Abstract Background: Breast cancer is the most common malignancy in women in the western world. The outcome of breast cancer would be strongly improved if patients could be diagnosed and treated early. This especially holds for patients with hereditary breast cancer. Aim: Our aim is to identify proteins that are associated with BRCA1 deficient hereditary breast cancer. These proteins could have potential use as screening, prognostic or predictive biomarkers. Approach: In-depth proteome profiling of tumor tissues of mouse breast cancer models was employed to identify BRCA1-associated proteins. To this end, tumor tissue lysates of five BRCA1 deficient and five proficient mouse models (Liu et al., 2007) were fractionated using SDS-PAGE followed by tryptic in-gel digestion, nanoLC-MS/MS and database searching. Normalized spectral counting was used for protein quantification and beta binomial statistics to discover significantly regulated proteins. Ingenuity Pathway Analysis and COFECO protein complex analysis was used to support data interpretation. The prognostic power was assessed by the use of publicly available gene expression human breast cancer data sets. Results: We identified a total of 3614 proteins, of which 804 were differential between the genomic instable BRCA1-deficient and the genomic stable BRCA1-proficient breast tumors. Pathway analysis and protein complex identified DNA-repair and associated function like chromatin modeling and RNA processing as the major functions associated with the upregulated proteins of the BRCA1 deficient tumors. We created a core DNA-repair protein signature using pathway and protein Complex analysis. When the signature proteins were mapped to human breast cancer gene-expression data sets, they were shown to have prognostic power. Conclusion: Proteomics of genetic mouse models for familial breast cancer is a powerful strategy to discover novel candidate BRCA1 deficiency proteins with human relevance. The major upregulation of DNA-repair complexes may indicate a compensatory mechanism for loss of BRCA1 DNA-repair. Further validation studies are required to investigate prognostic candidates in tissue microarrays. Integration with data on tumor and cancer cell-secreted proteins will pinpoint which of the BRCA1 deficiency associated proteins may have potential for screening of BRCA1 tumors and whether they have predictive value for sensitivity to PARP1 inhibition and Cisplatin treatment in BRCA1 as well as non-BRCA1-deficient tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5109. doi:10.1158/1538-7445.AM2011-5109