Unraveling the unknown areas of the human metabolome: the role of infrared ion spectroscopy

Combining Experimental with Computational Infrared and Mass Spectra for High-Throughput Nontargeted Chemical Structure Identification

The inability to identify the structures of most metabolites detected in environmental or biological samples limits the utility of nontargeted metabolomics. The most widely used analytical approaches combine mass spectrometry and machine learning methods to rank candidate structures contained in large chemical databases. Given the large chemical space typically searched, the use of additional orthogonal data may improve the identification rates and reliability. Here, we present results of combining experimental and computational mass and IR spectral data for high-throughput nontargeted chemical structure identification. Experimental MS/MS and gas-phase IR data for 148 test compounds were obtained from NIST. Candidate structures for each of the test compounds were obtained from PubChem (mean = 4444 candidate structures per test compound). Our workflow used CSI:FingerID to initially score and rank the candidate structures. The top 1000 ranked candidates were subsequently used for IR spectra prediction, scoring, and ranking using density functional theory (DFT-IR). Final ranking of the candidates was based on a composite score calculated as the average of the CSI:FingerID and DFT-IR rankings. This approach resulted in the correct identification of 88 of the 148 test compounds (59%). 129 of the 148 test compounds (87%) were ranked within the top 20 candidates. These identification rates are the highest yet reported when candidate structures are used from PubChem. Combining experimental and computational MS/MS and IR spectral data is a potentially powerful option for prioritizing candidates for final structure verification.

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

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.

New Approach for the Identification of Isobaric and Isomeric Metabolites

The structural elucidation of metabolite molecules is important in many branches of the life sciences. However, the isomeric and isobaric complexity of metabolites makes their identification extremely challenging, and analytical standards are often required to confirm the presence of a particular compound in a sample. We present here an approach to overcome these challenges using high-resolution ion mobility spectrometry in combination with cryogenic vibrational spectroscopy for the rapid separation and identification of metabolite isomers and isobars. Ion mobility can separate isomeric metabolites in tens of milliseconds, and cryogenic IR spectroscopy provides highly structured IR fingerprints for unambiguous molecular identification. Moreover, our approach allows one to identify metabolite isomers automatically by comparing their IR fingerprints with those previously recorded in a database, obviating the need for a recurrent introduction of analytical standards. We demonstrate the principle of this approach by constructing a database composed of IR fingerprints of eight isomeric/isobaric metabolites and use it for the identification of these isomers present in mixtures. Moreover, we show how our fast IR fingerprinting technology allows to probe the IR fingerprints of molecules within just a few seconds as they elute from an LC column. This approach has the potential to greatly improve metabolomics workflows in terms of accuracy, speed, and cost.

Glycosaminoglycans: What Remains To Be Deciphered?

Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conformations comprise "glycocodes" that are not yet fully deciphered. The molecular context also matters for GAG structures and functions, and the influence of the structure and functions of the proteoglycan core proteins on sulfated GAGs and vice versa warrants further investigation. The lack of dedicated bioinformatic tools for mining GAG data sets contributes to a partial characterization of the structural and functional landscape and interactions of GAGs. These pending issues will benefit from the development of new approaches reviewed here, namely (i) the synthesis of GAG oligosaccharides to build large and diverse GAG libraries, (ii) GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores, and molecular modeling to identify bioactive GAG sequences, biophysical methods to investigate binding interfaces, and to expand our knowledge and understanding of glycocodes governing GAG molecular recognition, and (iii) artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics.

Protonated Forms of Naringenin and Naringenin Chalcone: Proteiform Bioactive Species Elucidated by IRMPD Spectroscopy, IMS, CID-MS, and Computational Approaches

Naringenin (Nar) and its structural isomer, naringenin chalcone (ChNar), are two natural phytophenols with beneficial health effects belonging to the flavonoids family. A direct discrimination and structural characterization of the protonated forms of Nar and ChNar, delivered into the gas phase by electrospray ionization (ESI), was performed by mass spectrometry-based methods. In this study, we exploit a combination of electrospray ionization coupled to (high-resolution) mass spectrometry (HR-MS), collision-induced dissociation (CID) measurements, IR multiple-photon dissociation (IRMPD) action spectroscopy, density functional theory (DFT) calculations, and ion mobility-mass spectrometry (IMS). While IMS and variable collision-energy CID experiments hardly differentiate the two isomers, IRMPD spectroscopy appears to be an efficient method to distinguish naringenin from its related chalcone. In particular, the spectral range between 1400 and 1700 cm^-1 is highly specific in discriminating between the two protonated isomers. Selected vibrational signatures in the IRMPD spectra have allowed us to identify the nature of the metabolite present in methanolic extracts of commercial tomatoes and grapefruits. Furthermore, comparisons between experimental IRMPD and calculated IR spectra have clarified the geometries adopted by the two protonated isomers, allowing a conformational analysis of the probed species.

Characterization of Solar Radiation-Induced Degradation Products of the Plant Sunscreen Sinapoyl Malate

Agricultural activities at lower temperatures lead to lower yields due to reduced plant growth. Applying photomolecular heater agrochemicals could boost yields under these conditions, but UV-induced degradation of these compounds needs to be assessed. In this study, we employ liquid chromatography-mass spectrometry (LC-MS) coupled with infrared ion spectroscopy (IRIS) to detect and identify the degradation products generated upon simulated solar irradiation of sinapoyl malate, a proposed photomolecular heater/UV filter compound. All major irradiation-induced degradation products are identified in terms of their full molecular structure by comparing the IRIS spectra obtained after LC fractionation and mass isolation with reference IR spectra obtained from quantum-chemical calculations. In cases where physical standards are available, a direct experimental-to-experimental comparison is possible for definitive structure identification. We find that the major degradation products originate from trans-to-cis isomerization, ester cleavage, and esterification reactions of sinapoyl malate. Preliminary in silico toxicity investigations using the VEGAHUB platform suggest no significant concerns for these degradation products' human and environmental safety. The identification workflow presented here can analogously be applied to break down products from other agrochemical compounds. As the method records IR spectra with the sensitivity of LC-MS, application to agricultural samples, e.g., from field trials, is foreseen.

Differentiation between Isomeric 4,5-Functionalized 1,2,3-Thiadiazoles and 1,2,3-Triazoles by ESI-HRMS and IR Ion Spectroscopy

A large variety of 1,2,3-thiadiazoles and 1,2,3-triazoles are used extensively in modern pure and applied organic chemistry as important structural blocks of numerous valuable products. Creation of new methods of synthesis of these isomeric compounds requires the development of reliable analytical tools to reveal the structural characteristics of these novel compounds, which are able to distinguish between isomers. Mass spectrometry (MS) is a clear choice for this task due to its selectivity, sensitivity, informational capacity, and reliability. Here, the application of electrospray ionization (ESI) with ion detection in positive and negative modes was demonstrated to be useful in structural studies. Additionally, interconversion of isomeric 4,5-functionalized 1,2,3-triazoles and 1,2,3-thiadiazoles was demonstrated. Application of accurate mass measurements and tandem mass spectrometry in MS2 and MS3 modes indicated the occurrence of gas-phase rearrangement of 1,2,3-triazoles into 1,2,3-thiadiazoles under (+)ESI-MS/MS conditions, independent of the nature of substituents, in line with the reaction in the condensed phase. Infrared multiple photon dissociation (IRMPD) spectroscopy enabled the establishment of structures of some of the most crucial common fragment ions, including [M+H-N₂]⁺ and [M+H-N₂-RSO₂]⁺ species. The (-)ESI-MS/MS experiments were significantly more informative for the sulfonyl alkyl derivatives compared to the sulfonyl aryl ones. However, there was insufficient evidence to confirm the solution-phase transformation of 1,2,3-thiadiazoles into the corresponding 1,2,3-triazoles.

Structural Elucidation of Agrochemicals and Related Derivatives Using Infrared Ion Spectroscopy

Agrochemicals frequently undergo various chemical and metabolic transformation reactions in the environment that often result in a wide range of derivates that must be comprehensively characterized to understand their toxicity profiles and their persistence and outcome in the environment. In the development phase, this typically involves a major effort in qualitatively identifying the correct chemical isomer(s) of these derivatives from the many isomers that could potentially be formed. Liquid chromatography-mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy are often used in attempts to characterize such environment transformation products. However, challenges in confidently correlating chemical structures to detected compounds in mass spectrometry data and sensitivity/selectivity limitations of NMR frequently lead to bottlenecks in identification. In this study, we use an alternative approach, infrared ion spectroscopy, to demonstrate the identification of hydroxylated derivatives of two plant protection compounds (azoxystrobin and benzovindiflupyr) contained at low levels in tomato and spinach matrices. Infrared ion spectroscopy is an orthogonal tandem mass spectrometry technique that combines the sensitivity and selectivity of mass spectrometry with structural information obtained by infrared spectroscopy. Furthermore, IR spectra can be computationally predicted for candidate molecular structures, enabling the tentative identification of agrochemical derivatives and other unknowns in the environment without using physical reference standards.

Identification of Δ-1-pyrroline-5-carboxylate derived biomarkers for hyperprolinemia type II

Hyperprolinemia type II (HPII) is an inborn error of metabolism due to genetic variants in ALDH4A1, leading to a deficiency in Δ-1-pyrroline-5-carboxylate (P5C) dehydrogenase. This leads to an accumulation of toxic levels of P5C, an intermediate in proline catabolism. The accumulating P5C spontaneously reacts with, and inactivates, pyridoxal 5’-phosphate, a crucial cofactor for many enzymatic processes, which is thought to be the pathophysiological mechanism for HPII. Here, we describe the use of a combination of LC-QTOF untargeted metabolomics, NMR spectroscopy and infrared ion spectroscopy (IRIS) to identify and characterize biomarkers for HPII that result of the spontaneous reaction of P5C with malonic acid and acetoacetic acid. We show that these biomarkers can differentiate between HPI, caused by a deficiency of proline oxidase activity, and HPII. The elucidation of their molecular structures yields insights into the disease pathophysiology of HPII.

Combined metabolomics, NMR, and, IRIS identify biomarkers of hyperprolinemia type II (HPII) distinct from HPI and similar metabolic signatures as in patients with pyridoxine-dependent epilepsy.

How to proceed after "negative" exome: A review on genetic diagnostics, limitations, challenges, and emerging new multiomics techniques

Exome sequencing (ES) in the clinical setting of inborn metabolic diseases (IMDs) has created tremendous improvement in achieving an accurate and timely molecular diagnosis for a greater number of patients, but it still leaves the majority of patients without a diagnosis. In parallel, (personalized) treatment strategies are increasingly available, but this requires the availability of a molecular diagnosis. IMDs comprise an expanding field with the ongoing identification of novel disease genes and the recognition of multiple inheritance patterns, mosaicism, variable penetrance, and expressivity for known disease genes. The analysis of trio ES is preferred over singleton ES as information on the allelic origin (paternal, maternal, "de novo") reduces the number of variants that require interpretation. All ES data and interpretation strategies should be exploited including CNV and mitochondrial DNA analysis. The constant advancements in available techniques and knowledge necessitate the close exchange of clinicians and molecular geneticists about genotypes and phenotypes, as well as knowledge of the challenges and pitfalls of ES to initiate proper further diagnostic steps. Functional analyses (transcriptomics, proteomics, and metabolomics) can be applied to characterize and validate the impact of identified variants, or to guide the genomic search for a diagnosis in unsolved cases. Future diagnostic techniques (genome sequencing [GS], optical genome mapping, long-read sequencing, and epigenetic profiling) will further enhance the diagnostic yield. We provide an overview of the challenges and limitations inherent to ES followed by an outline of solutions and a clinical checklist, focused on establishing a diagnosis to eventually achieve (personalized) treatment.

Infrared multiple photon dissociation (IRMPD) spectroscopy and its potential for the clinical laboratory

Infrared multiple photon dissociation (IRMPD) spectroscopy is a powerful tool used to probe the vibrational modes-and, by extension, the structure-of an ion within an ion trap mass spectrometer. Compared to traditional FTIR spectroscopy, IRMPD spectroscopy has advantages including its sensitivity and its relative ability to handle complex mixtures. While IRMPD has historically been a technique for fundamental analyses, it is increasingly being applied in a more analytical fashion. Notable recent demonstrations pertinent to the clinical laboratory and adjacent interests include analysis of modified amino acids/residues and carbohydrates, structural elucidation (including isomeric differentiation) of metabolites, identification of novel illicit drugs, and structural studies of various biomolecules and pharmaceuticals. Improvements in analysis time, coupling to commercial instruments, and integration with separations methods are all drivers toward the realization of these analytical applications. Additional improvements in these areas, along with advances in benchtop tunable IR sources and increased cross-discipline collaboration, will continue to drive innovation and widespread adoption. The goal of this tutorial article is to briefly present the fundamentals and instrumentation of IRMPD spectroscopy, as an overview of the utility of this technique for helping to answer questions relevant to clinical analysis, and to highlight limitations to widespread adoption, as well as promising directions in which the field may be heading.

Gas-phase infrared spectroscopy of glycans and glycoconjugates

Glycans are intrinsically complex biomolecules that pose particular analytical challenges. Standard workflows for glycan analysis are based on mass spectrometry, often coupled with separation techniques such as liquid chromatography and ion mobility spectrometry. However, this approach does not yield direct structural information and cannot always distinguish between isomers. This gap might be filled in the future by gas-phase infrared spectroscopy, which has emerged as a promising structure-sensitive technique for glycan fingerprinting. This review highlights recent applications of gas-phase infrared spectroscopy for the analysis of synthetic and biological glycans and how they can be integrated into mass spectrometry-based workflows.

Metabolite Identification Using Infrared Ion Spectroscopy─Novel Biomarkers for Pyridoxine-Dependent Epilepsy

Untargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics strategies are being increasingly applied in metabolite screening for a wide variety of medical conditions. The long-standing "grand challenge" in the utilization of this approach is metabolite identification─confidently determining the chemical structures of m/z-detected unknowns. Here, we use a novel workflow based on the detection of molecular features of interest by high-throughput untargeted LC-MS analysis of patient body fluids combined with targeted molecular identification of those features using infrared ion spectroscopy (IRIS), effectively providing diagnostic IR fingerprints for mass-isolated targets. A significant advantage of this approach is that in silico-predicted IR spectra of candidate chemical structures can be used to suggest the molecular structure of unknown features, thus mitigating the need for the synthesis of a broad range of physical reference standards. Pyridoxine-dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine metabolism, resulting from a mutation in the ALDH7A1 gene that leads to an accumulation of toxic levels of α-aminoadipic semialdehyde (α-AASA), piperideine-6-carboxylate (P6C), and pipecolic acid in body fluids. While α-AASA and P6C are known biomarkers for PDE in urine, their instability makes them poor candidates for diagnostic analysis from blood, which would be required for application in newborn screening protocols. Here, we use combined untargeted metabolomics-IRIS to identify several new biomarkers for PDE-ALDH7A1 that can be used for diagnostic analysis in urine, plasma, and cerebrospinal fluids and that are compatible with analysis in dried blood spots for newborn screening. The identification of these novel metabolites has directly provided novel insights into the pathophysiology of PDE-ALDH7A1.

Evaluation of table-top lasers for routine infrared ion spectroscopy in the analytical laboratory

Infrared ion spectroscopy is increasingly recognized as a method to identify mass spectrometry-detected analytes in many (bio)chemical areas and its integration in analytical laboratories is now on the horizon. Commercially available quadrupole ion trap mass spectrometers are attractive ion spectroscopy platforms but operate at relatively high pressures. This promotes collisional deactivation which directly interferes with the multiple-photon excitation process required for ion spectroscopy. To overcome this, infrared lasers having a high instantaneous power are required and therefore a majority of analytical studies have been performed at infrared free electron laser facilities. Proliferation of the technique to routine use in analytical laboratories requires table-top infrared lasers and optical parametric oscillators (OPOs) are the most suitable candidates, offering both relatively high intensities and reasonable spectral tuning ranges. Here, we explore the potential of a range of commercially available high-power OPOs for ion spectroscopy, comparing systems with repetition rates of 10 Hz, 20 kHz, 80 MHz and a continuous-wave (cw) system. We compare the performance for various molecular ions and show that the kHz and MHz repetition-rate systems outperform cw and 10 Hz systems in photodissociation efficiency and offer several advantages in terms of cost-effectiveness and practical implementation in an analytical laboratory not specialized in laser spectroscopy.

Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go

We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.

Advanced tandem mass spectrometry in metabolomics and lipidomics-methods and applications

Metabolomics and lipidomics are new drivers of the omics era as molecular signatures and selected analytes allow phenotypic characterization and serve as biomarkers, respectively. The growing capabilities of untargeted and targeted workflows, which primarily rely on mass spectrometric platforms, enable extensive charting or identification of bioactive metabolites and lipids. Structural annotation of these compounds is key in order to link specific molecular entities to defined biochemical functions or phenotypes. Tandem mass spectrometry (MS), first and foremost collision-induced dissociation (CID), is the method of choice to unveil structural details of metabolites and lipids. But CID fragment ions are often not sufficient to fully characterize analytes. Therefore, recent years have seen a surge in alternative tandem MS methodologies that aim to offer full structural characterization of metabolites and lipids. In this article, principles, capabilities, drawbacks, and first applications of these "advanced tandem mass spectrometry" strategies will be critically reviewed. This includes tandem MS methods that are based on electrons, photons, and ion/molecule, as well as ion/ion reactions, combining tandem MS with concepts from optical spectroscopy and making use of derivatization strategies. In the final sections of this review, the first applications of these methodologies in combination with liquid chromatography or mass spectrometry imaging are highlighted and future perspectives for research in metabolomics and lipidomics are discussed.

High-Throughput Non-targeted Chemical Structure Identification Using Gas-Phase Infrared Spectra

The high-throughput identification of unknown metabolites in biological samples remains challenging. Most current non-targeted metabolomics studies rely on mass spectrometry, followed by computational methods that rank thousands of candidate structures based on how closely their predicted mass spectra match the experimental mass spectrum of an unknown. We reasoned that the infrared (IR) spectra could be used in an analogous manner and could add orthologous structure discrimination; however, this has never been evaluated on large data sets. Here, we present results of a high-throughput computational method for predicting IR spectra of candidate compounds obtained from the PubChem database. Predicted spectra were ranked based on their similarity to gas-phase experimental IR spectra of test compounds obtained from the NIST. Our computational workflow (IRdentify) consists of a fast semiempirical quantum mechanical method for initial IR spectra prediction, ranking, and triaging, followed by a final IR spectra prediction and ranking using density functional theory. This approach resulted in the correct identification of 47% of 258 test compounds. On average, there were 2152 candidate structures evaluated for each test compound, giving a total of approximately 555,200 candidate structures evaluated. We discuss several variables that influenced the identification accuracy and then demonstrate the potential application of this approach in three areas: (1) combining IR and mass spectra rankings into a single composite rank score, (2) identifying the precursor and fragment ions using cryogenic ion vibrational spectroscopy, and (3) the incorporation of a trimethylsilyl derivatization step to extend the method compatibility to less-volatile compounds. Overall, our results suggest that matching computational with experimental IR spectra is a potentially powerful orthogonal option for adding significant high-throughput chemical structure discrimination when used with other non-targeted chemical structure identification methods.

Untargeted metabolomics and infrared ion spectroscopy identify biomarkers for pyridoxine-dependent epilepsy

BackgroundPyridoxine-dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine catabolism that presents with refractory epilepsy in newborns. Biallelic ALDH7A1 variants lead to deficiency of α-aminoadipic semialdehyde dehydrogenase/antiquitin, resulting in accumulation of piperideine-6-carboxylate (P6C), and secondary deficiency of the important cofactor pyridoxal-5'-phosphate (PLP, active vitamin B6) through its complexation with P6C. Vitamin B6 supplementation resolves epilepsy in patients, but intellectual disability may still develop. Early diagnosis and treatment, preferably based on newborn screening, could optimize long-term clinical outcome. However, no suitable PDE-ALDH7A1 newborn screening biomarkers are currently available.MethodsWe combined the innovative analytical methods untargeted metabolomics and infrared ion spectroscopy to discover and identify biomarkers in plasma that would allow for PDE-ALDH7A1 diagnosis in newborn screening.ResultsWe identified 2S,6S-/2S,6R-oxopropylpiperidine-2-carboxylic acid (2-OPP) as a PDE-ALDH7A1 biomarker, and confirmed 6-oxopiperidine-2-carboxylic acid (6-oxoPIP) as a biomarker. The suitability of 2-OPP as a potential PDE-ALDH7A1 newborn screening biomarker in dried bloodspots was shown. Additionally, we found that 2-OPP accumulates in brain tissue of patients and Aldh7a1-knockout mice, and induced epilepsy-like behavior in a zebrafish model system.ConclusionThis study has opened the way to newborn screening for PDE-ALDH7A1. We speculate that 2-OPP may contribute to ongoing neurotoxicity, also in treated PDE-ALDH7A1 patients. As 2-OPP formation appears to increase upon ketosis, we emphasize the importance of avoiding catabolism in PDE-ALDH7A1 patients.FundingSociety for Inborn Errors of Metabolism for Netherlands and Belgium (ESN), United for Metabolic Diseases (UMD), Stofwisselkracht, Radboud University, Canadian Institutes of Health Research, Dutch Research Council (NWO), and the European Research Council (ERC).

Mass spectrometry-based identification of ortho-, meta- and para-isomers using infrared ion spectroscopy

Distinguishing positional isomers, such as compounds having different substitution patterns on an aromatic ring, presents a significant challenge for mass spectrometric analyses and is a frequently encountered difficulty in, for example, drug metabolism research. In contrast to mass spectrometry, IR spectroscopy is a well-known and powerful tool in the distinction of ortho-, meta- and para-isomers, but is not applicable to low-abundance compounds in complex mixtures such as often targeted in bioanalytical studies. Here, we demonstrate the use of infrared ion spectroscopy (IRIS) as a novel method that facilitates the differentiation between positional isomers of disubstituted phenyl-containing compounds and that can be applied in mass spectrometry-based complex mixture analysis. By analyzing different substitution patterns over several sets of isomeric compounds, we show that IRIS is able to consistently probe the diagnostic CH out-of-plane vibrations that are sensitive to positional isomerism. We show that these modes are largely independent of the chemical functionality contained in the ring substituents and of the type of ionization. We also show that IRIS spectra often identify the positional isomer directly, even in the absence of reference spectra obtained from physical standards or from computational prediction. We foresee that this method will be generally applicable to the identification of disubstituted phenyl-containing compounds.

Amadori rearrangement products as potential biomarkers for inborn errors of amino-acid metabolism

The identification of disease biomarkers plays a crucial role in developing diagnostic strategies for inborn errors of metabolism and understanding their pathophysiology. A primary metabolite that accumulates in the inborn error phenylketonuria is phenylalanine, however its levels do not always directly correlate with clinical outcomes. Here we combine infrared ion spectroscopy and NMR spectroscopy to identify the Phe-glucose Amadori rearrangement product as a biomarker for phenylketonuria. Additionally, we find analogous amino acid-glucose metabolites formed in the body fluids of patients accumulating methionine, lysine, proline and citrulline. Amadori rearrangement products are well-known intermediates in the formation of advanced glycation end-products and have been associated with the pathophysiology of diabetes mellitus and ageing, but are now shown to also form under conditions of aminoacidemia. They represent a general class of metabolites for inborn errors of amino acid metabolism that show potential as biomarkers and may provide further insight in disease pathophysiology.

Isomer-Specific Two-Color Double-Resonance IR2MS3 Ion Spectroscopy Using a Single Laser: Application in the Identification of Novel Psychoactive Substances

The capability of an ion trap mass spectrometer to store ions for an arbitrary amount of time allows the use of a single infrared (IR) laser to perform two-color double resonance IR–IR spectroscopic experiments on mass-to-charge (m/z) selected ions. In this single-laser IR²MS³ scheme, one IR laser frequency is used to remove a selected set of isomers from the total trapped ion population and the second IR laser frequency, from the same laser, is used to record the IR spectrum of the remaining precursor ions. This yields isomer-specific vibrational spectra of the m/z-selected ions, which can reveal the structure and identity of the initially co-isolated isomeric species. The use of a single laser greatly reduces the experimental complexity of two-color IR²MS³ and enhances its application in fields employing analytical MS. In this work, we demonstrate the methodology by acquiring single-laser IR²MS³ spectra in a forensic context, identifying two previously unidentified isomeric novel psychoactive substances (NPS) from a sample that was confiscated by the Amsterdam Police.

Quantification of Differential Metabolites in Dried Blood Spots Using Second-Tier Testing for SCADD/IBDD Disorders Based on Large-Scale Newborn Screening in a Chinese Population

Background: Although newborn screening (NBS) for metabolic defects using the marker butyl carnitine (C4) combined with the C4-to-acetylcarnitine ratio is adequate, the incorporation of novel parameters may improve differential testing for these disorders without compromising sensitivity. Methods: Analytical and clinical performance was evaluated by MS/MS using 237 initially positive neonatal samples between March 2019 and March 2020 at the Newborn Screening Center of Xuzhou Maternity and Child Health Care Hospital. Additionally, second-tier testing by ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) combined with the quantification of ethylmalonate (EMA) or isobutyryl-glycine (IBG) in dried blood spots (DBSs) was performed to reduce the false-positive rate. Results: We reviewed initial MS/MS data for DBSs from 469,730 neonates, and a second-tier test was performed using 237 samples that exceeded the C4 concentration cutoff value. Eleven variants of the ACADS gene were identified, with c.1031A>G (p.E344G) being the most common. Fifteen ACAD8 mutations were identified in seven patients, and Swiss modeling and amino acid conservation analyses were conducted for the novel variants. Based on a retrospective analysis of EMA and IBG, the application of second-tier tests before the release of neonatal screening results reduced referrals by over 91.89% and improved the positive predictive value (PPV) for short-chain acyl-CoA dehydrogenase deficiency/isobutyryl-CoA dehydrogenase deficiency (SCADD/IBDD) screening. Conclusion: A screening algorithm including EMA/IBG improves target differential testing for NBS and may eliminate unnecessary referrals while maintaining 100% sensitivity. Second-tier screening using UPLC-MS/MS as a rapid and convenient supplemental DNA sequencing method may be beneficial for differential detection.

Determination of Gossypol in Hamid and Bt (Seeni 1) Cottonseed Oil using Fourier Transform Infrared Spectroscopy

This study was conducted to determine the gossypol content in Bt cottonseed (Seeni-1) oil by using Fourier Transform Infrared (FTIR) spectroscopy with an Attenuated Total Reflectance (ATR) element. The wavelengths used were selected by spiking refined, bleached deodorized palm oil (RBDPO) to gossypol concentrations of 0-5% and noting the regions of maximal absorbance. Absorbance values of the wavelength regions 3700-2400 & 1900-750 cm-1 and a partial least squares (PLS) method were used to derive calibration models for Hamid cottonseed oil, Seeni-1 cottonseed oil, and gossypol-spiked RBDPO. The coefficients of determination (R2) for the calibration models were computed for the FTIR spectroscopy results against those found by using the wet chemical method AOCS method Ba 8�78. The R2 was 0.8916, 0.9581, and 0.9374 for Hamid cottonseed oil, Seeni-1 cottonseed oil, and gossypol-spiked RBDPO, respectively. The standard error (SE) of the calibration was 0.053, 0.078, and 0.062, respectively. The calibration models were validated using the cross-validation technique within the same set of oil samples. The results of FTIR spectroscopy as a useful technique determining gossypol content in crude cottonseed oil showed that there is a significant difference (p <0.05) in the amount of gossypol content in Hamid and Bt Seeni-1 cottonseed oils.

Development of a photoinduced fragmentation ion trap for infrared multiple photon dissociation spectroscopy

RATIONALE

Methods for isomer discrimination by mass spectroscopy are of increasing interest. Here we describe the development of a three-dimensional ion trap for infrared multiple photon dissociation (IRMPD) spectroscopy that enables the acquisition of the infrared spectrum of selected ions in the gas phase. This system is suitable for the study of a myriad of chemical systems, including isomer mixtures.

METHODS

A modified three-dimensional ion trap was coupled to a CO₂ laser and an optical parametric oscillator/optical parametric amplifier (OPO/OPA) system operating in the range 2300 to 4000 cm^-1 . Density functional theory vibrational frequency calculations were carried out to support spectral assignments.

RESULTS

Detailed descriptions of the interface between the laser and the mass spectrometer, the hardware to control the laser systems, the automated system for IRMPD spectrum acquisition and data management are presented. The optimization of the crystal position of the OPO/OPA system to maximize the spectroscopic response under low-power laser radiation is also discussed.

CONCLUSIONS

OPO/OPA and CO₂ laser-assisted dissociation of gas-phase ions was successfully achieved. The system was validated by acquiring the IRMPD spectra of model species and comparing with literature data. Two isomeric alkaloids of high economic importance were characterized to demonstrate the potential of this technique, which is now available as an open IRMPD spectroscopy facility in Brazil.

Mass-Spectrometry-Based Identification of Synthetic Drug Isomers Using Infrared Ion Spectroscopy

Infrared ion spectroscopy (IRIS), a mass-spectrometry-based technique exploiting resonant infrared multiple photon dissociation (IRMPD), has been applied for the identification of novel psychoactive substances (NPS). Identification of the precise isomeric forms of NPS is of significant forensic relevance since legal controls are dependent on even minor molecular differences such as a single ring-substituent position. Using three isomers of fluoroamphetamine and two ring-isomers of both MDA and MDMA, we demonstrate the ability of IRIS to distinguish closely related NPS. Computationally predicted infrared (IR) spectra are shown to correspond with experimental spectra and could explain the molecular origins of their distinctive IR absorption bands. IRIS was then used to investigate a confiscated street sample containing two unknown substances. One substance could easily be identified by comparison to the IR spectra of reference standards. For the other substance, however, this approach proved inconclusive due to incomplete mass spectral databases as well as a lack of available reference compounds, two common analytical limitations resulting from the rapid development of NPS. Most excitingly, the second unknown substance could nevertheless be identified by using computationally predicted IR spectra of several potential candidate structures instead of their experimental reference spectra.

Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications

Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.

Infrared ion spectroscopy: New opportunities for small-molecule identification in mass spectrometry - A tutorial perspective

Combining the individual analytical strengths of mass spectrometry and infrared spectroscopy, infrared ion spectroscopy is increasingly recognized as a powerful tool for small-molecule identification in a wide range of analytical applications. Mass spectrometry is itself a leading analytical technique for small-molecule identification on the merit of its outstanding sensitivity, selectivity and versatility. The foremost shortcoming of the technique, however, is its limited ability to directly probe molecular structure, especially when contrasted against spectroscopic techniques. In infrared ion spectroscopy, infrared vibrational spectra are recorded for mass-isolated ions and provide a signature that can be matched to reference spectra, either measured from standards or predicted using quantum-chemical calculations. Here we present an overview of the potential for this technique to develop into a versatile analytical method for identifying molecular structures in mass spectrometry-based analytical workflows. In this tutorial perspective, we introduce the reader to the technique of infrared ion spectroscopy and highlight a selection of recent experimental advances and applications in current analytical challenges, in particular in the field of untargeted metabolomics. We report on the coupling of infrared ion spectroscopy with liquid chromatography and present experiments that serve as proof-of-principle examples of strategies to address outstanding challenges.

Infrared Ion Spectroscopy of Environmental Organic Mixtures: Probing the Composition of α-Pinene Secondary Organic Aerosol

Characterizing the chemical composition of organic aerosols can elucidate aging mechanisms as well as the chemical and physical properties of the aerosol. However, the high chemical complexity and often low atmospheric abundance present a difficult analytical challenge. Milligrams or more of material may be needed for speciated spectroscopic analysis. In contrast, mass spectrometry provides a very sensitive platform but limited structural information. Here, we combine the strengths of mass spectrometry and infrared (IR) action spectroscopy to generate characteristic IR spectra of individual, mass-isolated ion populations. Soft ionization combined with in situ infrared ion spectroscopy, using the tunable free-electron laser FELIX, provides detailed information on molecular structures and functional groups. We apply this technique, along with quantum mechanical modeling, to characterize organic molecules in secondary organic aerosol (SOA) formed from the ozonolysis of α-pinene. Spectral overlap with a standard is used to identify cis-pinonic acid. We also demonstrate the characterization of isomers for multiple SOA products using both quantum mechanical computations and analyses of fragment ion spectra. These results demonstrate the detailed structural information on isolated ions obtained by combining mass spectrometry with fingerprint IR spectroscopy.

Translational Metabolism: A multidisciplinary approach towards precision diagnosis of inborn errors of metabolism in the omics era

The laboratory diagnosis of inborn errors of metabolism has been revolutionized in recent years, thanks to the amazing developments in the field of DNA sequencing including whole exome and whole genome sequencing (WES and WGS). Interpretation of the results coming from WES and/or WGS analysis is definitely not trivial especially since the biological relevance of many of the variants identified by WES and/or WGS, have not been tested experimentally and prediction programs like POLYPHEN-2 and SIFT are far from perfect. Correct interpretation of WES and/or WGS results can only be achieved by performing functional studies at multiple levels (different metabolomics platforms, enzymology, in vitro and in vivo flux analysis), often requires studies in model organisms like zebra fish, Caenorhabditis elegans, Saccharomyces cerevisiae, mutant mice and others, and also requires the input of many different disciplines to make this Translational Metabolism approach effective.

New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells

Mass-spectrometry based omics technologies - namely proteomics, metabolomics and lipidomics - have enabled the molecular level systems biology investigation of organisms in unprecedented detail. There has been increasing interest for gaining a thorough, functional understanding of the biological consequences associated with cellular heterogeneity in a wide variety of research areas such as developmental biology, precision medicine, cancer research and microbiome science. Recent advances in mass spectrometry (MS) instrumentation and sample handling strategies are quickly making comprehensive omics analyses of single cells feasible, but key breakthroughs are still required to push through remaining bottlenecks. In this review, we discuss the challenges faced by single cell MS-based omics analyses and highlight recent technological advances that collectively can contribute to comprehensive and high throughput omics analyses in single cells. We provide a vision of the potential of integrating pioneering technologies such as Structures for Lossless Ion Manipulations (SLIM) for improved sensitivity and resolution, novel peptide identification tactics and standards free metabolomics approaches for future applications in single cell analysis.

Conformational assignment of gas phase peptides and their H-bonded complexes using far-IR/THz: IR-UV ion dip experiment, DFT-MD spectroscopy, and graph theory for mode assignment

Graph theory based vibrational modes as new entities for vibrational THz spectroscopy.

The role of the clinician in the multi-omics era: are you ready?

Since Garrod's first description of alkaptonuria in 1902, and newborn screening for phenylketonuria introduced in the 1960s, P4 medicine (preventive, predictive, personalized, and participatory) has been a reality for the clinician serving patients with inherited metabolic diseases. The era of high-throughput technologies promises to accelerate its scale dramatically. Genomics, transcriptomics, epigenomics, proteomics, glycomics, metabolomics, and lipidomics offer an amazing opportunity for holistic investigation and contextual pathophysiologic understanding of inherited metabolic diseases for precise diagnosis and tailored treatment. While each of the -omics technologies is important to systems biology, some are more mature than others. Exome sequencing is emerging as a reimbursed test in clinics around the world, and untargeted metabolomics has the potential to serve as a single biochemical testing platform. The challenge lies in the integration and cautious interpretation of these big data, with translation into clinically meaningful information and/or action for our patients. A daunting but exciting task for the clinician; we provide clinical cases to illustrate the importance of his/her role as the connector between physicians, laboratory experts and researchers in the basic, computer, and clinical sciences. Open collaborations, data sharing, functional assays, and model organisms play a key role in the validation of -omics discoveries. Having all the right expertise at the table when discussing the diagnostic approach and individualized management plan according to the information yielded by -omics investigations (e.g., actionable mutations, novel therapeutic interventions), is the stepping stone of P4 medicine. Patient participation and the adjustment of the medical team's plan to his/her and the family's wishes most certainly is the capstone. Are you ready?