I measured the original concentration of my membrane protein after extraction. Then I immunoprecipitated it and eluted it in Laemmli buffer. How can I measure the concentration now before the downstream experiments? (Using the nanodrop)
You are able to measure the protein content of your sample in Laemmli buffer using the nanodrop. Set the nanodrop to read protein concentration and load 1uL of your sample. I would include a known BSA standard as a control to double check that you will get a correct measurement.
Glycerol absorbs strongly in the UV. You can try making your own Lamelli buffer using filtering the glycerol through activated charcoal , which should decrease the absorbance. The lamelli buffer needs to be used as a blank. If the Lamelli buffer already contains Comassie Blue or another dye you will not be able to detect the protein.
If you absolutely need the Lamelli buffer to elute, you can use other methods like BCA analysis or fluorescamine derivatization.