Screening food samples for contaminants, such as pesticides, requires the use of both GC-MS and LC-MS techniques. In order to cover a full suite of regulated compounds, several LC and GC methods are usually required that separately incorporate large suites of compounds, single residues and ‘troublesome’ compounds. Phthalimide fungicides, including captan and folpet, are compounds that are considered GC amenable pesticides, but are troublesome to analyze via standard GC analysis. In matrices containing chlorophyll, captan and folpet rapidly degrade in the injector port, making repeatable and robust analysis of these compounds very difficult. In this analysis, two LC ionization techniques (Electrospray and UniSpray) were assessed as to their ability to incorporate these problematic GC compounds into an LC method. Initial results show that captan and folpet can be analyzed in food matrix samples using an LC method using both ionization techniques. Method optimization was performed independently on each ionization technique prior to sample analysis. Linearity was assessed with the matrix samples having R2 values of > 0.99 for both compounds. The methods were also shown to be reproducible with matrix RSDs below 15%. The data presented demonstrates that the notoriously troublesome GC compounds captan and folpet can be analyzed using an LC-MS/MS via ESI or UniSpray ionization techniques.