Methods for protein analysis by capillary electrophoresis and mass spectrometry

Abstract: Protein analysis is important to understanding biological systems, but sample diversity necessitates a multitude of analysis techniques and methods. Challenges that are addressed include analysis of low abundance samples, fractionation to reduce sample complexity, and automation to reduce time and cost.Matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) is an important technique for protein characterization. In Paper I, the sensitivity of MALDI-MS was enhanced through the fabrication of a hydrophobic coating for the MALDI target plate, yielding analyte concentration. The plate outperformed a commercial concentration plate.Capillary electrophoresis (CE) separation offers low sample consumption and high efficiency, and in Paper II, offline CE-MALDI-MS fractionation was employed. A robot system for automation was constructed and used in analysis of spermatophore proteins from the butterfly Pieris napi. The robot was also used in automated on-target trypsin digestion under a lid of liquid fluorocarbons, a simpler and cheaper alternative to controlled humidity chambers. An indication of indigenous proteolysis of the sample was seen.Electrospray ionization (ESI) is the other technique for protein analysis in MS. In Paper III, the biomarker protein osteopontin (OPN) was analyzed by ESI-MS in order to find suitable conditions for its detection. A preliminary optimization of solvents and ionization conditions was done, and tandem MS (MSn) performed to increase the reliability of identification.