From our Trilogy optical specification guide, the Trilogy phycoerythrin module has an excitation LED of 530nm with excitation bandpass filter of 400-550 nm indicating that any light from the LED between those wavelengths is illuminated into the sample. The emission detected from any fluorescence is between 580nm and 640nm.

Likewise, the Trilogy Phycocyanin module has an excitation LED of 590nm with excitation bandpass filter of 400-600nm indicating that any light from the LED between those wavelengths is illuminated into the sample. The emission detected from any fluorescence is between 610nm and 670nm.

When in use with the article: Recent advances in production, purification and applications of phycobiliproteins (wjgnet.com)
In short, the Phyocyanin module can detect Phycoerythrin, significantly. From the article, Phycoerythrin can be excited by any light between 400nm and 590nm, but max excitation is around 550nm, which will cause fluorescence between 575nm and 650nm. This means the Phycocyanin module's LED can potentially excite Phycoerythrin pigment causing it to fluoresce and be detected by that same Phycocyanin module.

Also from the article, Phycocyanin can be excited by any light between 550nm and 650nmm, but max excitation is 590nm, which will cause fluorescence between 600nm and 680nm. This means the Phycoerythrin module's LED can potentially, although minimally since it's set to 530nm, excite PC pigment causing it to fluoresce. However, the fluorescence is again minimally detected by the PE module's filters which are set at a maximum of 640nm.

So, what you're seeing is that the Phycoerythrin module will minimally detect Phycocyanin, whereas the Phycocyanin module will have significant interferences with Phycoerythrin pigments in the same sample (i.e. you will significantly overestimate Phycocyanin if measuring a sample that contains both, however, you will have no significant interference from Phycocyanin pigments using the Phycoerythrin module if your sample contains both phycobilins).

Here's what you can do to get better representation of both pigments. Run your samples using both Trilogy modules. Your Phycocyanin module will give you an overestimate. If your Phycoerythrin module gives you very low values, then the Phycocyanin module is indicating that most of the pigment in the sample is Phycocyanin with very little to no interference from Phycoerythrin. If you find that your Phycocyanin values are way too high and you analyze that sample using the Phycoerythrin module and find the same thing, then you know for sure that your sample has a significant amount of Phycoerythrin in the sample in which case you can assess the phycobilin concentrations more accurately using the PE module.

We have other solutions for you if you're interested in assessing Phycocyanin containing cyanobacteria that will provide you with actual concentration estimates as well as abundance estimates without requiring you to extract your pigments (simply running live algal samples). The unit is called the CyanoFluor and it's specifically designed for this kind of research. Here's the link: https://www.turnerdesigns.com/cyanofluor-hab-indicator

Last thing to consider is dissolved organics for analysis for in vivo samples and how they can significantly interfere with your estimates. If working with organics and extracting proteins from solid materials, this would not pose a problem.