In this work, we evaluate the incorporation of an ultra-low flow interface for coupling capillary electrophoresis (CE) and mass spectrometry (MS), in combination with reversed-phase HPLC fractionation as an alternate workflow for quantitative proteomics. Proteins, extracted from a SILAC (stable isotope labeling by amino acids in cell culture) labeled and an unlabeled yeast strain were mixed and digested enzymatically in solution. The resulting peptides were fractionated using RP-HPLC and analyzed by CE-MS yielding a total of 28,538 quantified peptides that correspond to 3,272 quantified proteins. CE-MS analysis was performed using a neutral capillary coating, providing the highest separation efficiency at ultra-low flow conditions (<10 nL/min). Moreover, we were able to demonstrate that CE-MS is a powerful method for the identification of low abundance modified peptides within the same sample. Without any further enrichment strategies, we succeeded in quantifying 1,371 phosphopeptides present in the CE-MS dataset and found 49 phosphopeptides to be differentially regulated in the two yeast strains. Including acetylation, phosphorylation, deamidation and oxidized forms a total of 8,106 modified peptides could be identified in addition to 33,854 unique peptide sequences found. The work presented here shows the first quantitative proteomics approach that combines SILAC labeling with CE-MS analysis.