Automated Screening and Filtering Scripts for GC×GC-TOFMS Metabolomics Data

Comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) is a powerful tool for the analysis of complex mixtures, and it is ideally suited to discovery studies where the entire sample is potentially of interest. Unfortunately, when unit mass resolution mass spectrometers are used, many detected compounds have spectra that do not match well with libraries. This could be due to the compound not being in the library, or the compound having a weak/nonexistent molecular ion cluster. While high-speed, high-resolution mass spectrometers, or ion sources with softer ionization than 70 eV electron impact (EI) may help with some of this, many GC×GC systems presently in use employ low-resolution mass spectrometers and 70 eV EI ionization. Scripting tools that apply filters to GC×GC-TOFMS data based on logical operations applied to spectral and/or retention data have been used previously for environmental and petroleum samples. This approach rapidly filters GC×GC-TOFMS peak tables (or raw data) and is available in software from multiple vendors. In this work, we present a series of scripts that have been developed to rapidly classify major groups of compounds that are of relevance to metabolomics studies including: fatty acid methyl esters, free fatty acids, aldehydes, alcohols, ketones, amino acids, and carbohydrates.

Metabolomics Benefits from Orbitrap GC–MS—Comparison of Low- and High-Resolution GC–MS

The development of improved mass spectrometers and supporting computational tools is expected to enable the rapid annotation of whole metabolomes. Essential for the progress is the identification of strengths and weaknesses of novel instrumentation in direct comparison to previous instruments. Orbitrap liquid chromatography (LC)–mass spectrometry (MS) technology is now widely in use, while Orbitrap gas chromatography (GC)–MS introduced in 2015 has remained fairly unexplored in its potential for metabolomics research. This study aims to evaluate the additional knowledge gained in a metabolomics experiment when using the high-resolution Orbitrap GC–MS in comparison to a commonly used unit-mass resolution single-quadrupole GC–MS. Samples from an osmotic stress treatment of a non-model organism, the microalga Skeletonema costatum, were investigated using comparative metabolomics with low- and high-resolution methods. Resulting datasets were compared on a statistical level and on the level of individual compound annotation. Both MS approaches resulted in successful classification of stressed vs. non-stressed microalgae but did so using different sets of significantly dysregulated metabolites. High-resolution data only slightly improved conventional library matching but enabled the correct annotation of an unknown. While computational support that utilizes high-resolution GC–MS data is still underdeveloped, clear benefits in terms of sensitivity, metabolic coverage, and support in structure elucidation of the Orbitrap GC–MS technology for metabolomics studies are shown here.

Chlorine-initiated oxidation of <i>n</i>-alkanes under high-NO_<i>x</i> conditions: insights into secondary organic aerosol composition and volatility using a FIGAERO–CIMS

Chlorine-initiated oxidation of n-alkanes (C8−12) under high-nitrogen oxide conditions was investigated. Observed secondary organic aerosol yields (0.16 to 1.65) are higher than those for OH-initiated oxidation of C8−12 alkanes (0.04 to 0.35). A high-resolution time-of-flight chemical ionization mass spectrometer coupled to a Filter Inlet for Gases and AEROsols (FIGAERO–CIMS) was used to characterize the gas- and particle-phase molecular composition. Chlorinated organics were observed, which likely originated from chlorine addition to the double bond present on the heterogeneously produced dihydrofurans. A two-dimensional thermogram representation was developed to visualize the composition and relative volatility of organic aerosol components using unit-mass resolution data. Evidence of oligomer formation and thermal decomposition was observed. Aerosol yield and oligomer formation were suppressed under humid conditions (35 % to 67 % RH) relative to dry conditions (under 5 % RH). The temperature at peak desorption signal, Tmax, a proxy for aerosol volatility, was shown to change with aerosol filter loading, which should be constrained when evaluating aerosol volatilities using the FIGAERO–CIMS. Results suggest that long-chain anthropogenic alkanes could contribute significantly to ambient aerosol loading over their atmospheric lifetime.

Chlorine-initiated oxidation of n-alkanes under high NOx conditions: Insights into secondary organic aerosol composition and volatility using a FIGAERO-CIMS

Chlorine-initiated oxidation of n-alkanes (C8-12) under high nitrogen oxides conditions was investigated. Observed secondary organic aerosol yields (0.16 to 1.65) are higher than those for OH-initiated oxidation of C8-12 alkanes (0.04 to 0.35). A High-Resolution Time-of-Flight Chemical Ionization Mass Spectrometer coupled to a Filter Inlet for Gases and AEROsols (FIGAERO-CIMS) was used to characterize the gas- and particle-phase molecular composition. Chlorinated organics were observed, which likely originated from chlorine addition to the double bond present on the heterogeneously produced dihydrofurans. A two-dimensional thermogram representation was developed to visualize composition and relative volatility of organic aerosol components using unit-mass resolution data. Evidence of oligomer formation, thermal fragmentation and thermal decomposition was observed. Aerosol yield and oligomer formation were suppressed under humid conditions (35 to 67 % RH) relative to dry conditions (under 5 % RH). The temperature at peak desorption signal, Tmax, a proxy for aerosol volatility, was shown to change with aerosol filter loading, which should be constrained when evaluating aerosol volatilities using the FIGAERO-CIMS. Results suggest that long-chain anthropogenic alkanes could contribute significantly to ambient aerosol loading over their atmospheric lifetime.

Technical Note: Application of positive matrix factor analysis in heterogeneous kinetics studies utilizing the mixed-phase relative rates technique

The mixed-phase relative rates approach for determining aerosol particle organic heterogeneous reaction kinetics is often performed utilizing mass spectral tracers as a proxy for particle-phase reactant concentration. However, this approach may be influenced by signal contamination from oxidation products during the experiment. In the current study, the mixed-phase relative rates technique has been improved by combining a positive matrix factor (PMF) analysis with electron ionization aerosol mass spectrometry (unit-mass resolution), thereby removing the influence of m / z fragments from reaction products on the reactant signals. To demonstrate the advantages of this approach, the heterogeneous reaction between OH radicals and citric acid (CA) was investigated using a photochemical flow tube coupled to a compact time-of-flight aerosol mass spectrometer (C-ToF-AMS). The measured heterogeneous rate constant (k2) of citric acid toward OH was (3.31 ± 0.29) × 10−12 cm3 molecule−1 s−1 at 298 K and (30 ± 3)% relative humidity (RH) and was several times greater than the results utilizing individual m / z fragments. This phenomenon was further evaluated for particulate-phase organophosphates (triphenyl phosphate (TPhP), tris-1,3-dichloro-2-propyl phosphate (TDCPP) and tris-2-ethylhexyl phosphate (TEHP)), leading to k2 values significantly larger than previously reported. The results suggest that heterogeneous kinetics can be significantly underestimated when the structure of the products is highly similar to the reactant and when a non-molecular tracer is measured with a unit-mass resolution aerosol mass spectrometer. The results also suggest that the heterogeneous lifetime of organic aerosol in models can be overestimated due to underestimated OH uptake coefficients. Finally, a comparison of reported rate constants implies that the heterogeneous oxidation of aerosols will be dependent upon a number of factors related to the reaction system, and that a single rate constant for one system cannot be universally applied under all conditions.

Enhancing non-refractory aerosol apportionment from an urban industrial site through receptor modeling of complete high time-resolution aerosol mass spectra

Receptor modeling was performed on quadrupole unit mass resolution aerosol mass spectrometer (Q-AMS) sub-micron particulate matter (PM) chemical speciation measurements from Windsor, Ontario, an industrial city situated across the Detroit River from Detroit, Michigan. Aerosol and trace gas measurements were collected on board Environment Canada's Canadian Regional and Urban Investigation System for Environmental Research (CRUISER) mobile laboratory. Positive matrix factorization (PMF) was performed on the AMS full particle-phase mass spectrum (PMFFull MS) encompassing both organic and inorganic components. This approach compared to the more common method of analyzing only the organic mass spectra (PMFOrg MS). PMF of the full mass spectrum revealed that variability in the non-refractory sub-micron aerosol concentration and composition was best explained by six factors: an amine-containing factor (Amine); an ammonium sulfate- and oxygenated organic aerosol-containing factor (Sulfate-OA); an ammonium nitrate- and oxygenated organic aerosol-containing factor (Nitrate-OA); an ammonium chloride-containing factor (Chloride); a hydrocarbon-like organic aerosol (HOA) factor; and a moderately oxygenated organic aerosol factor (OOA). PMF of the organic mass spectrum revealed three factors of similar composition to some of those revealed through PMFFull MS: Amine, HOA and OOA. Including both the inorganic and organic mass proved to be a beneficial approach to analyzing the unit mass resolution AMS data for several reasons. First, it provided a method for potentially calculating more accurate sub-micron PM mass concentrations, particularly when unusual factors are present, in this case the Amine factor. As this method does not rely on a priori knowledge of chemical species, it circumvents the need for any adjustments to the traditional AMS species fragmentation patterns to account for atypical species, and can thus lead to more complete factor profiles. It is expected that this method would be even more useful for HR–ToF–AMS data, due to the ability to understand better the chemical nature of atypical factors from high-resolution mass spectra. Second, utilizing PMF to extract factors containing inorganic species allowed for the determination of the extent of neutralization, which could have implications for aerosol parameterization. Third, subtler differences in organic aerosol components were resolved through the incorporation of inorganic mass into the PMF matrix. The additional temporal features provided by the inorganic aerosol components allowed for the resolution of more types of oxygenated organic aerosol than could be reliably resolved from PMF of organics alone. Comparison of findings from the PMFFull MS and PMFOrg MS methods showed that for the Windsor airshed, the PMFFull MS method enabled additional conclusions to be drawn in terms of aerosol sources and chemical processes. While performing PMFOrg MS can provide important distinctions between types of organic aerosol, it is shown that including inorganic species in the PMF analysis can permit further apportionment of organics for unit mass resolution AMS mass spectra.

Enhancing non-refractory aerosol apportionment from an urban industrial site through receptor modelling of complete high time-resolution aerosol mass spectra

Receptor modelling was performed on quadrupole unit mass resolution aerosol mass spectrometer (Q-AMS) sub-micron particulate matter (PM) chemical speciation measurements from Windsor, Ontario, an industrial city situated across the Detroit River from Detroit, Michigan. Aerosol and trace gas measurements were collected on board Environment Canada's CRUISER mobile laboratory. Positive matrix factorization (PMF) was performed on the AMS full particle-phase mass spectrum (PMFFull MS) encompassing both organic and inorganic components. This approach was compared to the more common method of analysing only the organic mass spectra (PMFOrg MS). PMF of the full mass spectrum revealed that variability in the non-refractory sub-micron aerosol concentration and composition was best explained by six factors: an amine-containing factor (Amine); an ammonium sulphate and oxygenated organic aerosol containing factor (Sulphate-OA); an ammonium nitrate and oxygenated organic aerosol containing factor (Nitrate-OA); an ammonium chloride containing factor (Chloride); a hydrocarbon-like organic aerosol (HOA) factor; and a moderately oxygenated organic aerosol factor (OOA). PMF of the organic mass spectrum revealed three factors of similar composition to some of those revealed through PMFFull MS: Amine, HOA and OOA. Including both the inorganic and organic mass proved to be a beneficial approach to analysing the unit mass resolution AMS data for several reasons. First, it provided a method for potentially calculating more accurate sub-micron PM mass concentrations, particularly when unusual factors are present, in this case, an Amine factor. As this method does not rely on a priori knowledge of chemical species, it circumvents the need for any adjustments to the traditional AMS species fragmentation patterns to account for atypical species, and can thus lead to more complete factor profiles. It is expected that this method would be even more useful for HR-ToF-AMS data, due to the ability to better understand the chemical nature of atypical factors from high resolution mass spectra. Second, utilizing PMF to extract factors containing inorganic species allowed for the determination of extent of neutralization, which could have implications for aerosol parameterization. Third, subtler differences in organic aerosol components were resolved through the incorporation of inorganic mass into the PMF matrix. The additional temporal features provided by the inorganic aerosol components allowed for the resolution of more types of oxygenated organic aerosol than could be reliably resolved from PMF of organics alone. Comparison of findings from the PMFFull MS and PMFOrg MS methods showed that for the Windsor airshed, the PMFFull MS method enabled additional conclusions to be drawn in terms of aerosol sources and chemical processes. While performing PMFOrg MS can provide important distinctions between types of organic aerosol, it is shown that including inorganic species in the PMF analysis can permit further apportionment of organics for unit mass resolution AMS mass spectra.