Reproducible determination of dissolved organic matter photosensitivity: Data and code
Armstrong, Alec (2021), Reproducible determination of dissolved organic matter photosensitivity: Data and code, Dryad, Dataset, https://doi.org/10.5061/dryad.hmgqnk9d9
This dataset includes absorbance and fluourescence spectra used to compare the sensitivity of dissolved organic matter to experimental photodegradation. Spectra represent time series of measurements collected during 20-hour lab photodegradations. Nearly all experiments consisted of 60 absorbance and fluorescence measurements collected every 20 minutes as samples were exposed to simulated sunlight. A subset of these data were used to fit a parallel factor analysis (PARAFAC) model, onto which the entire data set was projected. Each experimental degradation fluorescence time series can then be expressed as relative change in PARAFAC component loadings, which are modeled with a biexpontial decay function. Fitted biexponential decay parameters may be indicators of relative photo-sensitivity useful in studies of dissolved organic matter. The dataset here includes individual spectra exported after some processing, Matlab scripts used to further process data and fit the PARAFAC model, exported PARAFAC model loadings, R scripts used to fit biexponential decay models to loss of PARAFAC components during photodegradation and compare fitted biexponential parameters, and the plots and tables related to this analysis.
Fluorescence excitation-emission matrices (EEMs) and absorbance spectra were collected with an Horiba Jobin Yvon Aqualog spectrofluorometer using a quartz flow cell with 1 cm path length. Absorbance/excitation wavelengths ranged from 600-230 nm in 3 nm intervals. Fluorescence spectra were collected at each excitation wavlength over an 8 pixel CCD (roughly every 3.24 nm) across the same wavelength range. Integration time was 1 s using "medium" gain setting in the Aqualog control software. Measurements were collected every 20 minutes using the "Sample Q" automatic measurement feature in the Aqualog software. Samples were continuously circulated between the spectrophotometer and a spiral exposure flow cell under an Oriel Sol2A solar simulator with a 1000 W Xe arc lamp equipped with a 1.5 air mass filter. Measurements were adjusted within the Aqualog software by subtracting a pure water blank, correcting fluorescence EEMs for inner filter effects, removing primary Rayleigh scatter, and normalizing each measurement by the integrated area under the Raman peak of water (347.5 nm). Spectra were imported to Matlab (R2018a) using the script and toolboxes included here, which also removed secondary Rayleigh scatter from EEMs. A subset of these data were fitted to a parallel factor analysis (PARAFAC) model onto which the entire dataset is projected, then model loadings for each EEM were exported (all using the drEEM toolbox) with the Matlab script. R (v. 3.6.0) was used to import model loadings and metadata and fit decay of PARAFAC components to an exponential decay model using the nlsLM function from the minpack.lm package.
Matlab and R scripts have been annotated to improve interpretation. Required R libraries are noted at the top of the script. R script requires user to define location of directory containing data to import (character variable "datadir") and location of directory to save plots (character variable "plotdir"). Matlab analysis script requires the drEEM toolbox (Murphy K.R., Stedmon C.A., Graeber D. and R. Bro, Fluorescence spectroscopy and multi-way techniques. PARAFAC, Anal. Methods, 2013, DOI:10.1039/c3ay41160e.), available for download at http://dreem.openfluor.org/ at time of writing.