Breast Cancer Degradomic View Figure 9. The differential degradation of other protein substrates observed for the tested BCP. (A) Pigment epithelium-derived factor; specific truncates from the N-terminal direction exist solely to produce the multiple BCP peptidome peptides. (B) Gelsolin; the sequence zone in the middle of the substrate sequences specifically produce the multiple BCP peptidome peptides. (C) Ceruloplasmin; the sequence zone toward the substrate C terminus specifically generated the multiple BCP peptidome peptides. (D) ApoA-IV; the cleavage P1-Leu, P1-Tyr, and Lys (labeled in the figure) specifically for the BCP exist to produce the multiple BCP peptidome peptides. The red, blue, and black lines along the amino acid sequences have the same significances as for Figure 7. doi:10.1371/journal.pone.0013133.g009 peptides and Xcorr .4.1 and DCn .0.16 or Xcorr .4.3 and DCn .0.05 for partially tryptic peptides; for charge state +3 peptides, Xcorr .1.5 and DCn .0.16, or Xcorr .1.8 and DCn .0.10, or Xcorr .2.9 and DCn .0.05 for fully tryptic peptides and Xcorr .4.8 and DCn .0.16 or Xcorr .5.1 and DCn .0.05 for partially tryptic peptides. Identified proteins were grouped to a nonredundant protein list using ProteinProphet [43] software, after which one protein IPI number was randomly selected to represent each corresponding protein group that consisted of a number of database entries. The identification details for each proteomic and peptidomic peptides were given in Data S1, and all spectra collected for the degradomic and proteomic analyses are accessible at http://www. ebi.ac.uk/pride/init.do. Supplementary materials are included with this manuscript. Ethics Statement We have obtained the written informed consent from all patients involved in this study. Supporting Information Table S1 The proteome tryptic peptides identified from the pooled breast cancer patients (BCP) and control healthy persons (HP) blood plasma samples. Found at: doi:10.1371/journal.pone.0013133.s001 (9.08 MB DOC) PLoS ONE | www.plosone.org 11 October 2010 | Volume 5 | Issue 10 | e13133