Mass spectrometry (MS) has been an important technique to ionize and sequence peptides, which makes MS indispensable in the field of proteomics. This dissertation contains studies of peptide ionization and dissociation using different methods. Various types of peptides were ionized with electrospray ionization (ESI) or matrix-assisted laser desorption ionization (MALDI) and dissociated by collision-induced dissociation (CID) or electron transfer dissociation (ETD). Mass spectra presented in this dissertation provide abundant information about peptide ionization and peptide sequencing. The addition of trivalent chromium, Cr(III), complexes to peptide solutions can increase the intensity of doubly protonated peptides, [M + 2H]2+, by ESI. Cr(H2O)63·3H2O and [Cr(THF)3]Cl3 work as reagents that provide the most abundant [M + 2H]2+, the greatest [M + 2H]2+ to [M + H]+ ratio, and the cleanest mass spectra. The requirement of the aqueous solution indicates that water is involved in the mechanism, and the effect of the ESI design suggests that this Cr(III)-induced effect occurs during the ESI desolvation process. Cr(III) complexes and iron oxide nanoparticles can not be used as MALDI matrices to analyze acidic peptides. Cr(III) complexes produce intense background ions, and no peptide ions were observed with any iron oxide nanoparticles due to adsorption interactions. In both positive and negative ion modes, high-energy CID produces greater sequence coverage and less abundant product ions containing neutral losses compared with low-energy and medium-energy CID. The formation of immonium ions and the side-chain fragmentation can indicate the presence of specific amino acid residues. High-energy CID from [M ? H]? provides complementary sequence information to results from [M + H]+. In addition, the absence of selective cleavage adjacent to proline from [M ? H]? is beneficial because y-ions from [M + H]+ commonly dominate the mass spectra. Selective cleavage adjacent to acidic residues and C-terminal residue exclusion occur in both ion modes. In ETD of doubly protonated ions, [M + 2H]2+, carboxylic acid groups from either the C-terminus or the side chains of acidic residues do not have a significant effect on sequence coverage of c- and z-ions. With permethylation (conversion of -COOH to -COOCH3), the zn//+ to zn/+ ratios increase only for peptides with basic residues at the C-terminus. Therefore, hydrogen bonding between a carboxylic acid group and a basic residue may interfere with zn//+ formation. The generation of y-ions may involve a CID-like mechanism and could be affected by deprotonation of either -COOH and -SH through zwitterion formation.