Application of Atmospheric Pressure Photo Ionization Hydrogen/Deuterium Exchange High-Resolution Mass Spectrometry for the Molecular Level Speciation of Nitrogen Compounds in Heavy Crude Oils

In-Electrospray source Hydrogen/Deuterium exchange coupled to multistage fragmentation for the investigation of the protonation and fragmentation pathways of gas phase ions

Identification of molecules in complex natural matrices relies on matching the fragmentation spectra of ions under investigation and the spectra acquired for the corresponding analytical standards. Currently, there are many databases of experimentally measured tandem mass spectrometry spectra (such as NIST, MzCloud, and Metlin), and considerable progress has been made in the development of software for predicting tandem mass spectrometry fragments in silico using combinatorial, machine learning, and quantum chemistry approaches (such as MetFrag, CFM-ID, and QCxMS). However, the electrospray ionization molecules can be ionized at different sites (protonated or deprotonated), and the fragmentation spectra of such ions are different. Here, we are using the combination of the in-ESI source hydrogen/deuterium exchange reaction and MSn fragmentation for the investigation of the fragmentation pathways for different protomers of organic molecules. It is shown that the distribution of the deuterium in the fragment ions reflects the presence of different protomers. For several molecules, the distribution of deuterium was traced up to the MS5 level of fragmentation revealing many unusual and unexpected effects. For example, we investigated the loss of HF from the ciprofloxacin and norfloxacin ions and observed that for ions protonated at -COOH group, the eliminating hydrogen always comes from -NH group. When ions are protonated at another site, the elimination of hydrogen with a probability of 30% occurs from the -NH group, and with a probability of 70%, it originates from other sites on the molecule. Such effects were not described previously. Quantum chemical simulation was used for the verification of the protonated structures and simulation of the corresponding fragmentation spectra.

Chemometric Analysis Combined with GC × GC-FID and ESI HR-MS to Evaluate Ultralow-Sulfur Diesel Stability

Diesel has been the most employed fuel in highway and nonhighway transportation systems. Many studies over the past years have attempted to classify diesel as a stable or unstable composition since this fuel can still degrade during storage or thermal oxidative processes. Products generated because of such degradation are the reason for the formation of soluble gums and insoluble organic particulates, which in turn cause a negative influence on engine performance. This work reports a detailed composition of nonpolar and polar compounds in many ultralow-sulfur diesel (ULSD) samples by comprehensive two-dimensional gas chromatography with a flame ionization detector (GC × GC-FID) and electrospray ionization high-resolution mass spectrometry (ESI HR-MS). In addition, chemometric approaches were applied for ULSD storage stability investigation. GC × GC-FID experiments achieved the nonpolar chemical characterization for the ULSD samples, including all main hydrocarbon classes: paraffins, mono- and dinaphthenics and olefins, and aromatics. The GC × GC-FID data combined with principal component analysis (PCA) described that the separation of the samples' concerning storage stability was mainly due to the contents of mono- and diaromatic compounds in the unstable ULSD samples. Moreover, PCA was also applied to the ESI (±) data set, and the results highlight the presence of compounds belonging to O class (natural antioxidants), which decrease the rate of oxygen consumption in the fuel, characterizing it as stable composition. The basic nitrogen compounds are mostly present in the stable ULSD samples indicating that they did not affect the stability of the fuel. On the other hand, the HC classes presented pronounced abundance among unstable ULSD samples suggesting that the fuel degradation may go through the oxidation of hydrocarbons and the formation of Ox compounds as byproducts. Furthermore, MS/MS experiments point to the formation of CcHhNnOo-like precursor species, which can react with each other and lead to the formation of gums and insoluble sediments in the fuel. In summary, the results express the potential of using the GC × GC-FID and ESI (±) Orbitrap MS techniques as valuable tools for diesel stability evaluations.

Hydrogen/deuterium exchange mass spectrometry in the world of small molecules

The combined use of hydrogen/deuterium exchange (HDX) and mass spectrometry (MS), referred to as HDX-MS, is a powerful tool for exploring molecular edifices and has been used for over 60 years. Initially for structural and mechanistic investigation of low-molecular weight organic compounds, then to study protein structure and dynamics, then, the craze to study small molecules by HDX-MS accelerated and has not stopped yet. The purpose of this review is to present its different facets with particular emphasis on recent developments and applications. Reversible H/D exchanges of mobilizable protons as well as stable exchanges of non-labile hydrogen are considered whether they are taking place in solution or in the gas phase, or enzymatically in a biological media. Some fundamental principles are restated, especially for gas-phase processes, and an overview of recent applications, ranging from identification to quantification through the study of metabolic pathways, is given.

Next Challenges for the Comprehensive Molecular Characterization of Complex Organic Mixtures in the Field of Sustainable Energy

The conversion of lignocellulosic biomass by pyrolysis or hydrothermal liquefaction gives access to a wide variety of molecules that can be used as fuel or as building blocks in the chemical industry. For such purposes, it is necessary to obtain their detailed chemical composition to adapt the conversion process, including the upgrading steps. Petroleomics has emerged as an integral approach to cover a missing link in the investigation bio-oils and linked products. It relies on ultra-high-resolution mass spectrometry to attempt to unravel the contribution of many compounds in complex samples by a non-targeted approach. The most recent developments in petroleomics partially alter the discriminating nature of the non-targeted analyses. However, a peak referring to one chemical formula possibly hides a forest of isomeric compounds, which may present a large chemical diversity concerning the nature of the chemical functions. This identification of chemical functions is essential in the context of the upgrading of bio-oils. The latest developments dedicated to this analytical challenge will be reviewed and discussed, particularly by integrating ion source features and incorporating new steps in the analytical workflow. The representativeness of the data obtained by the petroleomic approach is still an important issue.

PyFragMS-A Web Tool for the Investigation of the Collision-Induced Fragmentation Pathways

Dissociation induced by the accumulation of internal energy via collisions of ions with neutral molecules is one of the most important fragmentation techniques in mass spectrometry (MS), and the identification of small singly charged molecules is based mainly on the consideration of the fragmentation spectrum. Many research studies have been dedicated to the creation of databases of experimentally measured tandem mass spectrometry (MS/MS) spectra (such as MzCloud, Metlin, etc.) and developing software for predicting MS/MS fragments in silico from the molecular structure (such as MetFrag, CFM-ID, CSI:FingerID, etc.). However, the fragmentation mechanisms and pathways are still not fully understood. One of the limiting obstacles is that protomers (positive ions protonated at different sites) produce different fragmentation spectra, and these spectra overlap in the case of the presence of different protomers. Here, we are proposing to use a combination of two powerful approaches: computing fragmentation trees that carry information of all consecutive fragmentations and consideration of the MS/MS data of isotopically labeled compounds. We have created PyFragMS-a web tool consisting of a database of annotated MS/MS spectra of isotopically labeled molecules (after H/D and/or ¹⁶O/¹⁸O exchange) and a collection of instruments for computing fragmentation trees for an arbitrary molecule. Using PyFragMS, we investigated how the site of protonation influences the fragmentation pathway for small molecules. Also, PyFragMS offers capabilities for performing database search when MS/MS data of the isotopically labeled compounds are taken into account.

Solvent and Flow Rate Effects on the Observed Compositional Profiles and the Relative Intensities of Radical and Protonated Species in Atmospheric Pressure Photoionization Mass Spectrometry

Sample preparation and instrument parameters have regularly been demonstrated to impact upon the observed results in atmospheric pressure photoionization, mass spectrometry (MS), and analytical techniques in general but may be overlooked when such methods are applied to the characterization of real-world samples. An initial investigation into different solvent systems demonstrated that the inclusion of ethyl acetate inverted the ratio of relative intensities of radical and protonated species (R/P). Design of experiments was performed and indicated that the injection flow rate is also a significant factor. The impact of the solvent system and flow rate on signal intensity, the observed compositional profile, and R/P of selected molecular groups is demonstrated further. An inversion of R/P is observed at higher flow rates in solvent systems commonly used in petroleomics studies, effecting a loss of molecular speciation. The findings presented reiterate the critical importance in considering experimental parameters when interpreting the results of analytical procedures.

Analysis of environmental organic matters by Ultrahigh-Resolution mass spectrometry-A review on the development of analytical methods

Owing to the increasing environmental and climate changes globally, there is an increasing interest in the molecular-level understanding of environmental organic compound mixtures, that is, the pursuit of complete and detailed knowledge of the chemical compositions and related chemical reactions. Environmental organic molecule mixtures, including those in air, soil, rivers, and oceans, have extremely complex and heterogeneous chemical compositions. For their analyses, ultrahigh-resolution and sub-ppb level mass accuracy, achievable using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), are important. FT-ICR MS has been successfully used to analyze complex environmental organic molecule mixtures such as natural, soil, particulate, and dissolved organic matter. Despite its success, many limitations still need to be overcome. Sample preparation, ionization, structural identification, chromatographic separation, and data interpretation are some key areas that have been the focus of numerous studies. This review describes key developments in analytical techniques in these areas to aid researchers seeking to start or continue investigations for the molecular-level understanding of environmental organic compound mixtures.

Application of open port sampling interface mass spectrometry (OPSI-MS) to deuterium exchange as an aid for structural elucidation

RATIONALE

Deuterium exchange has been demonstrated to provide additional information to accurate mass measurement and collision-induced dissociation on unknown chemical structures. An enhanced method for rapid deuterium exchange could make this technique more routine for structural elucidation. Open port sampling interface mass spectrometry (OPSI-MS) with an aprotic solvent offers a rapid method for performing deuterium incorporation.

METHODS

Samples of standard drug molecules have been analysed by OPSI-MS directly from solids using a make-up flow of acetonitrile + 0.1% trifluoroacetic acid. The resultant spectra were compared with those obtained by OPSI-MS analysis of the samples dissolved in deuterium oxide (D₂ O). Solutions of these molecules in acetonitrile/D₂ O were analysed using an Atmospheric Solids Analysis Probe (ASAP) at different temperatures to compare the suitability of this technique.

RESULTS

The number of exchangeable hydrogens was obtained through deuterium exchange using the OPSI source, although there was some incomplete exchange or back-exchange observed. Molecules with one to five exchangeable hydrogens were successfully analysed. ASAP analysis produced more complicated spectra with higher levels of incomplete or back-exchanged ions; this was more pronounced at higher temperatures.

CONCLUSIONS

The use of OPSI provides a method for the rapid determination of the number of exchangeable hydrogens within a molecule. This yields useful information as an aid to the structural elucidation of unknowns. ASAP produces incomplete exchange and cannot be used for incorporation studies.

Speciation of organosulfur compounds in carbonaceous chondrites

Despite broad application of different analytical techniques for studies on organic matter of chondrite meteorites, information about composition and structure of individual compounds is still very limited due to extreme molecular diversity of extraterrestrial organic matter. Here we present the first application of isotopic exchange assisted Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for analysis of alkali extractable fraction of insoluble organic matter (IOM) of the Murchison and Allende meteorites. This allowed us to determine the individual S-containing ions with different types of sulfur atoms in IOM. Thiols, thiophenes, sulfoxides, sulfonyls and sulfonates were identified in both samples but with different proportions, which contribution corroborated with the hydrothermal and thermal history of the meteorites. The results were supported by XPS and thermogravimetric analysis coupled to FTICR MS. The latter was applied for the first time for analysis of chondritic IOM. To emphasize the peculiar extraterrestrial origin of IOM we have compared it with coal kerogen, which is characterized by the comparable complexity of molecular composition but its aromatic nature and low oxygen content can be ascribed almost exclusively to degradation of biomacromolecules.

Specification of the nitrogen functional group in a hydrotreated petroleum molecule using hydrogen/deuterium exchange electrospray ionization high-resolution mass spectrometry

Hydrotreatment is extensively used for the production of clean fuel. Attaining an understanding of the structural conversion of the nitrogen species during hydrotreatment is very challenging due to the compositional complexity and the absence of a proper characterization method. In the presented work, we coupled hydrogen/deuterium exchange (HDX) with positive-ion electrospray ionization high-resolution mass spectrometry ((+) ESI HR MS) to investigate the difference between the composition of the nitrogen-containing species and the functional groups before and after hydrotreatment. The solvent and additive were optimized for HDX (+) ESI HRMS through systematic evaluations on model nitrogen-containing compounds. We found that adding deuterated water (D₂O) and deuterated formic acid (DCOOD) significantly increased the degree of HDX and thus facilitated the identification of nitrogen functional groups. After application to the hydrotreated petroleum samples, the compositional variation of intermediate amine compounds during the heavy petroleum hydrotreatment process was clearly revealed.

Application of molecular dynamics simulation to improve the theoretical prediction for collisional cross section of aromatic compounds with long alkyl chains in crude oils

RATIONALE

Molecular dynamics (MD) simulations with finite temperature were performed to improve the theoretical prediction of collisional cross section (CCS) values, especially for aromatic compounds containing long alkyl chains.

METHODS

In this study, the CCS values of 11 aromatic compounds with long alkyl chains were calculated by MD simulations while considering internal energy at 300, 500, and 700 K, and the results were compared with experimentally determined values.

RESULTS

The CCS values calculated at higher energies showed better agreement with the experimental values. Polycyclic aromatic hydrocarbons (PAHs) such as pentacene and benz[b]anthracene were also investigated, and better agreement between the theoretical and experimental results was observed when higher temperature (or higher internal energy) was considered.

CONCLUSIONS

The data presented in this study show that the internal degrees of freedom of ions must be considered to accurately predict the CCS values of aromatic compounds with a flexible structure measured by ion mobility mass spectrometry.

High-Resolution Mass Spectrometry Study of the Bio-Oil Samples Produced by Thermal Liquefaction of Microalgae in Different Solvents

We have performed a comparative analysis of the bio-oil produced by thermal liquefaction of microalgae in different solvents using high-resolution Orbitrap mass spectrometry and GC-MS approach. Water, methanol, ethanol, butanol, isopropanol, acetonitrile, toluene, and hexane were used as solvents in which the liquefaction was performed. It was observed that all resulting oils demonstrate a considerable degree of similarity. For all samples, compounds containing 1 and 2 nitrogen atoms dominated in the positive ESI spectra, while a relative contribution of other compounds was small. In negative ESI mode, compounds having 2 to 7 oxygens were observed. Statistical analysis revealed that products can be combined in two groups depending on the solvent used for the liquefaction. To the first group, we can attribute the products obtained by using protic (alcohols) and to the second by using aprotic (acetonitrile, toluene) solvents. Nevertheless, based on our results, we concluded that solvent possesses a minor impact on molecular composition of bio-oil. We suggested that the driving force of the liquefaction reaction is the thermal dehydration of the carbohydrate in algae, resulting in water formation, which could be the trigger of the producing of bio-oil. To prove this hypothesis, we performed the reaction with the dry algae in the absence of the solvent and observed the formation of bio-oil. Graphical Abstract.

Characterization of Nitrogen-Containing Polycyclic Aromatic Heterocycles in Crude Oils and Refined Petroleum Products

A large amount of polycyclic aromatic hydrocarbons (PAHs) and their heterocyclic analogues (N, S, O) are released to the marine environment from natural oil seeps, oil spills, bilge discharges and input of land-based sources. Many of these compounds are toxic and have a deleterious effect on marine biota. Nitrogen-containing compounds in crude oils are typically present as cyclic compounds such as polycyclic aromatic nitrogen heterocycles (PANHs) and are generally classified into the two categories of nonbasic (N-PANHs) and basic compounds (B-PANHs). Chromatographic analyses of PANHs are easily to be interfered by other oil components without proper sample preparation prior to instrumental analysis. In this work, dual solid phase extraction columns of 3-(isocyanato)propyl-functionalized silica gel (Si-NCO) and silica gel were employed to efficiently separate both N-PANHs and B-PANHs from saturated and aromatic petroleum hydrocarbons, which enable simultaneous accurate analyses of these groups with single sample preparation. Crude oils studied contain various concentrations of N-PANHs including carbazole, benzocarbazole and B-PANHs including quinolone, acridine and benzoacridine as well as their alkylated homologues. These compounds in light fuel and lubricating oil are generally not detected or are only in trace concentration, but have considerable abundance in heavy fuel oils. Crude oils from different sources and various petroleum products have their unique absolute concentrations and relative distribution patterns of PANHs. Chemical fingerprints of PANHs can provide valuable information for forensic oil spill identification and improve the understanding of the fate, behaviour and chemical degradation of spilled crude oil.

Hydrogen/deuterium exchange in mass spectrometry

The isotopic exchange approach is in use since the first observation of such reactions in 1933 by Lewis. This approach allows the investigation of the pathways of chemical and biochemical reactions, determination of structure, composition, and conformation of molecules. Mass spectrometry has now become one of the most important analytical tools for the monitoring of the isotopic exchange reactions. Investigation of conformational dynamics of proteins, quantitative measurements, obtaining chemical, and structural information about individual compounds of the complex natural mixtures are mainly based on the use of isotope exchange in combination with high resolution mass spectrometry. The most important reaction is the Hydrogen/Deuterium exchange, which is mainly performed in the solution. Recently we have developed the approach allowing performing of the Hydrogen/Deuterium reaction on-line directly in the ionization source under atmospheric pressure. Such approach simplifies the sample preparation and can accelerate the exchange reaction so that certain hydrogens that are considered as non-labile will also participate in the exchange. The use of in-ionization source H/D exchange in modern mass spectrometry for structural elucidation of molecules serves as the basic theme in this review. We will focus on the mechanisms of the isotopic exchange reactions and on the application of in-ESI, in-APCI, and in-APPI source Hydrogen/Deuterium exchange for the investigation of petroleum, natural organic matter, oligosaccharides, and proteins including protein-protein complexes. The simple scenario for adaptation of H/D exchange reactions into mass spectrometric method is also highlighted along with a couple of examples collected from previous studies.

Investigation of bio-oil produced by hydrothermal liquefaction of food waste using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry

Recent research has revealed that more than 1.3 billion tons of food is wasted globally every year. The disposal of such huge biomass has become a challenge. In the present paper, we report the production of the bio-oil by hydrothermal liquefaction of three classes of food waste: meat, cheese and fruits. The highest yield of the bio-oil was observed for meat (∼60%) and cheese (∼75%), while for fruits, it was considerably low (∼10%). The molecular composition of the obtained bio-oil was investigated using ultrahigh resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry and was found to be similar to that obtained from algae. Several thousand heteroatom compounds (N, N₂, ON₂, etc. classes) were reliably identified from each sample. It was found that bio-oils produced from meat and cheese have many compounds (∼90%) with common molecular formulas, while bio-oil produced from fruits differs considerably (∼30% of compounds are unique).

Design and Validation of In-Source Atmospheric Pressure Photoionization Hydrogen/Deuterium Exchange Mass Spectrometry with Continuous Feeding of D2O

In this study, continuous in-source hydrogen/deuterium exchange (HDX) atmospheric pressure photoionization (APPI) mass spectrometry (MS) with continuous feeding of D₂O was developed and validated. D₂O was continuously fed using a capillary line placed on the center of a metal plate positioned between the UV lamp and nebulizer. The proposed system overcomes the limitations of previously reported APPI HDX-MS approaches where deuterated solvents were premixed with sample solutions before ionization. This is particularly important for APPI because solvent composition can greatly influence ionization efficiency as well as the solubility of analytes. The experimental parameters for APPI HDX-MS with continuous feeding of D₂O were optimized, and the optimized conditions were applied for the analysis of nitrogen-, oxygen-, and sulfur-containing compounds. The developed method was also applied for the analysis of the polar fraction of a petroleum sample. Thus, the data presented in this study clearly show that the proposed HDX approach can serve as an effective analytical tool for the structural analysis of complex mixtures. Graphical abstract ᅟ.

Online Simultaneous Hydrogen/Deuterium Exchange of Multitarget Gas-Phase Molecules by Electrospray Ionization Mass Spectrometry Coupled with Gas Chromatography

In this study, a hydrogen/deuterium (H/D) exchange method using gas chromatography-electrospray ionization/mass spectrometry (GC-ESI/MS) was first investigated as a novel tool for online H/D exchange of multitarget analytes. The GC and ESI source were combined with a homemade heated column transfer line. GC-ESI/MS-based H/D exchange occurs in an atmospheric pressure ion source as a result of reacting the gas-phase analyte eluted from GC with charged droplets of deuterium oxide infused as the ESI spray solvent. The consumption of the deuterated solvent at a flow rate of 2 μL min^-1 was more economical than that in online H/D exchange methods reported to date. In-ESI-source H/D exchange by GC-ESI/MS was applied to 11 stimulants with secondary amino or hydroxyl groups. After H/D exchange, the spectra of the stimulants showed unexchanged, partially exchanged, and fully exchanged ions showing various degrees of exchange. The relative abundances corrected for naturally occurring isotopes of the fully exchanged ions of stimulants, except for etamivan, were in the range 24.3-85.5%. Methylephedrine and cyclazodone showed low H/D exchange efficiency under acidic, neutral, and basic spray solvent conditions and nonexchange for etamivan with an acidic phenolic OH group. The in-ESI-source H/D exchange efficiency by GC-ESI/MS was sufficient to determine the number of hydrogen by elucidation of fragmentation from the spectrum. Therefore, this online H/D exchange technique using GC-ESI/MS has potential as an alternative method for simultaneous H/D exchange of multitarget analytes.

Application of Atmospheric Pressure Photoionization H/D-exchange Mass Spectrometry for Speciation of Sulfur-containing Compounds

Herein we report the observation of atmospheric pressure in-source hydrogen-deuterium exchange (HDX) of thiol group for the first time. The HDX for thiol group was optimized for positive atmospheric pressure photoionization (APPI) mass spectrometry (MS). The optimized HDX-MS was applied for 31 model compounds (thiols, thiophenes, and sulfides) to demonstrate that exchanged peaks were observed only for thiols. The optimized method has been successfully applied to the isolated fractions of sulfur-rich oil samples. The exchange of one and two thiol hydrogens with deuterium was observed in the thiol fraction; no HDX was observed in the other fractions. Thus, the results presented in this study demonstrate that the HDX-MS method using APPI ionization source can be effective for speciation of sulfur compounds. This method has the potential to be used to access corrosion problems caused by thiol-containing compounds. Graphical Abstract ᅟ.

High desolvation temperature facilitates the ESI-source H/D exchange at non-labile sites of hydroxybenzoic acids and aromatic amino acids

H/D exchange coupled with high-resolution mass spectrometry has become a powerful analytical approach for structural investigations of complex organic matrices.

Structure-dependent degradation of polar compounds in weathered oils observed by atmospheric pressure photo-ionization hydrogen/deuterium exchange ultrahigh resolution mass spectrometry

The resin fractions of fresh mixtures of three oils spilled during the M/V Hebei Spirit oil spill, as well as weathered oils collected at weathering stages II and IV from the oil spill site were analyzed and compared by atmospheric pressure photo-ionization hydrogen/deuterium exchange mass spectrometry (HDX MS). The significantly decreased abundance of N(+) and [N-H+D](+) ions suggested that secondary and tertiary amine-containing compounds were preferentially degraded during the early stage of weathering. [N+H](+) and [N+D](+) ions previously attributed to pyridine-type compounds degraded more slowly than secondary and tertiary amine-containing compounds. The preferential degradation of nitrogen-containing compounds was confirmed by photo-degradation experiments using 15 standard compounds. In addition, significant increases of [S1O1+H](+) and [S1O1+D](+) ions with higher DBE values were observed from fresh oil mixtures as compared to stages II and IV samples, and that could be linked with the decrease of higher DBE compounds of the S1 class. This study presented convincing arguments and evidence demonstrating that secondary and tertiary amines were more vulnerable to photo-degradation than compounds containing pyridine, and hence, preferential degradation depending on chemical structures must be considered in the production of hazardous or toxic components.

Optimization and Application of APCI Hydrogen-Deuterium Exchange Mass Spectrometry (HDX MS) for the Speciation of Nitrogen Compounds

A systematic study was performed to investigate the utility of atmospheric pressure chemical ionization hydrogen-deuterium exchange mass spectrometry (APCI HDX MS) to identify the structures of nitrogen-containing aromatic compounds. First, experiments were performed to determine the optimized experimental conditions, with dichloromethane and CH(3)OD found to be good cosolvents for APCI HDX. In addition, a positive correlation between the heated capillary temperature and the observed HDX signal was observed, and it was suggested that the HDX reaction occurred when molecules were contained in the solvent cluster. Second, 20 standard nitrogen-containing compounds were analyzed to investigate whether speciation could be determined based on the different types of ions produced from nitrogen-containing compounds with various functional groups. The number of exchanges occurring within the compounds correlated well with the number of active hydrogen atoms attached to nitrogen, and it was confirmed that APCI HDX MS could be used to determine speciation. The results obtained by APCI HDX MS were combined with the subsequent investigation of the double bond equivalence distribution and indicated that resins of shale oil extract contained mostly pyridine type nitrogen compounds. This study confirmed that APCI HDX MS can be added to previously reported chemical ionization, electrospray ionization, and atmospheric pressure photo ionization-based HDX methods, which can be used for structural elucidation by mass spectrometry.

Developments in FT-ICR MS instrumentation, ionization techniques, and data interpretation methods for petroleomics

Because of the increasing importance of heavy and unconventional crude oil as an energy source, there is a growing need for petroleomics: the pursuit of more complete and detailed knowledge of the chemical compositions of crude oil. Crude oil has an extremely complex nature; hence, techniques with ultra-high resolving capabilities, such as Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), are necessary. FT-ICR MS has been successfully applied to the study of heavy and unconventional crude oils such as bitumen and shale oil. However, the analysis of crude oil with FT-ICR MS is not trivial, and it has pushed analysis to the limits of instrumental and methodological capabilities. For example, high-resolution mass spectra of crude oils may contain over 100,000 peaks that require interpretation. To visualize large data sets more effectively, data processing methods such as Kendrick mass defect analysis and statistical analyses have been developed. The successful application of FT-ICR MS to the study of crude oil has been critically dependent on key developments in FT-ICR MS instrumentation and data processing methods. This review offers an introduction to the basic principles, FT-ICR MS instrumentation development, ionization techniques, and data interpretation methods for petroleomics and is intended for readers having no prior experience in this field of study.

Letter: Observation of the 16O/18O exchange during electrospray ionization

Isotopic exchange approach coupled to high-resolution mass spectrometry has become the power analytical approach for a wide range of analytical and bioanalyticall applications. Considerable efforts have been dedicated to developing fast exchange techniques directly in the ionization source. But all such methods are limited to the hydrogen/deuterium exchange approaches. In this paper we demonstrate that certain types of oxygen atoms can also be exchanged for (18)O on the time scale of the ionization process. Using HIO(3) and NaIO(4) and by infusing the heavy water H(2)(18)O in the ESI source we have demonstrated that it is possible to obtain a high level of oxygen exchange. It was observed that the rate of this exchange depends to a large extent on the temperature of the desolvating capillary of the mass spectrometer. Several other species, such as peptides, oligonucleotides and low weight organic molecules, were subjected to in-ESI (16)O/(18)O exchange but the exchange was not observed.

Letter: Analytical potential of the in-electrospray ionization source hydrogen/deuterium exchange for the investigation of oligonucleotides

It has previously been reported that different conformations of oligonucleotides may be detected using a gas-phase hydrogen/deuterium (H/D) exchange performed in the collision cell of a mass spectrometer. The presence of different conformers was postulated based on the bimodal shape of the deuterium distribution and on the ion mobility spectrometry data. Here we implement an in-electrospray ionization source H/D exchange to detect the different conformations of oligonucleotides in the region of ion formation. We observed that the number of H/D exchanges depends considerably on the temperature of the desolvating capillary and varies from 25% at 50°C to 80% at 450°C, but no bimodality in the shape of the deuterium distribution was observed. Such results indicate that in the region of ion formation different conformations of oligonucleotide ions rapidly interconvert one into another.

In ESI-source H/D exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa: the role of the temperature of the desolvating capillary on H/D exchange

Transition of proteins from the solution to the gas phase during electrospray ionization remains a challenging problem despite the large amount of attention it has received during the past few decades. One of the major questions relates to the extent to which proteins in the gas phase retain their condensed phase structures. We have used in-electrospray source hydrogen/deuterium exchange to determine the number of deuterium incorporations as a function of protein mass, charge state and temperature of the desolvating capillary where the reaction occurs. All experiments were performed on a Thermo LTQ FT Ultra equipped with a 7-T superconducting magnet. Ions were generated by an IonMax Electrospray ion source operated in the positive ESI mode. Deuterium exchange was performed by introducing a droplet of D2 O beneath the ESI capillary. We systematically investigated gas phase hydrogen/deuterium (H/D) exchange under atmospheric pressure for peptides and proteins of different molecular weights from 1 to 66 kDa. We observed that almost all proteins demonstrate similar exchange rates for all charge states and that these rates increase exponentially with the temperature of the desolvating capillary. We did not observe any clear correlation of the number of H/D exchanges with the value of the cross section for a corresponding charge state. We have demonstrated the possibility of performing in-ESI source H/D exchange of large proteins under atmospheric pressure. The simplicity of the experimental setup makes it a useful experimental technique that can be applied for the investigation of gas phase conformations of proteins.

QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure

Background

Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13. Recent studies demonstrated that high-performance mass spectrometers could resolve isotopic fine structure and eliminate this peak overlap, allowing direct detection and quantification of deuterium incorporation.

Results

Here, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure. Given a peptide sequence (or elemental formula) and charge state, the mass-to-charge ratios of deuterium-associated peaks of the specified ion is determined. Intensities of peaks in an experimental mass spectrum within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated based on the estimated distribution of deuterium exchange to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter. A tool is also incorporated into QUDeX-MS to help in assigning ion signals from peptides arising from enzymatic digestion of proteins. MATLAB-deployable and standalone versions are available for academic use at qudex-ms.sourceforge.net and agarlabs.com.

Conclusion

Isotopic fine structure HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mass accuracy and deconvolution of overlapping ion signals. As previously demonstrated, however, the data analysis workflow for HDX-MS data with resolved isotopic fine structure is distinct. QUDeX-MS we hope will aid in the adoption of isotopic fine structure HDX-MS by providing an intuitive workflow and interface for data analysis.