What follows is a step-by-step description of a simple protein CD measurement as I do it. I assumed you are working with a Jasco instrument, because this is by far the most common spectropolarimeter, but you will only need small adjustments for a different instrument. Good luck!
Sample preparation.
1. Choosing the right buffer.
Many of the protein samples a CD spectroscopist has to do with, come dissolved in buffers containing detergents, EDTA, high salts concentrations ... These buffers are far from optimum, because they are not transparent in the 180-210 wavelength region, where most of the protein secondary structure CD bands are. Some of them (e.g. the EDTA) not only obscura the spectrum , but also tend to give a signal so strong (that is to say in the JASCO instrument the potential signal is more than 700) that it exceeds the instrumental range so that damage can follows.
The subsequent buffer conditions should be OK for a proper measurement:
PiBuff: 1-20 mM
EDTA: <1 mM
Salt concentration: <50 mM
Detergent: none
Avoid if possible any other substance. If you are forced to use it, check the buffer transparency before doing any further measurement. To minimize buffer problems, you can use a short-pathlength cuvette (say 1mm), but this requires a more concentrated protein solution and a proper cuvette calibration.
2. Measuring the protein concentration.
First of all, take a look to table 2 to see what protein concentration is roughly required for a good CD.
Even when your sample comes with a "nominal" protein concentration, you MUST check it. Luckily, the degree of accuracy attainable measuring the absorbance of the aromatic sidechains (tyrosins and/or tryptophans only!) is generally enough. To do this, measure the absorbance of your sample (or of a dilution of it) at 280 nm. Then go to the Biopolymer Calculator of Yale University and calculate the molar extinction coefficient of your protein. Apply the Lambert & Beer law and get your protein concentration. Note that this is just an easy-to-do protocol: for more accurate results, or
when your protein contains no tyrosines and triptophanes, you may need some more accurate way to measure concentration.
The sample preparation is a very important step, I think the most important, so TAKE YOUR TIME HERE! Any inaccuracy here will result in the invalidation of the whole experiment.