Although capillary electrophoresis coupled to mass spectrometry (CE-MS) holds promise for urinary peptide profiling, only a limited number of studies have used CE-MS to study plasma peptides. Here we describe the establishment of a workflow, including sample preparation, CE-MS and MS/MS analyses, data processing and normalisation optimized for the analysis of plasma peptides. Using 293 plasma samples from 136 patients with end stage kidney failure (including pre- and post-dialysis samples) and 22 patients with chronic kidney disease, we identified and quantified the abundance of 3920 unique plasma peptides. The repeatability and intermediate precision of the analysis were high (with a coefficient of variation of 15% on average for all peptides). 644 out of 3920 peptides were sequenced by CE-MS/MS. These peptide fragments belonged to 129 parent proteins that were also found in Human Plasma PeptideAtlas. Using the pipeline, we identified 188 sequenced plasma peptides with different plasma abundance before and after dialysis. These peptides combined in a support vector machine (SVM) classifier successfully discriminated between pre- and post- dialysis samples in a blinded validation cohort of 45 dialysis patients. Enriched peptides after dialyses were for the major part associated to inflammation. In conclusion, this high-throughput strategy could contribute to address the need for reliable plasma biomarkers of disease.