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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.
