An automated system for intact protein analysis is described that combines capillary isoelectric focusing (CIEF), reversed-phase liquid chromatography (RPLC), and electrospray ionization-mass spectrometry (ESI-MS). Performance is demonstrated with a complex yeast enzyme concentrate. CIEF is performed with a microdialysis membrane-based cathodic cell that permits p/ fractions to be sampled and stored for subsequent LC-MS analysis. A total of 50 mu g protein is loaded onto the capillary. Ten fractions are stored which span the p/ range 3-10. Each fraction is subsequently cleaned on a reversed-phase trap column and then characterized by LC-MS. MaxEnt1 is used to deconvolute the raw mass spectra to obtain the molecular weight (MW) of intact proteins/peptides in the sample. A two-dimensional display of p/vs. MW is illustrated for the 500 most prevalent species as identified by MaxEnt1.