Cells respond to their environment with programmed changes in gene expression. Cataloging these changes at the protein level is key towards understanding the physiology of an organism. Multi-subunit and multi-protein complexes are also important and pathogenic and physiologic processes. In order to identify expressed proteins and potential protein complexes, we utilized a combination of non-denaturing chromatography and peptide mass fingerprinting. This approach allows us to identify the components of protein mixtures, as well as information lost in traditional proteomics, such as subunit associations. Applying this methodology to cells at both mid-exponential and stationary phase growth conditions, we identified several thousand proteins from each cell-state of E. coli corresponding to hundreds of unique gene products. The copurification of proteins when fractionated at varying pHs could suggest the components of higher order complexes. This non-denaturing proteomic approach should provide physiological data unavailable by other means. The components of several known cellular complexes were also evident in this analysis. To characterize proteins associated with nucleic acid binding, we also performed proteome analysis on log and stationary phase cells grown in LB separated over heparin chromatography at neutral pH, which enriches for these proteins. The complete analysis of these identifications is discussed.