International Workshop on Organic Matter Spectroscopy 2015


PhD course: Parallel factor analysis for interpreting organic matter fluorescence

Kate Murphy (Chalmers University of Technology)
Colin Stedmon (Danish Technical University)


PARAllel FACtor analysis (PARAFAC) is used to interpret natural organic matter (NOM) fluorescence when measured using excitation emission matrix (EEM) spectroscopy. PARAFAC resolves overlapping fluorescence signals into independent spectra representing different chemical components. When fluorescence signals conform to Beers Law, this process can lead to the identification and quantification of independently varying fluorophores. However, many practical and analytical hurdles stand between EEM datasets and their chemical interpretation. This course will provide instruction on best-practice application of PARAFAC to fluorescence datasets.

Topics to be covered
(1) PARAFAC model and assumptions;
(2) Experimental design considerations: measuring fluorescence;
(3) Organizing and importing raw data files into MATLAB and assembling a 3-way dataset;
(4) Corrections for spectral variability and inner filter effects;
(5) Preprocessing for non-trilinearity (scatter) and concentration variability;
(6) Identifying and treating outliers;
(7) Model development and visualization;
(8) Model validation: Split-half analysis, core consistency, residual analysis;
(9) Sensitivity analyses of larger datasets;
(10) Comparing PARAFAC spectra using the OpenFluor database.

Participants are expected to be at the postgraduate level (or equivalent) having a scientific or engineering background. In order to keep up at the course you will need to come prepared. You should arrive with (or submit prior to arrival):

(1) A set of fluorescence EEMs (alternatively, a tutorial dataset can be supplied).
(2) Correction files, if bringing your own data (Absorbance, Ex and Em correction factors).
(3) A sample log listing metadata related to each sample (e.g. site, date, pH, salinity, etc.).
(4) A laptop computer with MATLAB installed (2012 or later).
(5) The drEEM toolbox for MATLAB (
(6) A completed survey answering questions about your data, instrument and prior experience.

To obtain ETS points for your participation, you will need to:

(1) Read key literature distributed prior to the course, and come prepared (See above).
(2) Participate in the tutorial sessions.
(3) Create a range of PARAFAC models from a fluorescence EEM dataset.
(4) Submit the final validated PARAFAC spectra accompanied by a report documenting how you arrived at this model. The report deadline will be approx. 4 weeks after the course ends.

The course will be held during the WOMS2015 on Tuesday, 22 September 2015.