An In Silico Infrared Spectral Library of Molecular Ions for Metabolite Identification

Abstract

Infrared ion spectroscopy (IRIS) continues to see increasing use as an analytical tool for small-molecule identification in conjunction with mass spectrometry (MS). The IR spectrum of an m/z selected population of ions constitutes a unique fingerprint that is specific to the molecular structure. However, direct translation of an IR spectrum to a molecular structure remains challenging, as reference libraries of IR spectra of molecular ions largely do not exist. Quantum-chemically computed spectra can reliably be used as reference, but the challenge of selecting the candidate structures remains. Here, we introduce an in silico library of vibrational spectra of common MS adducts of over 4500 compounds found in the human metabolome database. In total, the library currently contains more than 75,000 spectra computed at the DFT level that can be queried with an experimental IR spectrum. Moreover, we introduce a database of 189 experimental IRIS spectra, which is employed to validate the automated spectral matching routines. This demonstrates that 75% of the metabolites in the experimental data set are correctly identified, based solely on their exact m/z and IRIS spectrum. Additionally, we demonstrate an approach for specifically identifying substructures by performing a search without m/z constraints to find structural analogues. Such an unsupervised search paves the way toward the de novo identification of unknowns that are absent in spectral libraries. We apply the in silico spectral library to identify an unknown in a plasma sample as 3-hydroxyhexanoic acid, highlighting the potential of the method.

Identification of Organic Micro-Pollutants in Surface Water Using Ms-Based Infrared Ion Spectroscopy

“…This reduces the weight of the more intense peaks and increases that of peaks with lower intensity; it also makes S less sensitive to intensity deviations between experimental and computed spectra, and therefore more sensitive to frequency overlap (Houthuijs et al, 2023). The scoring algorithm is also used to quantify the similarity between two experimental spectra; in this case, a common x-axis is ensured by linearly interpolating the intensities of both spectra onto a common frequency scale with 1 cm − 1 steps.…”

“…This demonstrates that care must be taken when using computational spectra as a reference and specifically that weak vibrational bands may be underrepresented in the experimental spectrum. The absolute similarity score is therefore not to be interpreted as a direct measure of structural identification, as true positives can have a wide range in scores (Houthuijs et al, 2023). Instead, the similarity score should be employed as a ranking of candidates, as is shown below.…”

“…For the proof-of-concept identification of gemfibrozil described above, we essentially generated a small reference library of in silico IR spectra of isomeric candidates. Alternatively, a more general molecular structure search can be conducted by employing a much larger in silico library, which was constructed in earlier work involving the Human Metabolome Database (HMDB) (Houthuijs et al, 2023). This library currently contains 75 941 computed IR spectra of ions derived from 4640 compounds and can be searched with or without m/z constraints.…”

“…Multiple candidate compounds can thus be screened efficiently based on matching their predicted spectra with the spectrum of the unknown. The recent development of an in silico IR spectral library of molecular ions based on the human metabolome database (HMDB) further exploits the use of predicted vibrational spectra to aid in the identification of unknowns (Houthuijs et al, 2023). Not only can searching the library with an unknown's IR spectrum lead to direct identification, it can also yield molecular structures highly similar to the unknown, opening a path towards de novo structural elucidation.…”

Infrared Photodissociation Spectroscopy of Water-Tagged Ions with a Widely Tunable Quantum Cascade Laser for Planetary Science Applications

“…Wavelength agile IR photodissociation techniques are increasingly showing promise as analytical tools for the interrogation of a variety of biomolecule classes − including structural isomer differentiation. − Unfortunately, most implementations present insurmountable barriers for adaptation to space-borne sensors, which place stringent demands on system size, weight, and power. Immediately disqualified are direct multiphoton action spectroscopic techniques which require intense user facility photon sources .…”