An open platform for Aerosol InfraRed Spectroscopy analysis – AIRSpec

Abstract

Abstract. AIRSpec is a platform consisting of several chemometric packages developed for analysis of Fourier transform infrared (FTIR) spectra of atmospheric aerosols. The packages are accessible through a browser-based interface, which also generates the necessary input files based on user interactions for provenance management and subsequent use with a command-line interface. The current implementation includes the task of baseline correction, organic functional group (FG) analysis, and multivariate calibration for any analyte with absorption in the mid-infrared. The baseline correction package uses smoothing splines to correct the drift of the baseline of ambient aerosol spectra given the variability in both environmental mixture composition and substrates. The FG analysis is performed by fitting individual Gaussian line shapes for alcohol (aCOH), carboxylic acid (COOH), alkane (aCH), carbonyl (CO), primary amine (aNH2), and ammonium (ammNH) for each spectrum. The multivariate calibration model uses the spectra to estimate the concentration of relevant target variables (e.g., organic or elemental carbon) measured with different reference instruments. In each of these analyses, AIRSpec receives spectra and user choices on parameters for model computation; input files with parameters that can later be used with a command-line interface for batch computation are returned together with diagnostic figures and tables in text format. AIRSpec is built using the open-source software consisting of R and Shiny and is released under the GNU Public License v3. Users can download, modify, and extend the package, or access its functionality through the web application (http://airspec.epfl.ch, last access: 3 April 2019) hosted at the École polytechnique fédérale de Lausanne (EPFL). AIRSpec provides a unified framework by which different chemometric techniques can be shared and accessed, and its underlying suite of packages provides the basic functionality for extending the platform with new types of analyses. For example, basic functionality includes operations for populating and accessing spectra residing in in-memory arrays or relational databases, input and output of spectra and results of computation, and user interface development. Moreover, AIRSpec facilitates the exploratory work, can be used by FTIR spectra acquired with different methods, and can be extended easily with new chemometric packages when they become available. Therefore AIRSpec provides a framework for centralizing and disseminating such algorithms. This paper describes the modular architecture and provides examples of the implemented packages using the spectra of aerosol samples collected on PM2.5 polytetrafluoroethylene (Teflon) filters.

Characterization of primary and aged wood burning and coal combustion organic aerosols in an environmental chamber and its implications for atmospheric aerosols

“…The RONO 2 group abundances were not quantified due to the extensive overlap of its absorbances with other compounds and in order to keep the MIR estimates consistent with those of AMS, for which only total (organic plus inorganic) nitrate was estimated. After estimating FG abundances, the O : C, H : C, and OM : OC ratios were calculated with a few assumptions about the number of carbon atoms attached to each FG (refer to Chhabra et al, 2011b;Russell, 2003;Maria et al, 2002).…”

“…In addition, exposure to ambient fine PM is estimated to have caused 8.9 million premature deaths worldwide per year (in 2015; Burnett et al, 2018). Organic matter (OM), which constitutes up to 90 % of total fine atmospheric PM, is a key factor in aerosol-related phenomena (Russell, 2003;Shiraiwa et al, 2017). However, its chemical com-…”

Characterization of primary and aged wood burning and coal combustion organic aerosols in environmental chamber and its implications for atmospheric aerosols

“…After baseline correction and blank subtraction, the multiple peak-fitting algorithm described by Takahama et al (2013) and implemented by Reggente et al (2019b), functioning based on non-linear least squares analysis, was applied to the spectra to obtain major FG abundances of aCOH, COOH, aCH, and naCO , manuscript in preparation). The RONO 2 group abundances were not quantified due to extensive overlap of its absorbances with other compounds and in order to keep 6 https://doi.org/10.5194/acp-2020-924 Preprint.…”

Beyond the Ångström Exponent: Probing Additional Information in Spectral Curvature and Variability of In Situ Aerosol Hyperspectral (0.3–0.7 μm) Optical Properties

“…The Teflon filter set was analyzed by FT‐IR at the University of California, Davis, CA, using a Tensor II (Bruker Optics, Billerica, MA), infrared spectrometer equipped with a liquid nitrogen‐cooled mercury cadmium telluride detector (see Section S4 in Supporting Information S1 for details). Spectra are baseline corrected prior to peak‐fitting to estimate concentrations of organic functional groups that include aliphatic C‐H (aCH), alcohol OH (aCOH), carboxylic acids (COOH), and non‐acid carbonyls (naCO) (Reggente et al., 2019 and references therein).…”