Approaches towards the automated interpretation and prediction of electrospray tandem mass spectra of non‐peptidic combinatorial compounds

Abstract

Combinatorial chemistry is widely used within the pharmaceutical industry as a means of rapid identification of potential drugs. With the growth of combinatorial libraries, mass spectrometry (MS) became the key analytical technique because of its speed of analysis, sensitivity, accuracy and ability to be coupled with other analytical techniques. In the majority of cases, electrospray mass spectrometry (ES-MS) has become the default ionisation technique. However, due to the absence of fragment ions in the resulting spectra, tandem mass spectrometry (MS/MS) is required to provide structural information for the identification of an unknown analyte. This work discusses the first steps of an investigation into the fragmentation pathways taking place in electrospray tandem mass spectrometry. The ultimate goal for this project is to set general fragmentation rules for non-peptidic, pharmaceutical, combinatorial compounds. As an aid, an artificial intelligence (AI) software package is used to facilitate interpretation of the spectra. This initial study has focused on determining the fragmentation rules for some classes of compound types that fit the remit as outlined above. Based on studies carried out on several combinatorial libraries of these compounds, it was established that different classes of drug molecules follow unique fragmentation pathways. In addition to these general observations, the specific ionisation processes and the fragmentation pathways involved in the electrospray mass spectra of these systems were explored. The ultimate goal will be to incorporate our findings into the computer program and allow identification of an unknown, non-peptidic compound following insertion of its ES-MS/MS spectrum into the AI package. The work herein demonstrates the potential benefit of such an approach in addressing the issue of high-throughput, automated MS/MS data interpretation.

Advances in structure elucidation of small molecules using mass spectrometry

“…13), oligosaccharides [332], glycans [333], and peptides [334]. For example, compound libraries from combinatorial synthesis show common neutral mass losses when studied under electrospray conditions [335]. Another study used neural networks to simulate 70-eV electron ionization mass spectra of alkanes [336].…”

Computational mass spectrometry for small molecules

“…For tandem MS, the fragmentation behavior of small molecules under varying fragmentation energies is not completely understood [156], and has been investigated in many studies to find general fragmentation rules [188,189]. Mass Frontier (see below) currently contains the largest fragmentation library, manually curated from several thousand publications [33].…”

Gas-phase reactions of protonated tryptophan

“…(J Am Soc Mass Spectrom 2004, 15, 65-76) © 2004 American Society for Mass Spectrometry U nderstanding the fragmentation reactions of protonated amino acids is not only important from an analytical perspective for diagnosis of inherited disorders of metabolism [1], and for automated interpretation and prediction of electrospray tandem mass spectra (ESI/MS/MS) [2], but also as models for developing the tools and concepts used to understand the mechanisms for the fragmentation mechanisms of protonated peptides (For studies on the mechanism of the fragmentation reactions of protonated amino acids see reference [3]). The loss of ammonia from protonated tryptophan is observed as the primary fragmentation pathway, with concomitant formation of a [M ϩ H Ϫ NH 3 ] ϩ ion by nucleophilic attack from the C3 position of the indole side chain.…”