Although tandem mass spectrometry has revolutionized the identification and structural characterization of peptides and proteins, future advances in comprehensive proteome analysis will depend on the development of improved methods for ion activation that yield greater sequence information, and with selective control over the fragmentation chemistry. This report presents initial findings that demonstrate the utility of a novel ion activation method using ultrashort (approximate to 30 fs) laser pulses as a means to overcome the limitations of current technologies, while opening the door to solving significant challenges in protein and peptide analysis.