Try to perform a titration assay by varying the concentration from as low as 10uM to as high as 1 mM and record the ThT fluoroscence in each case by using any of the spectrofluorimeter (LS55 lying in the lab). Identify a particular concentration beyond which the signal does not increase any further. That should be your optimum ThT concentration for your assay!!! Gud Luck!!!
That is the reason why 5 ul of 2.5 mM ThT is added to 120 ul of polyGln aggregate sample. This corresponds to a final concentration of about 100 uM of ThT in solution, which should even compensate the maximum peptide concentration if used in the reaction.
I use it to stain cells that have amyloid aggregates. I use 0.005% w/v dissolved in water. I do not filter or run through cotton or anything, just add it directly to the cells to stain aggregates for 5 min. Then do 3 washes with absolute ethanol 3-5 min/wash and then once with water and you're good to go.