Current proteomics technologies based on miniaturized on-line liquid chromatography (LC) coupled with mass spectrometry (MS) allow us to analyze protein expression profiling with a high throughput. Compared to genome sequencing and microarray-based transcriptomics, however, proteomics is still under development to achieve coverage of the entire proteome. In this commentary, the optimization of proteomic nanoLC/MS systems is described. In addition, future development of the analytical systems to achieve the coverage of the entire proteome is discussed.