I figured it might be beneficial for me to do a little reading and post a summary of how the EPO test works.
1. EPO is a glycoprotein - that is a protein with attached sugars (oligosaccharides)
2. Different oligosaccharides have different charges. Some will be more acidic (negatively charged) while others will be more basic (positively charged).
3. The combination of oligosaccharides attached to the EPO protein will affect the entire charge of the protein. Endogenous EPO is fairly neutral in charge. Exogenous EPO, which is synthesized in cell culture, has different oligosaccharides attached than the endogenous EPO, and tends to be basic (rhEPO) or acidic (Aranesp).
4. Proteins can be separated on the basis of charge by a technique called isoelectric focusing, and this is the basis of the EPO test.
Below is a picture of a hypothetical EPO test. As you can see, it doesn't matter about the absolute levels of EPO in the urine sample, the charge will still be different if there is synthetic EPO in the sample and thus easily detectable.
(taken from Delanghe et al. 2008. Am J Hematol. 83:237-241)