A method (100) and a system (200) for processing mammalian bodily fluids to isolate target peptides and proteins. The method can include the steps of passing a mammalian bodily fluid through at least one ion exchange column (204). The ion exchange column can include an anionic resin and/or a cationic resin. The ion exchange column can be selected to remove large particles at a first pH level selected to remove such large particles at a maximum fluid pressure of 30 pounds per square inch (psi), for example less than 10 psi. The large particles can be released from the ion exchange column with a rinse solution having a pH selected for releasing the large particles. The pH of the fluid then can be adjusted to be a value less than 5.0, and the fluid can be filtered with a microfilter or ultrafilter (210).