Design of the First Analytical Platform for Automated Top Down Proteomics With quadrupole/Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

118 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2004.The enclosed writing details technology development leading to the first high-throughput proteome analysis of Methanosarcina acetivorans utilizing a custom FT mass spectrometer. It outlines a two dimensional separations platform that utilizes a 96 well plate nanospray robot to facilitate automated analysis on the mass spectrometer. This thesis also highlights instrument advancements required to improve throughput for observation of protein intact masses and methods used to obtain robust fragmentation. Included within the automation platform is software developed for efficiently managing intact protein and MS/MS data. Also, a novel fragmentation method has been developed to extend dynamic range for fragmentation of intact proteins as large as 60 kDa. The enclosed work is the foundation for the first fully automated platform for intact protein analysis by tandem MS. With the identification of hundreds of proteins from a single run, the high-throughput Top Down proteome analysis of intact proteins is now a reality.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD