This dataset accompanies a publication in which we present a strategy for acquisition and effective de novo peptide sequencing of complementary CID and 351 nm ultraviolet photodissociation (UVPD) MS/MS pairs. E. coli whole cell lysate is carbamylated to block lysine side chains, digested with trypsin (now active only at Arg residues), and N-terminally tagged with the chromophore AMCA. Three technical replicates were analyzed using a Thermo Velos Pro dual linear ion trap mass spectrometer coupled to a Coherent 351 nm excimer laser. Each precursor ion is isolated twice with the mass spectrometer switching between CID and UVPD activation modes to obtain a complementary MS/MS pair. We modified our UVnovo de novo sequencing software to automatically learn from and interpret fragmentation spectra from any combination of complementary activation methods, and we used this to analyze the CID/UVPD paired spectra. This performance exceeds that of PEAKS and PepNovo on the CID spectra alone and demonstrates that CID/UPVD brings significant advantages for comprehensive and accurate de novo peptide sequencing.