This dataset contains mass spectrometry measurements acquired to verify peptide products generated by a peptide asparaginyl ligase (PAL)-catalyzed reaction, including (i) peptide substrate cyclization and hydrolysis side product formation, and (ii) protein–peptide ligation. For cyclization, the linear peptide GL12 (GIARGDYKSNSL) was processed by PAL to yield the cyclic product cGN10 (GIARGDYKSN, head-to-tail cyclized) and a linear hydrolysis by-product GN10 (GIARGDYKSN). For ligation, an affibody protein (ABY) was conjugated at its C-terminus to a short fluorescent/azide-containing peptide FL (GWSK(5-FAM)K(N3)-NH2), generating the ligation product ABY–FL. Raw MS files and deconvoluted peak lists/summaries are provided for intact mass confirmation of reactants and products.