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

Abstract. The Orbitrap mass spectrometer has recently been proved to be a powerful instrument to accurately measure gas-phase and particle-phase organic compounds with a greater mass resolving power than other widely used online mass spectrometers in atmospheric sciences. We develop an open-source software tool (Orbitool, https://orbitrap.catalyse.cnrs.fr, last access: 4 February 2021) to facilitate the analysis of long-term online Orbitrap data. Orbitool can average long-term data while improving the mass accuracy by re-calibrating each mass spectrum, assign molecular formulae of compounds and their isotopes to measured signals, and export time series and mass defect plots. The noise reduction procedure in Orbitool can separate signal peaks from noise and reduce the computational and storage expenses. Chemical ionization Orbitrap data from laboratory experiments on ozonolysis of monoterpenes and ambient measurements in urban Shanghai were used to test Orbitool. For the test dataset, the average mass accuracy was improved from <2 to <0.5 ppm by mass calibrating each spectrum. The denoising procedure removed 97 % of the noise peaks from a spectrum averaged for 30 min while maintaining the signal peaks, substantially helping the automatic assignment of unknown species. To illustrate the capabilities of Orbitool, we used the most challenging and complex dataset we have collected so far, which consists of ambient gas-phase measurements in urban Shanghai. These tests showed that Orbitool was able to automatically assign hundreds of molecular formulae as well as their isotopes with high accuracy.

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High mass accuracy and high mass resolving power FT-ICR secondary ion mass spectrometry for biological tissue imaging

Analytical and Bioanalytical Chemistry ◽

10.1007/s00216-013-7048-1 ◽

2013 ◽

Vol 405 (18) ◽

pp. 6069-6076 ◽

Cited By ~ 44

Author(s):

Donald F. Smith ◽

Andras Kiss ◽

Franklin E. Leach ◽

Errol W. Robinson ◽

Ljiljana Paša-Tolić ◽

...

Keyword(s):

Mass Spectrometry ◽

Secondary Ion Mass Spectrometry ◽

Mass Accuracy ◽

Resolving Power ◽

Tissue Imaging ◽

High Mass ◽

High Mass Accuracy ◽

Mass Resolving Power ◽

Secondary Ion ◽

Ft Icr

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C60 Secondary Ion FT-ICR Mass Spectrometry: High Mass Resolving Power and High Mass Accuracy SIMS

Microscopy and Microanalysis ◽

10.1017/s1431927613005291 ◽

2013 ◽

Vol 19 (S2) ◽

pp. 660-661

Author(s):

L. Pasa-Tolic ◽

D.F. Smith ◽

F.E. Leach ◽

E.W. Robinson ◽

R.M. Heeren

Keyword(s):

Mass Spectrometry ◽

Mass Accuracy ◽

Resolving Power ◽

High Mass ◽

High Mass Accuracy ◽

Mass Resolving Power ◽

Secondary Ion ◽

Ft Icr

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.

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Ultra-High Mass Resolving Power, Mass Accuracy, and Dynamic Range MALDI Mass Spectrometry Imaging by 21-T FT-ICR MS

Analytical Chemistry ◽

10.1021/acs.analchem.9b04768 ◽

2020 ◽

Vol 92 (4) ◽

pp. 3133-3142 ◽

Cited By ~ 5

Author(s):

Andrew P. Bowman ◽

Greg T. Blakney ◽

Christopher L. Hendrickson ◽

Shane R. Ellis ◽

Ron M. A. Heeren ◽

...

Keyword(s):

Mass Spectrometry Imaging ◽

Dynamic Range ◽

Maldi Mass Spectrometry ◽

Mass Accuracy ◽

Resolving Power ◽

High Mass ◽

Mass Resolving Power ◽

Ft Icr Ms ◽

Maldi Mass Spectrometry Imaging ◽

Ft Icr

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OLYMPIA - a compact laboratory Orbitrap-based high-resolution mass spectrometer laboratory set-up: Performance studies for gas composition measurement in analogues of planetary environments

10.5194/egusphere-egu21-8424 ◽

2021 ◽

Author(s):

Illia Zymak ◽

Arnaud Sanderink ◽

Bertrand Gaubicher ◽

Jan Žabka ◽

Jean-Pierre Lebreton ◽

...

Keyword(s):

Organic Compounds ◽

Mass Resolution ◽

Resolving Power ◽

High Mass ◽

Ionization Source ◽

Mass Spectrometers ◽

Mass Resolving Power ◽

Set Up ◽

Almost All ◽

Complex Organic

In situ composition measurements at Saturn and its moons (Cassini-Huygens1,2) and at comet 67P/Churyumov-Gerasimenko (Rosetta3,4) unveiled the complexity of the atmospheric chemical composition and high abundance of organic compounds in the environments of Solar System bodies. The deciphering of the measurements, obtained by current state-of-the-art instruments, to obtain the composition of complex gas mixtures that include polyatomic molecules and volatile organic compounds (VOCs) often requires having recourse to instrument response modeling supplemented by theoretical chemical models.One of the limitations in currently flown mass spectrometers is their limited mass resolving power. High mass-resolving power offers the capability to identify unambiguously almost all complex organic compounds. Such technique offers identification of almost all complex organic compounds without application of complementary separation techniques, e.g. chromatography, spectroscopy or collision induced dissociation. A new generation of space mass spectrometers under development (MASPEX5, MULTUM6, CORALS7, CRATER7, among others), aims at reaching mass resolution of > 50 000. CORALS and CRATER are Orbitrap-based instruments using CosmOrbitrap elements.In collaboration with J. Herovsky institute, the Laboratoire de Physique et de Chimie de l'Environnement et de l'Espace (LPC2E) has developed a new laboratory test-bench based on the Orbitrap&#8482; technology OLYMPIA (Orbitrap anaLYseur MultiPle IonisAtion) to evaluate several space applications of an Orbitrap-based space instrument using different ionization techniques. OLYMPIA is a compact, transportable set-up and is intended to be used as a stand-alone device (currently with an EI ionization source), but later intended to be coupled to different sources of ions. The next step in the next few months is to couple it with the LLILBID set-up in Berlin8.OLYMPIA is currently directly coupled with a first prototype of a compact electron impact ionization source. A single shot provides a useful signal duration of 200-250ms second before it decays to the noise level, and provide mass resolution for Kr ion isotopes of the order of 30 000 and on C2H4 on fragments of the order of 40 000. Kr is mostly being used to characterize the isotopic measurement capability of OLYMPIA and mixtures of C2H4, CO and N2gases in different proportions.&#160; In this presentation we concentrate on the capability to detect low ethylene lighter VOC concentration in different mixtures of CO and N2. Sensitivity of the instrument is sufficient to detect traces of the carbon dioxide gas in mixture with molecular nitrogen abundant in less than 1% volume ratio.1 Waite, J. H. et al. Space Sci. Rev. 114, 113&#8211;231 (2004)2 Coates, A. J. et al. Geophys. Res. Lett. 34, (2007)3 Balsiger, H. et al. Space Sci. Rev. 128, 745&#8211;801 (2007)4 Le Roy, L. et al. A&A 583, (2015)5 Brockwell, T. G. et al. in 2016 IEEE Aerospace Conference 1&#8211;17 (2016)6 Shimma, S. et al. Anal. Chem. 82, 8456&#8211;8463 (2010)7 Arevalo Jr, R. et al. Rapid Commun. Mass Spectrom. 32, 1875&#8211;1886 (2018)8 Klenner, F. et al. Astrobiology 20, 179&#8211;189 (2019)

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Calculation of the Ion Optical Properties of Inhomogeneous Magnetic Sector Fields Part 3: Oblique Incidence and Exit at Curved Boundaries

Zeitschrift für Naturforschung A ◽

10.1515/zna-1959-0911 ◽

1959 ◽

Vol 14 (9) ◽

pp. 822-827 ◽

Cited By ~ 22

Author(s):

H. A. Tasman ◽

A. J. H. Boerboom ◽

H. Wachsmuth

Keyword(s):

Oblique Incidence ◽

Normal Incidence ◽

Second Order ◽

Resolving Power ◽

High Mass ◽

Curved Boundaries ◽

Magnetic Sector ◽

Mass Resolving Power ◽

Mass Dispersion ◽

Fringing Fields

In previous papers 1.2we presented the radial second order imaging properties of inhomogeneous magnetic sector fields with normal incidence and exit at plane boundaries. These fields may provide very high mass resolving power and mass dispersion without increase in radius or decrease of slit widths. In the present paper the calculations are extended to include the effect of oblique incidence and exit at curved boundaries. The influence of the fringing fields on axial focusing when the boundaries are oblique, is accounted for. It is shown that the second order angular aberration may Le eliminated by appropriate curvature of the boundaries.

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Numerical analysis of trajectories in a Cassinian ion trap of second order with trap door ion inlet

European Journal of Mass Spectrometry ◽

10.1177/1469066720984380 ◽

2021 ◽

Vol 27 (1) ◽

pp. 3-12

Author(s):

Bjoern Raupers ◽

Hana Medhat ◽

Juergen Grotemeyer ◽

Frank Gunzer

Keyword(s):

Ion Trap ◽

Ion Traps ◽

Second Order ◽

Resolving Power ◽

Periodic Pattern ◽

Ion Motion ◽

Trap Door ◽

Mass Resolving Power ◽

Long Time ◽

The Fourier Transform

Ion traps like the Orbitrap are well known mass analyzers with very high resolving power. This resolving power is achieved with help of ions orbiting around an inner electrode for long time, in general up to a few seconds, since the mass signal is obtained by calculating the Fourier Transform of the induced signal caused by the ion motion. A similar principle is applied in the Cassinian Ion Trap of second order, where the ions move in a periodic pattern in-between two inner electrodes. The Cassinian ion trap has the potential to offer mass resolving power comparable to the Orbitrap with advantages regarding the experimental implementation. In this paper we have investigated the details of the ion motion analyzing experimental data and the results of different numerical methods, with focus on increasing the resolving power by increasing the oscillation frequency for ions in a high field ion trap. In this context the influence of the trap door, a tunnel through which the ions are injected into the trap, on the ion velocity becomes especially important.

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Evaluations of Surface PM10 Concentration and Chemical Compositions in MERRA-2 Aerosol Reanalysis over Central and Eastern China

Remote Sensing ◽

10.3390/rs13071317 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1317

Author(s):

Xiaodan Ma ◽

Peng Yan ◽

Tianliang Zhao ◽

Xiaofang Jia ◽

Jian Jiao ◽

...

Keyword(s):

Eastern China ◽

Mainland China ◽

Chemical Components ◽

Chemical Compositions ◽

Observation Data ◽

Causative Factors ◽

Routine Sampling ◽

Aerosol Compositions ◽

Modern Era

The chemical composition dataset of Aerosol Reanalysis of NASA’s Modern-Era Retrospective Analysis for Research and Application, version 2 (MERRAero) has not been thoroughly evaluated with observation data in mainland China due to the lack of long-term chemical components data. Using the 5-year data of PM10 mass concentrations and chemical compositions obtained from the routine sampling measurements at the World Meteorological Organization the Global Atmosphere Watch Programme regional background stations, Jing Sha (JS) and Lin’An (LA), in central and eastern China, we comprehensively evaluate the surface PM10 concentrations and chemical compositions such as sulfate (SO42−), organic carbon (OC) and black carbon (BC) derived from MERRAero. Overall, the concentrations of PM10, SO42−, OC and BC from the MERRAero agreed well with the measurements, despite a slight and consistent overestimation of BC concentrations and a moderate and persistent underestimation of PM10 concentrations throughout the study period. The MERRAero reanalysis of aerosol compositions performs better during the summertime than wintertime. By considering the nitrate particles in PM10 reconstruction, MERRAero performance can be significantly improved. The unreasonable seasonal variations of PM10 chemical compositions at station LA by MERRAero could be causative factors for the larger MERRAero discrepancies during 2016–2017 than the period of 2011–2013.

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ESA’s X-Ray Astronomy Mission, XMM

International Astronomical Union Colloquium ◽

10.1017/s0252921100076971 ◽

1990 ◽

Vol 123 ◽

pp. 129-140

Author(s):

B.G. Taylor ◽

A. Peacock

Keyword(s):

Resolving Power ◽

Science Program ◽

Eccentric Orbit ◽

Ccd Cameras ◽

Optical Telescope ◽

X Ray ◽

Medium Resolution ◽

Reflection Gratings ◽

Better Than

AbstractESA’s X-ray Astronomy Mission, XMM, scheduled for launch in 1998, is the second of four cornerstones of ESA’s long term science program Horizon 2000. Covering the range from about 0.1 to 10 keV, it will provide a high throughput of 5000 cm2 at 7 keV with three independant telescopes, and have a spatial resolution better than 30 arcsec. Broadband spectrophotometry is provided by CCD cameras while reflection gratings provide medium resolution spectroscopy (resolving power of about 400) in the range 0.3–3 keV. Long uninterrupted observations will be made from the 24 hr period, highly eccentric orbit, reaching a sensitivity approaching 10−15 erg cm−2 s−1 in one orbit. A 30 cm UV/optical telescope is bore-sighted with the x-ray telescopes to provide simultaneous optical counterparts to the numerous serendipitous X-ray sources which will be detected during every observation.

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