Phycobiliproteins are a family of water-soluble pigment proteins that play an important role as accessory or antenna pigments and absorb in the green part of the light spectrum poorly used by chlorophyll a. The phycoerythrins (PEs) are one of four types of phycobiliproteins that are generally distinguished based on their absorption properties. As PEs are water soluble, they are generally not captured with conventional pigment analysis. Here we present a statistical model based on in situ measurements of three transatlantic cruises which allows us to derive relative PE concentration from standardized hyperspectral underwater radiance measurements (Lu). The model relies on Empirical Orthogonal Function (EOF) analysis of Lu spectra and, subsequently, a Generalized Linear Model with measured PE concentrations as the response variable and EOF loadings as predictor variables. The method is used to predict relative PE concentrations throughout the water column and to calculate integrated PE estimates based on those profiles.