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Abstract
Shotgun proteomics involves digestion of a protein mixture followed by separation of the peptides and subsequent analysis by mass spectrometry. Our approach to shotgun proteomics relies on accurate mass measurement of peptides by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). This thesis describes two different strategies to improve proteomic analysis. The first approach uses mass defect labeling of cysteine residues in order to improve peptide assignment. The improvement originates from decongestion of the mass spectra due to the mass shift exhibited by the cysteine-containing peptides. The second approach targets a critical step for any shotgun proteomic analysis which is the proteolysis of the protein mixture. An aqueous-organic solvent system is proposed to improve the specificity of the peptides generated by trypsin and also to reduce significantly the time required for digestion.