Femtosecond laser pulses have been widely used as a tool to study molecular ionization and fragmentation. This article bridges the application of femtosecond laser technology in early research focused on small isolated molecules with that in modern biological mass spectrometry for proteomics and metabolomic analysis on large (140+ atoms) biomolecules. The single-shot interaction of a femtosecond laser with neutral para-nitrotoluene (pNT) is investigated with time-of-flight mass spectrometry and compared with the ultrafast photodissociation of protonated pNT in an ion trap mass spectrometer accumulated over ∼1000 pulses. The ion trap experiment is then extended to longer biomolecules. As demonstrated in the examples of vasopressin and tomatine, this novel ion activation method provides greater sequence coverage and nonstatistical fragmentation, leading to valuable information complementary to conventional methods for structural analysis.