Aerosol Mass Spectrometry (AMS) has emerged as the principal tool for aerosol analysis and soft ionization techniques are an important subset particularly suited for chemical speciation investigations. This dissertation presents the use of soft ionization AMS for the analysis of complex organic aerosols in laboratory studies, both as models for Primary and Secondary Organic Aerosol (POA and SOA). An established technique (PERCI-AMS) is used to identify the resonance capture mechanisms for cysteine containing peptide residues. This technique is then applied to investigate the ozonolysis of mixed particles representative of biogenic rich organic aerosol as is common for marine aerosols. In order to apply soft ionization AMS to lower concentrations of particle mass more representative of ambient aerosol loadings and thus allow SOA investigations, an entirely new AMS technique was developed and is presented utilizing Near-Infrared Laser-Desorption-Ionization (NIR-LDI-AMS). The advantages this technique are exemplified by an analysis of limonene ozonolysis SOA whereby first generation homogeneous oxidation products are delineated from second generation heterogeneous oxidation products.