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) to facilitate the analysis of long-term online Orbitrap data. Orbitool can average long-term data while maintaining the mass accuracy by re-calibrating each mass spectrum, identify chemical compositions and isotopes of measured signals, and export time series and mass defect plots. The noise reduction procedure in Orbitool can separate signal peaks from noise and greatly 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 successfully test Orbitool. For the test dataset, the average mass accuracy was improved from < 2 ppm 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, greatly helping the automatic identification of unknown species. To illustrate the capabilities of Orbitool, we used the most challenging/complex dataset we have collected so far, which consists of ambient measurements in urban Shanghai. These tests showed that Orbitool was able to automatically separate and identify hundreds of compounds as well as their isotopes with a very high accuracy.