Orbitool: a software tool for analyzing online Orbitrap mass spectrometry data

Cai, Runlong; Li, Yihao; Clément, Yohann; Li, Dandan; Dubois, Clement; Fabre, Marlène; Besson, L.; Perrier, S.; George, Christian; Ehn, Mikael; Huang, Cheng; Yi, Ping; Ma, Yingge; Riva, Matthieu

doi:10.5194/amt-14-2377-2021

Cited by 14 publications

(14 citation statements)

References 38 publications

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“…Externally, the Orbitrap can be calibrated by the traditional electrospray ionization source with a 2 mM sodium acetate solution, which can provide a series of negative adduct ions in the measurement range (mass to charge ratio ( m / z ), 50–750). Internally, due to the lack of standards for radicals and closed-shell products, the Orbitrap was mass-calibrated using mass spectra obtained from the ozonolysis of monoterpenes in ambient indoor air conditions . Data analyses were conducted using the XCalibur 4.1 (Thermo Scientific) and OrbiTool software.…”

Section: Experimental Sectionmentioning

confidence: 99%

“…Internally, due to the lack of standards for radicals and closed-shell products, the Orbitrap was mass-calibrated using mass spectra obtained from the ozonolysis of monoterpenes in ambient indoor air conditions . Data analyses were conducted using the XCalibur 4.1 (Thermo Scientific) and OrbiTool software. During online CI measurements, mass shift in mass accuracy was within 2 ppm.…”

Section: Experimental Sectionmentioning

confidence: 99%

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Field Detection of Highly Oxygenated Organic Molecules in Shanghai by Chemical Ionization–Orbitrap

Zhang

et al. 2022

Environ. Sci. Technol.

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Secondary organic aerosol, formed through atmospheric oxidation processes, plays an important role in affecting climate and human health. In this study, we conducted a comprehensive campaign in the megacity of Shanghai during the 2019 International Import Expo (EXPO), with the first deployment of a chemical ionization Orbitrap mass spectrometer for ambient measurements. With the ultrahigh mass resolving power of the Orbitrap mass analyzer (up to 140,000 Th/Th) and capability in dealing with massive spectral data sets by positive matrix factorization, we were able to identify the major gas-phase oxidation processes leading to the formation of oxygenated organic molecules (OOM) in Shanghai. Nine main factors from three independent sub-range analysis were identified. More than 90% of OOM are of anthropogenic origin and >60% are nitrogen-containing molecules, mainly dominated by the RO 2 + NO and/or NO 3 chemistry. The emission control during the EXPO showed that even though the restriction was effectual in significantly lowering the primary pollutants (20−70% decrease), the secondary oxidation products responded less effectively (14% decrease), or even increased (50 to >200%) due to the enhancement of ozone and the lowered condensation sink, indicating the importance of a stricter multi-pollutant coordinated strategy in primary and secondary pollution mitigation.

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Section: Experimental Sectionmentioning

confidence: 99%

Section: Experimental Sectionmentioning

confidence: 99%

Field Detection of Highly Oxygenated Organic Molecules in Shanghai by Chemical Ionization–Orbitrap

Zhang

et al. 2022

Environ. Sci. Technol.

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“…C) are expected to show a lower signal than the value predicted using natural abundances (e.g., 13 C: 12 C = 1.12%) if sensitivity is a function of concentration. As shown in Figure 4a, the relative abundance of measured isotopic OOMs compared to theoretical isotopic abundance does indeed decrease with decreasing intensity.…”

Section: ■ Results and Discussionmentioning

confidence: 81%

“…The limited resolving power of online ToF-MS may cause interferences among ion signals, which unavoidably introduce uncertainties to the identification of numerous vapors in complex atmospheric conditions, 10,11 especially for polluted environments with various nitrogen-containing OOMs. 12,13 Replacing conventional online ToF-MS with high-resolution Orbitrap MS can greatly improve atmospheric vapor identification. The mass resolving power of a Q Exactive Orbitrap 14 be in excess of 100,000.…”

Section: ■ Introductionmentioning

confidence: 99%

Improving the Sensitivity of Fourier Transform Mass Spectrometer (Orbitrap) for Online Measurements of Atmospheric Vapors

et al. 2022

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Orbitrap Fourier transform mass spectrometry coupled with chemical ionization (CI) is a new-generation technique for online analysis in atmospheric chemistry. The advantage of the high resolving power of the CI-Orbitrap has been compromised by its relatively low sensitivity to trace compounds (e.g., <106 molecules cm–3) in complex gaseous mixtures, limiting its application in online atmospheric measurements. In this study, we improve the sensitivity of a Q Exactive Orbitrap by optimizing the parameters governing the signal-to-noise ratio. The influence of other parameters related to ion transmission and fragmentation is also discussed. Using gaseous compounds in an environmental chamber, we show that by increasing the number of ions in the analyzer, the number of microscans (i.e., transients), and the averaging time, the sensitivity of the CI-Orbitrap to trace compounds can be substantially improved, and the linear detection range can be extended by a factor of 50 compared to standard settings. The CI-Orbitrap with optimized parameters is then used to measure oxygenated organic molecules in the atmosphere. By improving the sensitivity, the number of detected compounds above the 50% sensitivity threshold (i.e., the signal intensity at which the sensitivity is decreased by half) is increased from 129 to 644 in the atmospheric measurements. The Q Exactive CI-Orbitrap with improved sensitivity can detect ions with concentrations down to ∼5 × 104 molecules cm–3 (1 h averaging), and its 50% sensitivity threshold is now below 105 molecules cm–3.

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“…We preprocessed the raw data generated by the CI-Orbitrap using a new software called Orbitool (Orbitool version 1.40) developed specifically for the data-analysis of time series data from Orbitrap (Cai et al, 2021). We denoised, mass calibrated, and time-averaged the data into 30-minute steps using Orbitool.…”

Section: Discussionmentioning

confidence: 99%

Selective deuteration as a tool for resolving autoxidation mechanisms in α-pinene ozonolysis

Meder

Peräkylä²,

Varelas³

et al. 2022

Preprint

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Abstract. Highly oxygenated organic molecules (HOM) from α-pinene ozonolysis have been shown to be significant contributors to secondary organic aerosol (SOA), yet our mechanistic understanding of how the peroxy radical-driven autoxidation leads to their formation in this system is still limited. The involved isomerisation reactions such as H-atom abstractions followed by O2 additions can take place on sub-second time-scales in short-lived intermediates, making the process challenging to study. Similarly, while the end products and sometimes radical intermediates can be observed using mass spectrometry, their structures remain elusive. Therefore, we propose a method utilising selective deuterations for unveiling the mechanisms of autoxidation, where the HOM products can be used to infer which C-atoms have taken part in the isomerisation reactions. This relies on the fact that if a C−D bond is broken due to an abstraction by a peroxy group forming a −OOD hydroperoxide, the D-atom will become labile and able to be exchanged with a hydrogen atom in water vapour (H2O), effectively leading to loss of the D-atom from the molecule. In this study, we test the applicability of this method using three differently deuterated versions of α-pinene with the newly developed chemical ionisation Orbitrap (CI-Orbitrap) mass spectrometer to inspect the oxidation products. The high mass resolving power of the Orbitrap is critical, as it allows the unambiguous separation of molecules with a D-atom (mD=2.0141) from those with two H-atoms (mH2=2.0157). We found that the method worked well and we could deduce that two of the three tested compounds had lost D-atoms during oxidation, suggesting that those deuterated positions were actively involved in the autoxidation process. Surprisingly, the deuterations were not observed to decrease HOM molar yields, as would have been expected due to kinetic isotope effects. This may be an indication that the relevant H (or D) abstractions were fast enough that no competing pathways were of relevance despite slower abstraction rates of the D-atom. We show that selective deuteration can be a very useful method for studying autoxidation on a molecular level, and likely not limited to the system of α-pinene ozonolysis tested here.

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Orbitool: a software tool for analyzing online Orbitrap mass spectrometry data

Cited by 14 publications

References 38 publications

Field Detection of Highly Oxygenated Organic Molecules in Shanghai by Chemical Ionization–Orbitrap

Field Detection of Highly Oxygenated Organic Molecules in Shanghai by Chemical Ionization–Orbitrap

Improving the Sensitivity of Fourier Transform Mass Spectrometer (Orbitrap) for Online Measurements of Atmospheric Vapors

Selective deuteration as a tool for resolving autoxidation mechanisms in α-pinene ozonolysis

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