CHOPPI (CHO protein predicted immunogenicity) is a web-based immunoinformatics tool for assessing the immunogenicity risk of CHO proteins (CHOPs). These process-related impurities may contribute to immune responses against biologics. CHOPPI users can analyze individual CHOPs or filter the entire CHO genome for immunogenic potential. CHOPPI also characterizes similarity with human proteins at the T cell epitope level, since CHOPs that are similar but not identical to human in terms of epitope content may elicit unfavorable immune responses. © 2014 Wiley Periodicals, Inc. 111 11 November 2014 10.1002/bit.25286 Article Articles Bioprocess Engineering and Supporting Technologies © 2014 Wiley Periodicals, Inc. Despite high quality standards and continual process improvements in manufacturing, host cell protein (HCP) process impurities remain a substantial risk for biological products. Even at low levels, residual HCPs can induce a detrimental immune response compromising the safety and efficacy of a biologic. Consequently, advanced-stage clinical trials have been cancelled due to the identification of antibodies against HCPs. To enable earlier and rapid assessment of the risks in Chinese Hamster Ovary (CHO)-based protein production of residual CHO protein impurities (CHOPs), we have developed a web tool called CHOPPI, for CHO Protein Predicted Immunogenicity. CHOPPI integrates information regarding the possible presence of CHOPs (expression and secretion) with characterizations of their immunogenicity (T cell epitope count and density, and relative conservation with human counterparts). CHOPPI can generate a report for a specified CHO protein (e.g., identified from proteomics or immunoassays) or characterize an entire specified subset of the CHO genome (e.g., filtered based on confidence in transcription and similarity to human proteins). The ability to analyze potential CHOPs at a genomic scale provides a baseline to evaluate relative risk. We show here that CHOPPI can identify clear differences in immunogenicity risk among previously validated CHOPs, as well as identify additional "risky" CHO proteins that may be expressed during production and induce a detrimental immune response upon delivery. We conclude that CHOPPI is a powerful tool that provides a valuable computational complement to existing experimental approaches for CHOP risk assessment and can focus experimental efforts in the most important directions. Biotechnol. Bioeng. 2014;111: 2170-2182. © 2014 Wiley Periodicals, Inc.