Please consult the manual or customer service. There should be some built-in procedure to adjust the energy levels, so that there is no jump at the filter switching wavelengths. Apart from the jumps, the spectrum looks rather ugly and not like a spectrum of a single emitting species. What did you measure?

Dear Dr. Menges,

Thank you for the response. I will confirm it again to the customer service. Actually, I have asked this but still no solution. That is actually not a fluorescence measurement, that is only a diffuse reflectance of the light source taken by using the diffuser (TiO2 surface if I am not mistaken) with synchronous measurement mode (delta wavelength = 0). However, that broken spectra sometimes also appeared in the EEM if the internal filters are used, especially if I used front face measurement method. That is why I asked this.

From a grating-based monochromator, you also get some light at the double wavelength from the second order diffraction. JASCO calls them "automatic cut filter". Normally, they are short pass optical filters, that cut off the double wavelength. Several such filters are needed to cover the complete excitation wavelength range. As each of these filter has different transmission, the intensity jump at the switching wavelength needs to be corrected for. Customer support should be able to fix this easily, or else they don't deserve their name...

When measuring EEM fluorescence data without cut filters, you can see the second order excitation peaks easily as another diagonal line at the doubled excitation wavelength. My spectroscopy software SPEKWIN32 has some functionality to cope with this distortions post-measurement: http://effemm2.de/spekwin/spekwin_man_2d_en.html

Thanks a lot for the answer! So I think I will not use the filters for my measurement until I have got confirmation about how to handle the effect of the filters from the CS. 

As I understood, was your intention just to have a look to lamp spectrum? To get lamp spectrum you may need to split emission channel and detection channel measurement., as Peter wrote. With some additional measurements (e.g. external calibrated ligth source with known spectrum) you got possibility to get correction of emission channel. From there you migth be able to do a conclusion on ecxitation correction. (But its is quite tricky to get it with small uncertainties). Another way could be correction by an known dye set to get a correction function, as decribed here: https://www.researchgate.net/publication/221872001_State-of-the_Art_Comparability_of_Corrected_Emission_Spectra_2_Field_Laboratory_Assessment_of_Calibration_Performance_Using_Spectral_Fluorescence_Standards

Article State-of-the Art Comparability of Corrected Emission Spectra...

Thank you Dr. Jan,

My intention, actually, is to correct the Fluorescence EEM, because I observed strange broken spectra appear on the EEM when I set the measurement using an internal filter. I measure the lamp spectra just to show and confirm that the broken spectra are because of the internal filter. I have already tried to make a correction data using external calibrated source and rhodamin B, and applied it to the raw EEM. But the correction data did not remove the broken spectra. I think this was because when we make the correction data the external calibrated light source was measured from different position, so the light beam did not pass through the internal filter. That is why the correction data could not removed the effect of the internal filter. (Maybe). 

I think the method to make the correction data need to be improved for this spectrofluorometer. BTW, I don't have experience using another type of spectrofluorometer.

Currently, for my previous data, I use some smoothing method to reduce that 'ugly' broken spectra, since I need to remove it to do some calculation using the EEM. But in the future, maybe I would not use the internal filter, even the higher order diffraction will appear in the EEM. Or as Peter wrote, we need another spectrofluorometer (If we have a funding again next time, ;))

Increase pressure on JASCO support, they have to give guidance on the proper functioning of their products. Threaten to give the spectrometer back. Publicly shame them on social web sites and give negative reviews...

Perhaps also of interest:

https://www.researchgate.net/publication/272672488_Procedures_for_Wavelength_Calibration_and_Spectral_Response_Correction_of_CCD_Array_Spectrometers

Article Procedures for Wavelength Calibration and Spectral Response ...

Do you have any update on this? I am having a similar issue.

Osman Doluca : Sorry, I have no update so far, If you really don't want that broken spectra you can turn off Internal Filter option. However the spectra will be cut in specific area where 1st and 2nd order Rayleigh scattering occurs. Don't forget also to make spectra correction data with same setting. Spectra pre-processing is another option to solve this or just leave it like that if your region of interest in EEM are not at that internal filter cut off...