Evaluating the Accuracy of the QCEIMS Approach for Computational Prediction of Electron Ionization Mass Spectra of Purines and Pyrimidines

Mass spectrometry is the most commonly used method for compound annotation in metabolomics. However, most mass spectra in untargeted assays cannot be annotated with specific compound structures because reference mass spectral libraries are far smaller than the complement of known molecules. Theoretically predicted mass spectra might be used as a substitute for experimental spectra especially for compounds that are not commercially available. For example, the Quantum Chemistry Electron Ionization Mass Spectra (QCEIMS) method can predict 70 eV electron ionization mass spectra from any given input molecular structure. In this work, we investigated the accuracy of QCEIMS predictions of electron ionization (EI) mass spectra for 80 purine and pyrimidine derivatives in comparison to experimental data in the NIST 17 database. Similarity scores between every pair of predicted and experimental spectra revealed that 45% of the compounds were found as the correct top hit when QCEIMS predicted spectra were matched against the NIST17 library of >267,000 EI spectra, and 74% of the compounds were found within the top 10 hits. We then investigated the impact of matching, missing, and additional fragment ions in predicted EI mass spectra versus ion abundances in MS similarity scores. We further include detailed studies of fragmentation pathways such as retro Diels–Alder reactions to predict neutral losses of (iso)cyanic acid, hydrogen cyanide, or cyanamide in the mass spectra of purines and pyrimidines. We describe how trends in prediction accuracy correlate with the chemistry of the input compounds to better understand how mechanisms of QCEIMS predictions could be improved in future developments. We conclude that QCEIMS is useful for generating large-scale predicted mass spectral libraries for identification of compounds that are absent from experimental libraries and that are not commercially available.

Development and application of an in-house library and workflow for gas chromatography–electron ionization–accurate-mass/high-resolution mass spectrometry screening of environmental samples

This work presents an optimized gas chromatography–electron ionization–high-resolution mass spectrometry (GC-EI-HRMS) screening method. Different method parameters affecting data processing with the Agilent Unknowns Analysis SureMass deconvolution software were optimized in order to achieve the best compromise between false positives and false negatives. To this end, an accurate-mass library of 26 model compounds was created. Then, five replicates of mussel extracts were spiked with a mixture of these 26 compounds at two concentration levels (10 and 100 ng/g dry weight in mussel, 50 and 500 ng/mL in extract) and injected in the GC-EI-HRMS system. The results of these experiments showed that accurate mass tolerance and pure weight factor (combination of reverse-forward library search) are the most critical factors. The validation of the developed method afforded screening detection limits in the 2.5–5 ng range for passive sampler extracts and 1–2 ng/g for mussel sample extracts, and limits of quantification in the 0.6–3.2 ng and 0.1–1.8 ng/g range, for the same type of samples, respectively, for 17 model analytes. Once the method was optimized, an accurate-mass HRMS library, containing retention indexes, with ca. 355 spectra of derivatized and non-derivatized compounds was generated. This library (freely available at https://doi.org/10.5281/zenodo.5647960), together with a modified Agilent Pesticides Library of over 800 compounds, was applied to the screening of passive samplers, both of polydimethylsiloxane and polar chemical integrative samplers (POCIS), and mussel samples collected in Galicia (NW Spain), where a total of 75 chemicals could be identified.

Benchmark PhotoIonization Cross-Sections of Neutral Scandium from the Ground and Excited States

The B-spline R-matrix method has been used to investigate cross-sections for photoionization of neutral scandium from the ground and excited states in the energy region from the 3d and 4s valence electron ionization thresholds to 25 eV. The initial bound states of Sc and the final residual Sc+ ionic states have been accurately calculated by combining the multiconfiguration Hartree-Fock method with the frozen-core close-coupling approach. The lowest 20 bound states of Sc I belonging to the ground 3d4s2 and excited 3d24s, 3d24p, 3d4s4p, 4s24p, and 3d3 configurations have been considered as initial states. The 81 LS final ionic states of Sc+ belonging to the terms of 3p63d2, 3p63d4l (l = 0–3), 3p63d5l (l = 0–3), 3p63d6s, 3p64s2, 3p64s4l (l = 0–3), 3p64s5l (l = 0–1), and 3p64p2 configurations have been included in the final-state close-coupling expansion. The cross-sections are dominated by complicated resonance structures in the low energy region converging to several Sc+ ionic thresholds. The inclusion of all these final ionic states has been noted to significantly impact the near-threshold resonance structures and background cross-sections. The important scattering channels for leaving the residual ion in various final states have been identified, and the 3d electron ionization channels have been noted to dominate the cross-sections at higher photon energies.