Ultrafast Ionization and Fragmentation: From Small Molecules to Proteomic Analysis

Abstract

Proteomic analysis offers great diagnostic relevance, because unlike DNA, different cells in an organism express different proteins. In fact, the cellular proteome can vary as a function of time or in response to stimuli. Beyond amino acid sequence, protein function depends on chemical modifications known as post-translational modifications (PTMs) that serve as “switches” and “signals” that activate or inhibit vital functions. Despite advances in mass spectrometry, which have led to the development of fully automated protein sequencing instruments, the mapping of PTMs remains a challenge. The interaction of intense near-infrared femtosecond laser pulses with isolated molecules or ions leads to the creation of radical-ion species through an ultrafast process known as tunnel ionization. The resulting unstable ions fragment according to predictable dissociation pathways. Progress analyzing and controlling the fundamental processes taking place during photoionization and fragmentation of small polyatomic molecules has led to the development of femtosecond laser-induced ionization/dissociation (fs-LID) for proteomic analysis. Fs-LID has been proven effective for the mapping of phosphorylation sites as well as other PTMs along the peptide backbone. The fundamental steps involved in fs-LID, which permits cleavage of strong bonds while leaving chemically labile bonds intact, are discussed. Numerous examples are given to illustrate this exciting new ion activation method, and potential applications are identified.