Analyses of crude samples from biotechnology processes are often required in order to demonstrate that residual host cell impurities are reduced or eliminated during purification. In later stages of development, as the processes are further developed and finalized, there is a tremendous volume of testing required to confirm the absence of residual host cell proteins (HCP) and DNA. Analytical tests for these components are very challenging since (1). they may be present at levels that span a million-fold range, requiring substantial dilutions; (2). are not a single component, often existing as fragments and a variety of structures; (3). require high sensitivity for final steps in process; and (4). are present in very complex matrices including other impurities, the product, buffers, salts and solvents. Due to the complex matrices and the variety of potential analytes, the methods of analysis are not truly quantitative for all species. Although these limitations are well known, the assays are still very much in demand since they are required for approval of new products. Methods for final products, described elsewhere, focus on approaches to achieve regulatory requirements. The study described herein will describe the technical rationale for measuring the clearance of HCP and DNA in the entire bioprocessing to purification from an Escherichia coli-derived expression system. Three analytical assays, namely, reversed-phase high-performance liquid chromatography (RP-HPLC), enzyme-linked immunosorbent assay (ELISA), and Threshold Total DNA Assay, were utilized to quantify the protein product, HCP and DNA, respectively. Product quantification is often required for yield estimation and is useful since DNA and HCP results are best expressed as a ratio to product for calculation of relative purification factors. The recombinant E. coli were grown to express the protein of interest as insoluble inclusion bodies (IB) within the cells. The IB were isolated by repeated homogenization and centrifugation and the inclusion body slurry (IBS) was solubilized with urea. After refolding the product, the solution was loaded on several commonly used ion exchangers (CM, SP, DEAE, and Q). Product was eluted in a salt gradient mode and fractions were collected and analyzed for product, HCP and DNA. The IBS used for this study contained about 15 mg/ml product, 38 mg/ml HCP and 1.1 mg/ml DNA. Thus, the relative amounts of HCP and DNA in the IBS was excessive, and about 10(3) times greater than typical (because the cells and IB were not processed with the normal number of washing steps during isolation). This was of interest since similar samples may be encountered when working with non-inclusion body systems, such as periplasmic expressions, or in cases where the upstream unit operations under-perform in IB cleaning. The study described herein describes the development of three robust methods that provide the essential process data needed. These findings are of general interest to other projects since applications of similar analytical technology may be used as a tool to develop processes, evaluate clearance of impurities, and produce a suitable product.