# Analysis of spectra

Spectroscopy is one of the most common techniques for measurement of atmospheric chemical composition in the vapor phase. Fourier transform infrared (FTIR) spectroscopy is also one of the earliest techniques for observing chemical characteristics of atmospheric aerosol (Allen and Palen, 1989; Mader et al., 1952; McClenny et al., 1985; Volz, 1972). Given that many structural features (polarity, aromaticity) exhibit molecular response in the mid-infrared, FTIR spectra can be informative if not complex to analyze.

The first step to analysis is a qualitative appreciation for spectral features. While there is no shortage of tutorials avaliable online, one is an example of one that is particularly simple and practical.

• Visualize spectra and compare against blank samples.
• Check peaks in “spectra-structure correlation tables” to confirm the presence of certain functional groups.

IR spectra databases and structure-spectra correlation tables:

The second step is to perform quantitative analysis, which draws on techniques in chemometrics, statistical learning, and machine learning. Examples include:

• Baseline correction: regression and cluster analysis (for mixture models)
• Peak fitting: regression
• Multivariate calibration: regression
• Spectra type identification: cluster and classification analyses
• Receptor modeling: exploratory factor analysis

General resources for techniques relevant for chemometrics:

Other textbooks useful for IR spectra analysis:

• Bellamy (1980)
• Harris and Bertolucci (1989)
• Mayo et al. (2004)
• Smith (1995)
• Lambert et al. (1998)
• Chalmers and Griffiths (2002)
• Stuart (2004)
• Griffiths and Haseth (2007)
• Pavia et al. (2008)
• Kelley (2013)
• Hasegawa (2017)

References for terminology and nomenclature:

# Implementation of Spectral Analysis Tools in R

• R programmers and developers can access full functionality through R.
• Non-programmers can access common functionality through command-line interface (CLI) or browser that call pre-defined scripts.
• Additional analyses not specific to FTIR can be performed outside of R after exporting files to a common data exchange format.

## Libraries:

The following R libraries consolidate operations for spectral analysis of environmental samples (specifically, chemical mixtures found in atmospheric particles). The objective is not to reproduce interactive tools available for single spectrum analysis (e.g., Bruker OPUS), or general chemometric tools (e.g., CAMO The Unscrambler), but to provide a method for distributing algorithms that have worked for analysis of atmospheric spectra.

Installation procedures are described in the README file for each package. The simplest spectra object used by these packages inherts from an R’s fundamental matrix class, which can be used with the widest range of statistical functions available in R with minimal manipulation of data forms. There is additional functionality in other R packages that can be leveraged for further analysis:

## Tutorials

The following tutorials accompany the Atmospheric Measurement Techniques Discussion (AMTD) article (under review) introducing these packages (Reggente et al., 2018). Reggente et al. (2018) describes scripts and example ouputs distributed with the packages; more details on the underlying code are presented in these vignettes.

# References

Allen, D. T. and Palen, E.: Recent advances in aerosol analysis by infrared spectroscopy, Journal of Aerosol Science, 20(4), 441–455, doi:10.1016/0021-8502(89)90078-5, 1989.

Bellamy, L. J.: The infrared spectra of complex molecules: Volume two advances in infrared group frequencies, Springer, Netherlands., 1980.

Bishop, C. M.: Pattern recognition and machine learning, Springer, New York, NY., 2009.

Chalmers, J. M. and Griffiths, P. R.: Handbook of vibrational spectroscopy, John Wiley & Sons, Inc., 2002.

Coates, J.: Interpretation of infrared spectra, a practical approach, in Encyclopedia of analytical chemistry, John Wiley & Sons, Ltd., 2006.

Griffiths, P. and Haseth, J. A. D.: Fourier transform infrared spectrometry, 2nd ed., John Wiley & Sons, In., 2007.

Harris, D. C. and Bertolucci, M. D.: Symmetry and Spectroscopy: An Introduction to Vibrational and Electronic Spectroscopy, Dover Publications, New York., 1989.

Hasegawa, T.: Quantitative infrared spectroscopy for understanding of a condensed matter, Springer Japan., 2017.

Hastie, T., Tibshirani, R. and Friedman, J.: The elements of statistical learning: data mining, inference, and prediction, Springer Verlag., 2009.

Kelley, A. M.: Condensed-Phase Molecular Spectroscopy and Photophysics, John Wiley & Sons, Hoboken, NJ., 2013.

Lambert, J. B., Shurvell, H. F., Lightner, D. and Cooks, R. G.: Organic structural spectroscopy, Prentice Hall., 1998.

Mader, P. P., MacPhee, R. D., Lofberg, R. T. and Larson, G. P.: Composition of organic portion of atmospheric aerosols in the los angeles area, Industrial & Engineering Chemistry, 44(6), 1352–1355, doi:10.1021/ie50510a047, 1952.

Massart, D. L., Vandeginste, B. G. M., Deming, S. N., Michotte, Y. and Kaufman, L. and: Chemometrics: A textbook, Elsevier Science., 1988.

Mayo, D., Miller, F. and Hannah, R.: Course notes on the interpretation of infrared and raman spectra, John Wiley & Sons., 2004.

McClenny, W. A., Childers, J. W., Rōhl, R. and Palmer, R. A.: FTIR transmission spectrometry for the nondestructive determination of ammonium and sulfate in ambient aerosols collected on teflon filters, Atmospheric Environment, 19(11), 1891–1898, doi:10.1016/0004-6981(85)90014-9, 1985.

Pavia, D., Lampman, G. and Kriz, G.: Introduction to spectroscopy, Brooks/Cole Pub Co., Belmont, CA., 2008.

Reggente, M., Höhn, R. and Takahama, S.: An open platform for aerosol infrared spectroscopy analysis – airspec, Atmospheric Measurement Techniques Discussions, 2018, 1–28, doi:10.5194/amt-2018-332, 2018.

Shurvell, H.: Spectra–structure correlations in the mid- and far-infrared, in Handbook of vibrational spectroscopy, John Wiley & Sons, Ltd., 2006.

Smith, B.: Fundamentals of Fourier transform infrared spectroscopy, Taylor & Francis., 1995.

Stuart, B. H.: Infrared spectroscopy: Fundamentals and applications, John Wiley & Sons Ltd, Chichester., 2004.

Volz, F. E.: Infrared absorption by atmospheric aerosol substances, Journal of Geophysical Research, 77(6), 1017–1031, doi:10.1029/JC077i006p01017, 1972.