Capillary isoelectric focusin g (clEF) coupled to mass spectrometry (cIEF-MS) offers a potentially very powerful analytical tool for the investigation of physiological samples. The high resolvin g capabilities of clEF in combination with the high sensitivity and enhanced structural information provided by MS is highly desirable for the analysis of complex samples. How ever a major limitation of the technique has alw ays been the requ irement to desalt samples pr ior to clEF analysis. Such desalting normally occurs off-line and therefore adds complexity and the possibility of sample loss or contamina tion. In this study we demonstrate the use of a modified clEF protocol which enables samples containing ph ysiological levels of salts to be de salted on-line, within the clEF capillary. This new technique is very fast and efficient, allowi ng the direct analysis of a ph ysiologically derived fluid that contains a complex mix of proteins, such as human cerebrospinal fluid by clEF-MS in a single step experiment. C apillary isoelectric focus ing (clEF) carried ou t in fused silica capillaries was orig inally demonstrated by Hjerten and Zhu over ten years ago [1]. It has subsequently found widespread use in the separation and analysis of polypeptide and protein mixtures [2-4]. The two major advantages of clEF over conventional slab gel electrophoresis are the enhanced separation efficiencies as well as a substantial reduction in Joule heating [5]. Experimentally, the clEF proc ess consists of an initi al focusing step that is based on the isoelectric point (pl) values of ind ividual anal ytes. It is subseque ntly followed by an analyte mobilization stage affected either by electrophoresi s or pressure [6]. This is shown schema tically in Figure 1. Capillary IEF has been used exten sively with conv entional UV detection; however, the use of clEF coupled to mass spe ctrometry (clEF-MS) has to date received scant attention [7,8). The us e of clEF-MS affords a highl y efficient sepa ration technique with the capability to stru cturally characterize anal ytes deri ved from complex mixtures. This is Add ress repri nt requ ests to Stephen Nay lor, Biomedical Mass Spectrometry Facility,