Get Coble Peaks and other fluorescence indicies
eem_coble_peaks2.RdModified from 'eem_coble_peaks' from eemR package to include some additional indices and modified definitions of Coble peaks. For indices that are ratios, the values in the ratio must be 5 times (or specifed amount) greater than the area below the 1:1 line (considered noise). If the desired wavelength is not explicitly measured the EEM will be interpolated using the interp2 function from the pracma library.
Arguments
- eem
an object of class eem or eemlist
- abs_data
dataframe of absorbance data matching the samples, used to calculate relative fluorescence efficiency
- noise_ratio
numeric indicating the noise threshold for ratio calculations
- verbose
logical determining if additional messages should be printed
Details
Coble peaks are based on Coble et al. 2014 and are defined as follows:
Peak B (pB): ex = 270:280 nm, em = 300:320 nm, Tyrosine-like
Peak T (pT): ex = 270:280 nm, em = 320:350 nm, Tryptophan-like
Peak A (pA): ex = 250:260 nm, em = 380:480 nm, Humic-like.
Peak M (pM): ex = 310:320 nm, em = 380:420 nm, Marine humic-like
Peak C (pC): ex = 330:350 nm, em = 420:480 nm, Humic-like
Peak D (pD): ex = 390 nm, em = 509 nm, Soil fulvic acid
Peak E (pE): ex = 455 nm, em = 521 nm, Soil fulvic acid
Peak N (pN): ex = 280 nm, em = 370 nm, Plankton derived
Given that peaks A, B, C, M, and T are not defined at fixed excitation and emission wavelength, the maximum fluorescence value in the region is extracted.
Additional fluorescence indices are based on Hansen et al. 2016. Measurements are defined as follows:
rAT: The ratio of peak A to peak T, indication of the amount of humic like (recalcitrant) to fresh (liable) DOM.
rCA: The ratio of peak C to peak A, indication of the amount of humic like to fumic like DOM.
rCM: The ratio of peak C to peak M, indication of the amount of diagenetically altered (blueshifted) DOM.
rCT: The ratio of peak C to peak T, indication of the amount of humic like (recalcitrant) to fresh (liable) DOM.
Fluorescence Index (FI): Ratio of fluorescence at ex = 370 nm, em = 470 nm to em = 520 nm. Identifies the relative contributions of terrestrial to microbial DOM sources.
Max Wavelength of FI (FI_max): The location (wavelength) of the maxiumum emission peak at ex= 370 nm. This is typically around 470 nm for natural materials however recent work has shown that this can change considerably for pyrogenic organic matter (Egan et al. 2023).
Humification Index (HIX): ex = 254 nm, em =\(\sum\)435:480 divided by em =\(\sum\)300:345. HIX proposed by Zsolnay (2002). An indication of humic substances or extent of humification. Higher values indicate an higher degree of humification.
Freshness Index (\(\beta:\alpha\), fresh): ex = 310 nm, ratio of em = 380 nm to max in em = 420:435 nm. An indication of recently produced DOM, higher values indicate more recently produced DOM.
Relative Fluorescence Efficiency (RFE): Ratio of fluorescence at ex = 370 nm, em = 460 nm to absorbance at 370 nm. An indicator of the relative amount of algal to non-algal DOM.
Biological Index (BIX): ex = 310 nm, ratio of em = 380 nm to em = 430 nm. An indicator of autotrophic productivity, values above 1 indicate recently produced autochthonous DOM.
References
Coble, P. G., Lead, J., Baker, A., Reynolds, D. M., & Spencer, R. G. M. (Eds.). (2014). Aquatic Organic Matter Fluorescence. Cambridge: Cambridge University Press. https://doi.org/10.1017/CBO9781139045452
Hansen, A. M., Kraus, T. E. C., Pellerin, B. A., Fleck, J. A., Downing, B. D., & Bergamaschi, B. A. (2016). Optical properties of dissolved organic matter (DOM): Effects of biological and photolytic degradation. Limnology and Oceanography, 61(3), 1015–1032. https://doi.org/10.1002/lno.10270
Egan, J. K., McKnight, D. M., Bowman, M. M., SanClements, M. D., Gallo, A. C., Hatten, J. A., & Matosziuk, L. M. (2023). Identifying photochemical alterations of dissolved pyrogenic organic matter using fluorescence spectroscopy. Aquatic Sciences, 85(2), 38. https://doi.org/10.1007/s00027-022-00919-7