Increasing Polyaromatic Hydrocarbon (PAH) Molecular Coverage during Fossil Oil Analysis by Combining Gas Chromatography and Atmospheric-Pressure Laser Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS)

Ion Source Complementarity for Characterization of Complex Organic Mixtures Using Fourier Transform Mass Spectrometry: A Review

Complex organic mixtures are found in many areas of research, such as energy, environment, health, planetology, and cultural heritage, to name but a few. However, due to their complex chemical composition, which holds an extensive potential of information at the molecular level, their molecular characterization is challenging. In mass spectrometry, the ionization step is the key step, as it determines which species will be detected. This review presents an overview of the main ionization sources employed to characterize these kinds of samples in Fourier transform mass spectrometry (FT-MS), namely electrospray (ESI), atmospheric pressure photoionization (APPI), atmospheric pressure chemical ionization (APCI), atmospheric pressure laser ionization (APLI), and (matrix-assisted) laser desorption ionization ((MA)LDI), and their complementarity in the characterization of complex organic mixtures. First, the ionization techniques are examined in the common direct introduction (DI) usage. Second, these approaches are discussed in the context of coupling chromatographic techniques such as gas chromatography, liquid chromatography, and supercritical fluid chromatography.

Hyphenation of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with separation methods: The art of compromises and the possible - A review

This review provides an overview of the online hyphenation of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) with separation methods to date. The online coupling between separation techniques (gas and liquid chromatography, capillary electrophoresis) and FT-ICR MS essentially raises questions of compromise and is not look as straightforward as hyphenation with other analyzers (QTOF-MS for instance). FT-ICR MS requires time to reach its highest resolving power and accuracy in mass measurement capabilities whereas chromatographic and electrophoretic peaks are transient. In many applications, the strengths and the weaknesses of each technique are balanced by their hyphenation. Untargeted "Omics" (e.g. proteomics, metabolomics, petroleomics, …) is one of the main areas of application for FT-ICR MS hyphenated to online separation techniques because of the complexity of the sample. FT-ICR MS achieves the required high mass measurement accuracy to determine accurate molecular formulae and resolution for isobar distinction. Meanwhile separation techniques highlight isomers and reduce the ion suppression effects extending the dynamic range. Even if the implementation of FT-ICR MS hyphenated with online separation methods is a little trickier (the art of compromise), this review shows that it provides unparalleled results to the scientific community (the art of the possible), along with raising the issue of its future in the field with the relentless technological progress.

Revealing the Reactivity of Individual Chemical Entities in Complex Mixtures: the Chemistry Behind Bio-Oil Upgrading

Bio-oils are precursors for biofuels but are highly corrosive necessitating further upgrading. Furthermore, bio-oil samples are highly complex and represent a broad range of chemistries. They are complex mixtures not simply because of the large number of poly-oxygenated compounds but because each composition can comprise many isomers with multiple functional groups. The use of hyphenated ultrahigh-resolution mass spectrometry affords the ability to separate isomeric species of complex mixtures. Here, we present for the first time, the use of this powerful analytical technique combined with chemical reactivity to gain greater insights into the reactivity of the individual isomeric species of bio-oils. A pyrolysis bio-oils and its esterified bio-oil were analyzed using gas chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry, and in-house software (KairosMS) was used for fast comparison of the hyphenated data sets. The data revealed a total of 10,368 isomers in the pyrolysis bio-oil and an increase to 18,827 isomers after esterification conditions. Furthermore, the comparison of the isomeric distribution before and after esterification provide new light on the reactivities within these complex mixtures; these reactivities would be expected to correspond with carboxylic acid, aldehyde, and ketone functional groups. Using this approach, it was possible to reveal the increased chemical complexity of bio-oils after upgrading and target detection of valuable compounds within the bio-oils. The combination of chemical reactions alongside with in-depth molecular characterization opens a new window for the understanding of the chemistry and reactivity of complex mixtures.

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.

Advances in Chemical Analysis of Oil Spills Since the Deepwater Horizon Disaster

Analytical techniques for chemical analysis of oil, oil photochemical and biological transformation products, and dispersants and their biodegradation products benefited significantly from research following the 2010 Deepwater Horizon (DWH) disaster. Crude oil and weathered-oil matrix reference materials were developed based on the Macondo well oil and characterized for polycyclic aromatic hydrocarbons, hopanes, and steranes for use to assure and improve the quality of analytical measurements in oil spill research. Advanced gas chromatography (GC) techniques such as comprehensive two-dimensional GC (GC × GC), pyrolysis GC with mass spectrometry (MS), and GC with tandem MS (GC-MS/MS) provide a greater understanding at the molecular level of composition and complexity of oil and weathering changes. The capabilities of high-resolution MS (HRMS) were utilized to extend the analytical characterization window beyond conventional GC-based methods to include polar and high molecular mass components (>400 Da) and to provide new opportunities for discovery, characterization, and investigation of photooxidation and biotransformation products. Novel separation approaches to reduce the complexity of the oil and weathered oil prior to high-resolution MS and advanced fluorescence spectrometry have increased the information available on spilled oil and transformation products. HRMS methods were developed to achieve the required precision and sensitivity for detection of dispersants and to provide molecular-level characterization of the complex surfactants. Overall, research funding following the DWH oil spill significantly advanced and expanded the use of analytical techniques for chemical analysis to support petroleum and dispersant characterization and investigations of fate and effects of not only the DWH oil spill but future spills.

Predicting ion mobility as a function of the electric field for small ions in light gases

High resolution mobility devices such as Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) and Differential Mobility spectrometers (DMS) use strong electric fields to gas concentration ratios, E/N, to separate ions in the gas phase. While extremely successful, their empirical results show a non-linear, ion-dependent relation between mobility K and E/N that is difficult to characterize. The one-temperature theory Mason-Schamp equation, which is the most widely used ion mobility equation, unfortunately, cannot capture this behavior. When the two-temperature theory is used, it can be shown that the K-E/N behavior can be followed quite closely numerically by equating the effect of increasing the field to an increase in the ion temperature. This is attempted here for small ions in a Helium gas environment showing good agreement over the whole field range. To improve the numerical characterization, the Lennard-Jones (L-J) potentials may be optimized. This is attempted for Carbon, Hydrogen, Oxygen and Nitrogen at different degrees of theory up to the fourth approximation, which is assumed to be exact. The optimization of L-J improves the accuracy yielding errors of about 3% on average. The fact that a constant set of L-J potentials work for the whole range of E/N and for several molecules, also suggests that inelastic collisions can be circumvented in calculations for He. The peculiar K-E/N hump behaviors are studied, and whether mobility increases or decreases with E/N is shown to derive from a competition between relative kinetic energy and the interaction potentials.

Vacuum Laser Photoionization inside the C-trap of an Orbitrap Mass Spectrometer: Resonance-Enhanced Multiphoton Ionization High-Resolution Mass Spectrometry

State-of-the-art mass spectrometry with ultraviolet (UV) photoionization is mostly limited to time-of-flight (ToF) mass spectrometers with 1000-10 000 m/Δm mass resolution. However, higher resolution and higher spectral dynamic range mass spectrometry may be indispensable in complex mixture characterization. Here, we present the concept, implementation, and initial evaluation of a compact ultrahigh-resolution mass spectrometer with gas-phase laser ionization. The concept is based on direct laser photoionization in the ion accumulation and ejection trap (C-trap) of an Orbitrap mass spectrometer. Resonance-enhanced multiphoton ionization (REMPI) using 266 nm UV pulses from a frequency-quadrupled Nd:YAG laser was applied for selective and efficient ionization of monocyclic and polycyclic aromatic hydrocarbons. The system is equipped with a gas inlet for volatile compounds and a heated gas chromatography coupling. The former can be employed for rapid system m/z-calibration and performance evaluation, whereas the latter enables analysis of semivolatile and higher-molecular-weight compounds. The capability to evaluate complex mixtures is demonstrated for selected petrochemical materials. In these experiments, several hundred to over a thousand compounds could be attributed with a root-mean-square mass error generally below 1 ppm and a mass resolution of over 140 000 at 200 m/z. Isobaric interferences could be resolved, and narrow mass splits, such as 3.4 mDa (SH₄/C₃), are determined. Single laser shots provided limits of detection in the 20-ppb range for p-xylene and 1,2,4-trimethylbenzene, similar to compact vacuum REMPI-ToF systems.

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) peak intensity normalization for complex mixture analyses

RATIONALE

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a preferred technique for analyzing complex organic mixtures. Currently, there is no consensus normalization approach, nor an objective method for selecting one, for quantitative analyses of FT-ICR-MS data. We investigate a method to evaluate and score the amount of bias various normalization approaches introduce into the data.

METHODS

We evaluate the ability of the Statistical Procedure for the Analysis of Normalization Strategies (SPANS) to guide the selection of appropriate normalization approaches for two different FT-ICR-MS data sets. Furthermore, we test the robustness of SPANS results to changes in SPANS parameter values and assess the impact of using various normalization approaches on downstream statistical analyses.

RESULTS

The normalization approach identified by SPANS differed for the two data sets. Normalization methods impacted the statistical significance of peaks differently, underscoring the importance of carefully evaluating potential methods. More consistent SPANS scores resulted when at least 120 significant peaks are used, where larger sets of peaks were obtained by increasing the p-value threshold. Interestingly, we show that total sum scaling and highest peak normalization, used in previous studies, underperformed relative to SPANS-recommended normalization approaches.

CONCLUSIONS

Although there is no single, best normalization method for all data sets, SPANS provides a mechanism to identify an appropriate normalization method for analyzing FT-ICR-MS data quantitatively. The number of peaks used in the background distributions of SPANS contributes more significantly to the reproducibility of results than the p-value thresholds used to obtain those peaks.

Comprehensive Screening of Polycyclic Aromatic Hydrocarbons and Similar Compounds Using GC-APLI-TIMS-TOFMS/GC-EI-MS

In the present work, a novel workflow based on complementary gas-phase separations for the identification of isomeric PAHs from complex mixtures is described. This is the first report on the coupling of gas chromatography (GC), atmospheric pressure laser ionization (APLI), and trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) for the characterization of polycyclic aromatic hydrocarbons. Over a hundred known unknowns are uniquely identified based on the molecular ion retention indices I (5%), mobility (RSD < 0.6% and R = 50-90 with S_r = 0.18 V/ms), mobility-based theoretical candidate assignment (<3%), accurate mass chemical formula assignment (<2 ppm), and electron impact fragmentation pattern and database search. The advantages of theoretical modeling of PAHs and similar compounds were evaluated using candidate structures ranked by retention indices and fragmentation pattern from GC-EI-MS data sets. Over 20 PAH isomeric and deuterated standards were utilized for the GC-APLI-TIMS-TOF MS workflow validation. Noteworthy is the analytical capability for untargeted screening of isomeric and isobaric compounds with additional characterization metrics not available in traditional GC-EI-MSⁿ workflows.

Petroleomics: Tools, Challenges, and Developments

The detailed molecular characterization of petroleum-related samples by mass spectrometry, often referred to as petroleomics, continues to present significant analytical challenges. As a result, petroleomics continues to be a driving force for the development of new ultrahigh resolution instrumentation, experimental methods, and data analysis procedures. Recent advances in ionization, resolving power, mass accuracy, and the use of separation methods, have allowed for record levels of compositional detail to be obtained for petroleum-related samples. To address the growing size and complexity of the data generated, vital software tools for data processing, analysis, and visualization continue to be developed. The insights gained impact upon the fields of energy and environmental science and the petrochemical industry, among others. In addition to advancing the understanding of one of nature's most complex mixtures, advances in petroleomics methodologies are being adapted for the study of other sample types, resulting in direct benefits to other fields.

Trace-Level Persistent Organic Pollutant Analysis with Gas-Chromatography Orbitrap Mass Spectrometry-Enhanced Performance by Complementary Acquisition and Processing of Time-Domain Data

The range of commercial techniques for high-resolution gas-chromatography-mass spectrometry (GC-MS) has been recently extended with the introduction of GC Orbitrap Fourier transform mass spectrometry (FTMS). We report on progress with quantitation performance in the analysis of persistent organic pollutants (POP), by averaging of time-domain signals (transients), from a number of GC-FTMS experiment replicates. Compared to a standard GC-FTMS measurement (a single GC-FTMS experiment replicate, mass spectra representation in reduced profile mode), for the 10 GC-FTMS technical replicates of ultratrace POP analysis, sensitivity improvement of up to 1 order of magnitude is demonstrated. The accumulation method was implemented with an external high-performance data acquisition system and dedicated data processing software to acquire the time-domain data for each GC-FTMS replicate and to average the acquired GC-FTMS data sets. Concomitantly, the increased flexibility in ion signal detection allowed the attainment of ultrahigh-mass resolution (UHR), approaching R = 700 000 at m/z = 200.

Petroleomic depth profiling of Staten Island salt marsh soil: 2ω detection FTICR MS offers a new solution for the analysis of environmental contaminants

Staten Island is located in one of the most densely populated regions of the US: the New York/New Jersey Estuary. Marine and industrial oil spills are commonplace in the area, causing the waterways and adjacent marshes to become polluted with a range of petroleum-related contaminants. Using Rock-Eval pyrolysis, the hydrocarbon impact on a salt marsh was assessed at regular intervals down to 90 cm, with several key sampling depths of interest identified for further analysis. Ultrahigh resolution data are obtained by direct infusion (DI) atmospheric pressure photoionization (APPI) on a 12 T solariX Fourier transform ion cyclotron resonance mass spectrometer (FTICR MS) allowing trends in the compositional profile with depth to be observed, such as changes in the relative hydrocarbon intensity and the relative contributions from oxygen- and sulfur-containing groups. These trends may correlate with the timing of major oil spills and leaks of petroleum and other industrial chemicals into the waterways. The use of gas chromatography (GC) coupled to a 7 T solariX 2XR FTICR MS equipped with an atmospheric pressure chemical ionization (APCI) ion source offers retention time resolved and extensive compositional information for the complex environmental samples complementary to that obtained by DI-APPI. The compositional profile observed using GC-APCI FTICR MS includes contributions from phosphorous-containing groups, which may be indicative of contamination from other anthropogenic sources.

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 GC/MS studies of a light crude oil fraction

The continuous development in analytical instrumentation has brought the newly developed Orbitrap-based gas chromatography / mass spectrometry (GC/MS) instrument into the forefront for the analysis of complex mixtures such as crude oil. Traditional instrumentation usually requires a choice to be made between mass resolving power or an efficient chromatographic separation, which ideally enables the distinction of structural isomers that is not possible by mass spectrometry alone. Now, these features can be combined, thus enabling a deeper understanding of the constituents of volatile samples on a molecular level. Although electron ionization is the most popular ionization method employed in GC/MS analysis, the need for softer ionization methods has led to the utilization of atmospheric pressure ionization sources. The last arrival to this family is the atmospheric pressure photoionization (APPI), which was originally developed for liquid chromatography / mass spectrometry (LC/MS). With a newly developed commercial GC-APPI interface, it is possible to extend the characterization of unknown compounds. Here, first results about the capabilities of the GC/MS instrument under high or low energy EI or APPI are reported on a volatile gas condensate. The use of different ionization energies helps matching the low abundant molecular ions to the structurally important fragment ions. A broad range of compounds from polar to medium polar were successfully detected and complementary information regarding the analyte was obtained.

Evaluation of coal-related model compounds using tandem mass spectrometry

RATIONALE

Gas chromatography/mass spectrometry (GC/MS) is a routine and basic instrumental method for the analysis of complex coal conversion products in the chemical industry. To further enhance the practical potential of GC/MS in chemical industry, a tandem MS method for the selection of ion pairs applied in monitoring coal conversions was established using GC/quadrupole time-of-flight MS (GC/Q-TOF MS). The corresponding fragmentation pathways were explored and suitable ion pairs were screened.

METHODS

Fourteen coal-related model compounds (CRMCs) were analyzed using GC/Q-TOF MS with different collision-induced dissociation (CID) energies (5-20 eV). The fragmentation pathways can offer a better understanding of chemical bond breaking, hydrogen transfer, rearrangement reactions and elimination of neutral fragments for CRMCs during the CID process.

RESULTS

The precursor ions of aromatic hydrocarbons without alkyl chains were difficult to fragment with a CID energy of 20 eV. But aromatic hydrocarbons with branched chains were prone to fragment via the loss of alkyl chains and further fragmented through ring-opening reactions. Compared with the C_alk C_ar bond, the C_ar C_ar bond was difficult to fragment due to its high bond dissociation energy. The existence of heteroatoms facilitated fragmentation that was conducive to the screening of ion pairs.

CONCLUSIONS

The CID technique of GC/Q-TOF MS will contribute to studies on the organic composition of coals and to building monitoring methods for coal conversions via fragmentation and ion pair selection.

Increasing Analytical Separation and Duty Cycle with Nonlinear Analytical Mobility Scan Functions in TIMS-FT-ICR MS

In this work, nonlinear, stepping analytical mobility scan functions are implemented to increase the analytical separation and duty cycle during tandem Trapped Ion Mobility Spectrometry and FT-ICR MS operation. The differences between linear and stepping scan functions are described based on length of analysis, mobility scan rate, signal-to-noise, and mobility resolving power. Results showed that for the linear mobility scan function only a small fraction of the scan is sampled, resulting in the lowest duty cycle 0.5% and longest experiment times. Implementing nonlinear targeted scan functions for analysis of known mobilities resulted in increased duty cycle (0.85%) and resolving powers (R up to 300) with a 6-fold reduction in time from 30 to 5 min. For broad range characterization, a nonlinear mobility stepping scan function provided the best sensitivity, resolving power, duty cycle (4%), and points per peak. The applicability of nonlinear mobility scan functions for the analysis of complex mixtures is illustrated for the case of a direct infusion of a MCF-7 breast cancer cell digest, where isobaric peptides (e.g., DFTPAELR and TTILQSTGK) were separated in the mobility domain (R_IMS: 110) and identified based on their CCS, accurate mass (R_MS: 550k), and tandem MS using IRMPD in the ICR cell.

Normal-phase liquid chromatography retention behavior of polycyclic aromatic sulfur heterocycles and alkyl-substituted polycyclic aromatic sulfur heterocycle isomers on an aminopropyl stationary phase

Retention indices for 67 polycyclic aromatic sulfur heterocycles (PASHs) and 80 alkyl-substituted PASHs were determined using normal-phase liquid chromatography (NPLC) on an aminopropyl (NH₂) stationary phase. The retention behavior of PASH on the NH₂ phase is correlated with the number of aromatic carbon atoms and two structural characteristics have a significant influence on their retention: non-planarity (thickness, T) and the position of the sulfur atom in the bay-region of the structure. Correlations between solute retention on the NH₂ phase and T of PASHs were investigated for three cata-condensed (cata-) PASH isomer groups: (a) 13 four-ring molecular mass (MM) 234 Da cata-PASHs, (b) 20 five-ring MM 284 Da cata-PASHs, and (c) 12 six-ring MM 334 Da cata-PASHs. Correlation coefficients ranged from r = -0.49 (MM 234 Da) to r = -0.65 (MM 334 Da), which were significantly lower than structurally similar PAH isomer groups (r = -0.70 to r = -0.99). The NPLC retention behavior of the PASHs are compared to similar results for PAHs.

Analysis of Photoirradiated Water Accommodated Fractions of Crude Oils Using Tandem TIMS and FT-ICR MS

For the first time, trapped ion mobility spectrometry (TIMS) in tandem with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is applied to the analysis of the low energy water accommodated fraction (WAF) of a crude oil as a function of the exposure to light. The TIMS-FT-ICR MS analysis provided, in addition to the heteroatom series identification, new insights into the WAF isomeric complexity (e.g., [m/z; chemical formula; collision cross section] data sets) for a better evaluation of the degree of chemical and structural photoinduced transformations. Inspection of the [m/z; chemical formula; collision cross section] data sets shows that the WAF composition changes as a function of the exposure to light in the first 115 h by initial photosolubilization of HC components and their photo-oxidation up to O_4-5 of mainly high double bond equivalence species (DBE > 9). The addition of high resolution TIMS (resolving power of 90-220) to ultrahigh resolution FT-ICR MS (resolving power over 400k) permitted the identification of a larger number of molecular components in a single analysis (e.g., over 47k using TIMS-MS compared to 12k by MS alone), with instances of over 6-fold increase in the number of molecular features per nominal mass due to the WAF isomeric complexity. This work represents a stepping stone toward a better understanding of the WAF components and highlights the need for better experimental and theoretical approaches to characterize the WAF structural diversity.

Chemical Analysis of Water-accommodated Fractions of Crude Oil Spills Using TIMS-FT-ICR MS

Multiple chemical processes control how crude oil is incorporated into seawater and also the chemical reactions that occur overtime. Studying this system requires the careful preparation of the sample in order to accurately replicate the natural formation of the water-accommodated fraction that occurs in nature. Low-energy water-accommodated fractions (LEWAF) are carefully prepared by mixing crude oil and water at a set ratio. Aspirator bottles are then irradiated, and at set time points, the water is sampled and extracted using standard techniques. A second challenge is the representative characterization of the sample, which must take into consideration the chemical changes that occur over time. A targeted analysis of the aromatic fraction of the LEWAF can be performed using an atmospheric-pressure laser ionization source coupled to a custom-built trapped ion mobility spectrometry-Fourier transform-ion cyclotron resonance mass spectrometer (TIMS-FT-ICR MS). The TIMS-FT-ICR MS analysis provides high-resolution ion mobility and ultrahigh-resolution MS analysis, which further allow the identification of isomeric components by their collision cross-sections (CCS) and chemical formula. Results show that as the oil-water mixture is exposed to light, there is significant photo-solubilization of the surface oil into the water. Over time, the chemical transformation of the solubilized molecules takes place, with a decrease in the number of identifications of nitrogen- and sulfur-bearing species in favor of those with a greater oxygen content than were typically observed in the base oil.

Comprehensive chemical comparison of fuel composition and aerosol particles emitted from a ship diesel engine by gas chromatography atmospheric pressure chemical ionisation ultra-high resolution mass spectrometry with improved data processing routines

The analysis of petrochemical materials and particulate matter originating from combustion sources remains a challenging task for instrumental analytical techniques. A detailed chemical characterisation is essential for addressing health and environmental effects. Sophisticated instrumentation, such as mass spectrometry coupled with chromatographic separation, is capable of a comprehensive characterisation, but needs advanced data processing methods. In this study, we present an improved data processing routine for the mass chromatogram obtained from gas chromatography hyphenated to atmospheric pressure chemical ionisation and ultra high resolution mass spectrometry. The focus of the investigation was the primary combustion aerosol samples, i.e. particulate matter extracts, as well as the corresponding fossil fuels fed to the engine. We demonstrate that utilisation of the entire transient and chromatographic information results in advantages including minimisation of ionisation artefacts and a reliable peak assignment. A comprehensive comparison of the aerosol and the feed fuel was performed by applying intensity weighted average values, compound class distribution and principle component analysis. Certain differences between the aerosol generated with the two feed fuels, diesel fuel and heavy fuel oil, as well as between the aerosol and the feed were revealed. For the aerosol from heavy fuel oil, oxidised species from the CHN and CHS class precursors of the feed were predominant, whereas the CHO_x class is predominant in the combustion aerosol from light fuel oil. Furthermore, the complexity of the aerosol increases significantly compared to the feed and incorporating a higher chemical space. Coupling of atmospheric pressure chemical ionisation to gas chromatography was found to be a useful additional approach for characterisation of a combustion aerosol, especially with an automated utilisation of the information from the ultra-high resolution mass spectrometer and the chromatographic separation.