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Chapter 1-4 describes computational studies, using molecular dynamics, on in-silico mass spectra of small molecules generation. Chapter 5 provides another routine from experimental side to help unknown metabolites identification with methane chemical ionization and quadrupole-time of flight mass spectrometry.

We tested methane chemical ionization on 367 trimethylsilylated (TMS) derivatized metabolites using quadrupole time-of-flight detector (QTOF). We developed an algorithm to automatically detect molecular ion species and tested SIRIUS software on how accurate the determination of molecular formulas.

We chose 816 trimethylsilyl derivatives of organic acids, alcohols, amides, amines, and thiols to compare in silico-generated spectra against the experimental EI mass spectra from the NIST17 library, suggesting that QCEIMS methods can be extended to compounds that are not present in experimental databases.

We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.