I am having trouble recognizing whether the emission picks that I am seeing are from the light source of the instrument or from my sample?? is there a way to better discriminate them?
(I am not talking about the excitation wavelength)
Arezoo Setayesh, you should measure your spectrum without a sample (Io(lambda), where lambda is lights wavelength) and spectrum with sample (I(lambda)). Then you can calculate the spectrum of your sample as
S(lambda) = I(lambda) / Io(lambda)
This is a correct operation if you avoid saturation of your receiver for any spectral range, otherwise, you should adjust incident light intensity or receiver's sensitivity.
In fact, this is an extended version of Gerhard Martens answer.
in order to overcome (at least partly) the experimental challenges mentioned by Valeriy Sterligov , you may use a so-called 'white reference' instead of the sample. The white reference will give you approximately the same spectrum as the source, but at decreased photon flux.
Furthermore, there is no necessity to change the geometry of your experimental set up when changing between the acquisition of the sample spectrum and that of the source.
You may 'google' for 'white reference'; a lot of suppliers will be provided by that search...