Abstract

Mass spectrometry (MS) is a powerful analytical technique used in many fields, including proteomics, metabolomics, drug discovery and many more areas relying on compound identifications. Even though nowadays MS is a standard and popular method, there are many compounds which lack experimental spectra. In those cases, predicting mass spectra from the chemical structure can reveal useful information, help in compound identification and expand the spectral databases, improving the accuracy and efficiency of database search. [,].

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• Can I predict QC-based mass spectra starting from SMILES?
• How can I run those computationally heavy predictions?
• Can I take into account different conformers?

Learning Objectives

• To prepare structure-data format (SDF) files for further operations analysis, starting from chemical structure descriptors in simplified molecular-input line-entry system (SMILES) format.
• To generate 3D conformers and optimise them using semi-empirical quantum mechanical (SQM) methods.
• To produce simulated mass spectra for a given molecule in MSP (text based) format.