Breast Cancer Degradomic View Figure 4. The net cleavage specificity of BCP and HP proteases for the degradome individual substrate. Protein substrate apoA-IV is used for this examination. The counts and frequencies (percentages) for amino acids at P1 in the BCP and HP are used to present the specificity. The BCP degradome proteases are more active than the HP ones to cleave more sites at P1-Ala, Lys, Leu, Arg, and Tyr. For the BCP, the P1-Leu, Tyr, and Ala are relatively preferred for cleavage in comparison with other P1-amino acids. doi:10.1371/journal.pone.0013133.g004 reported in this work can be directly applied for the diagnostic purpose. We are now developing high-through measurement capabilities based on the accurate mass and time tags approach [38], [39] to support such extensive degradomic-peptidomic investigations, and the work reported herein is the impetus driving these efforts. We also note that degradomic-peptidomic analysis of blood plasma is highly sensitive to a variety of conditions such as specimen collection and storage, peptidomic sample processing, sample analysis processes etc. For extensive comparative studies, standard operation procedures need to be established and executed to minimize the unnecessary variation that could affect the analytical results. The present study, albeit with the relatively small cohort size, used carefully selected patient and healthy control samples that were collected using the same laboratory protocol and processed in parallel. The data generated with our global peptidomic strategy are highly suggestive and provide a foundation for future efforts in this area. Methods Human blood plasma samples and collection procedure Human blood plasma samples were collected from the BCP and HP at the University of Texas M. D. Anderson Cancer Center (Houston, TX), following the same strict laboratory protocol for each sample. Approval for conducting this study was obtained from the Institutional Review Boards of the University of Texas M. D. Anderson Cancer Center and the Pacific Northwest National Laboratory in accordance with federal regulations. The 15 breast cancer subjects selected for this study are patients with ER/PR positive and Her2 negative invasive ductal carcinoma; 5 are stages I, 7 are stage II and 3 are stage III; 11 PLoS ONE | www.plosone.org 6 October 2010 | Volume 5 | Issue 10 | e13133