The proteomics field has shifted over recent years from two-dimensional gel electrophoresis (2-DE)-based approaches to SDS-PAGE or gel-free workflows because of the tremendous developments in isotopic labeling techniques, nano-liquid chromatography, and high-resolution mass spectrometry. However, 2-DE still offers the highest resolution in protein separation. Therefore, we combined stable isotope labeling with amino acids in cell culture of controls and apoptotic HeLa cells with 2-DE and the subsequent analysis of tryptic peptides via nano-liquid chromatography coupled to an LTQ-Orbitrap mass spectrometer to obtain quantitative data using the methods with the highest resolving power on all levels of the proteomics workflow. More than 1,200 proteins with more than 2,700 protein species were identified and quantified from 816 Coomassie Brilliant Blue G-250 stained 2-DE spots. About half of the proteins were identified and quantified only in single 2-DE spots. The majority of spots revealed one to five proteins; however, in one 2-DE spot, up to 23 proteins were identified. Only half of the 2-DE spots represented a dominant protein with more than 90% of the whole protein amount. Consequently, quantification based on staining intensities in 2-DE gels would in approximately half of the spots be imprecise, and minor components could not be quantified. These problems are circumvented by quantification using stable isotope labeling with amino acids in cell culture. Despite challenges, as shown in detail for lamin A/C and vimentin, the quantitative changes of protein species can be detected. The combination of 2-DE with high-resolution nano-liquid chromatography-mass spectrometry allowed us to identify proteomic changes in apoptotic cells that would be unobservable using any of the other previously employed proteomic workflows. The large-scale analysis of proteins was made possible by high-resolution protein and peptide separation technologies such as two-dimensional gel electrophoresis (2-DE) 1 (1) and capillary chromatography (2) combined with the development of matrix-assisted laser desorption ionization (MALDI) (3) and electrospray ionization (ESI) (4) mass spectrometry (MS), two soft ionization techniques that enable the analysis of large biomolecules. 2-DE allows the highest resolution of protein separation, with up to 10,000 spots (5). Typically, 2-DE was combined with protein identification via peptide mass fingerprinting using MALDI-MS, often supported by tandem MS (MS/MS) produced with post-source decay (6). In 1996, the term "proteome" was defined as the protein composition of a cell, organism, organelle, tissue, or body fluid at a given time (7). However, the proteome is not the direct complement of the genome because of alternative splice variants, post-trans- 1 The abbreviations used are: 2-DE, two-dimensional gel electrophoresis; emPAI, exponentially modified protein abundance index; ESI, electrospray ionization; H/L, heavy-to-light; LC, liquid chromatography; MALDI, matrix-assisted laser desorption ionizat...