The total-ion-yield (TIY) near-edge X-ray absorption fine-structure (NEXAFS) spectra of two dipeptides were measured and analyzed to identify the excitation sites of core electrons and the corresponding destination molecular orbitals. Peptide molecules were transferred to the gaseous phase using traditional heating and MALDI methods, ensuring that the resulting NEXAFS spectra and fragmentation products were consistent across both approaches. Mass spectra obtained at various excitation energies revealed the branching ratios of products at each energy level, offering insights into specific dissociation phenomena. Notably, variations in excitation energy demonstrated a selective dissociation process, with certain products forming more efficiently. This specificity appears closely linked to dissociations near the peptide bond, where the nodal planes of destination molecular orbitals are located. These findings were validated using both small peptide models and peptoid molecules, highlighting consistent patterns in the dissociation behavior.