Hi Liliana,
You can turn on the three different FP measurements at the bottom of the user interface to measure the three different proteins.
The selection of filters/LEDs is complicated – it depends on both the emission and excitation spectra of the proteins. You need to ideally select ones that align with their peaks, but also since you are measuring them all together at the same time you will need to ensure that you are selecting filters in such a way to avoid too much overlap between adjacent proteins (i.e. you don’t want to be significantly exciting two at the same time).
This may take some trial and error.
Also, to improve your chances if you are measuring multiple proteins you ideally would use media with low auto-fluroescene (ie. don’t use LB), make sure the FPs are being expressed in fairly large amounts, and finally you would ideally pick proteins with long stokes-shift so that you can maximise the signal-to-noise (ie. reduce the amount of excitation light entering the emission filter).