Proteolysis products of proteins damaged by glycation, oxidation, and nitration—glycated, oxidized, and nitrated amino acids (glycation, oxidation, and nitration free adducts)—are waste products normally excreted in urine and cleared in peritoneal dialysate. Glucose degradation products in peritoneal dialysis (PD) fluids may increase protein damage, giving rise to increased protein glycation, oxidation, and nitration adduct residues of proteins and increased flux of glycation, oxidation, and nitration free adducts. Increased protein damage has been linked to mortality in end-stage renal disease. Reliable quantitation of markers for adducts of protein glycation, oxidation, and nitration is required for mechanistic studies and for morbidity and mortality risk analysis in PD patients. We review the available analytical techniques for such quantitation. Stable isotopic dilution analysis with tandem mass spectrometry is the “gold standard.” This method needs to be applied further in the study of PD and to validate other techniques so that the effect of PD on the metabolism and clearance of damaged proteins and related products can be quantified, and so that best-practice fluid management can be established to minimize cardiovascular risk.