Molecular Structure and Identification Through G-SIMS and SMILES

Abstract

In this chapter, we discuss the use of G-SIMS (gentle secondary ion mass spectrometry) and SMILES (simplified molecular input line entry specification) for analyzing biologically relevant materials and molecules. G-SIMS is an easy-to-use method that considerably simplifies complex static secondary ion mass spectrometry (SSIMS) spectra into spectra with only those ions that are highly characteristic of the surface. G-SIMS provides information about the molecular structure that is not directly available from the mass spectrum, allowing the identification of unknown materials without the need for experimental library spectra. For complex molecules such as biomolecules, identification of the most characteristic fragment ions alone may be insufficient to uniquely identify a molecule because of the combinatorial chemical possibilities available within the achievable mass accuracy. The molecular structure can be reassembled by following the fragmentation pathways (by varying the G-SIMS surface plasma temperature); this technique is known as G-SIMS-FPM (G-SIMS fragmentation pathway mapping). This provides powerful capability analogous to MS/MS experiments traditionally used in mass spectrometry. A simple method, using SMILES, is used to simulate the fragmentation pathways that occur in G-SIMS. These pathways are found to have good agreement with the G-SIMS fragmentation pathways. The simulated pathways help analysts deduce the molecular structure, leading to refined identification. A rapid method to establish a foundational database of simulated pathways using the SIMS community and a web-based system is being developed.