to numerous limitations of 2D-GE, high-throughput alternatives have been sought out. Shotgun proteomics allows for the analysis of an entire proteome simultaneously through batch digestion of whole-cell lysates. Proteins can be identified from the resulting complex mixture from accurate mass measurements of their constituent peptides. Fourier transform mass spectrometry (FTMS) is capable of achieving the part-per-million mass accuracy and ultra-high mass resolution needed for these measurements. This thesis details a high-throughput proteomic method using LCMALDI- FTMS to analyze a protein standard and a cell lysate. Additionally, a novel technique called mass defect labeling is described as a way to increase the specificity of accurate mass measurements.