For example, less than 30% of all detected peaks can be identified in GC–MS based metabolomics. That means there is a large discrepancy between compounds and associated reference mass spectra. Yet, current mass spectral libraries are still insufficient in breadth and scope to identify all chemicals detected: there are only 306,622 EI-MS compound spectra in the NIST 17 mass spectral database, while PubChem has recorded 102 million known chemical compounds of which 14 million are commercially available. Gas chromatography coupled to mass spectrometry (GC/MS) is frequently used for such molecules and has been standardized with electron ionization (EI) at 70 eV more than 50 years ago. Mass spectrometry is the most important analytical technique to detect and analyze small molecules. Improved methods to calculate potential energy surfaces (PES) are still needed before QCEIMS mass spectra of novel molecules can be generated at large scale. Overall, QCEIMS can predict 70 eV electron ionization spectra of chemicals from first principles. Conformational flexibility was not correlated to the accuracy of predictions. The parameter space was probed to increase prediction accuracy including initial temperatures, the number of MD trajectories and impact excess energy (IEE). Organic oxygen compounds had a lower matching accuracy, while computation time exponentially increased with molecular size. The compounds covered 43 chemical classes, ranging up to 358 Da.
To test the accuracy of predictions, in silico mass spectra of 451 small molecules were generated and compared to experimental spectra from the NIST 17 mass spectral library.
Here, we test quantum chemistry methods (QCEIMS) to generate in silico EI mass spectra (MS) by combining molecular dynamics (MD) with statistical methods. While there are over 102 million compounds in PubChem, less than 300,000 curated electron ionization (EI) mass spectra are available from NIST or MoNA mass spectral databases. Compound identification by mass spectrometry needs reference mass spectra.