Breast cancer is known as the most common cancer in women population, especially in developed countries. Improved prognosis and effective treatment are needed to reduce the mortality of the disease. Doxorubicin, a topoisomerase II-targeting chemotherapeutic drug has been widely used to treat breast cancer. The rapidly evolved proteomics techniques, especially LC-MS/MS analysis, has been used in protein profiling in body fluids as well as cells, which provide us with a deep comprehension in drugs mechanism and patients response to the treatment. This new method can be extended in biomarker identification to improve diagnosis and monitoring of treatment. Effective treatment of breast cancer by Doxorubicin has been complicated by the single nucleotide polymorphism (SNP 309) in MDM 2 gene. The polymorphism is caused by substitution of Guanine over Thymine in its promoter. SNP 309 can be homozygous (GG) or heterozygous (TG) with different frequency in the general population. This polymorphism promotes tumor susceptibility and resistance to topoisomerase II-targeting agents. We aim to identify plasma proteins which correlate with a particular SNP309 genotype by using LC-MS/MS proteomics approach. The main objective of this research is to find the effective expressed biomarkers which should facilitate the monitoring of Doxorubicin treatment. Two different targets were selected in this study: 1) thirty breast cancer patients' on Doxorubicin treatment; 2) breast cancer-derived MCF7 cell line incubated with Doxorubicin. The plasma samples from the patients selected in this study were separated in three groups based on MDM2 single nucleotide polymorphism. The identified proteins from plasma samples with heterozygous (TG) and homozygous (GG) mutant genotypes were categorized in two groups: up-regulated proteins and downregulated proteins were identified with significant {p < 0.05) changes from the view of statistic. In the GG genotype group of samples, three proteins including a-1-antitrypsin, ceruloplasmin and Serotransferrin were up-regulated while hemoglobin subunit p and a2 macroglobulin were down regulated. In TG genotype group of samples, Serotransferrin, Apolipoprotein A-l and Clusterin were down-regulated whereas ceruloplasmin were up regulated. The protein profiling MCF7 cells incubated with Doxorubicin as compared with untreated MCF7 cells indicated that 10 cellular proteins were down-regulated and 13 others upregulated. These included HSP 90, glyceraldehyde-3-phosphate dehydrogenase, peroxiredoxin-1, and Calreticulin precursor. It is to be hoped that proteins identified in our study can be candidate biomarkers in monitoring Doxorubicin therapy in patients. 4