Breast Cancer Degradomic View Figure 6. Selective degradation of ITI HC1-3 observed for the tested BCP. (A) The peptidome peptides were observed solely from the HC1 main chain, not from the two propeptides (blank-filled ovals). (B) The peptidome peptides were observed dominantly from the HC2 main chain, except for one (not labeled) from the propeptide (black color-filled oval). (C) The peptidome peptides were observed solely from the HC3 main chain, not from the two propeptides (blank-filled ovals). doi:10.1371/journal.pone.0013133.g006 using the area under the curve (peak area) as a measurement. To compile quantitative measurement of the identified peptides, the datasets for the two samples were processed for finding features (unique mass classes) based on the algorithm described previously [41]. Abundance of a feature is defined as sum of the individual spectrum abundances and log10 of this value is used as the abundance value without any further processing or normalization. Several heuristics principles were used for reducing quantitation information to unique peptide forms for presentation. In many reported cases multiple charge states for the detected features were observed, and the abundant, identical charge states were reported for those having the same abundance ratio between the various charge state distributions. In a few cases where the abundance ratio was not preserved for the different charge state distributions, manual inspection and correction of abundance value were applied and indicated in the data list (Table S2). The quantitative data include following two categories: 1) peptides were identified by the FT MS/MS-UStags for both the BCP and HP samples and 2) peptides were identified for either the BCP or HP sample. For situation 2, the unique mass classes between the two samples were matched according to the FT MS measured masses (5 ppm error tolerance) and the HRLC elution time (10% variance tolerance). When the peptides identified from one sample were not matched to species from the other sample, the species were declared not found in the other sample. The not-found species were assigned to have the abundance values of the background intensity scaled for summing over the features based on the same condition as the identified peptides correspondingly. PLoS ONE | www.plosone.org 8 October 2010 | Volume 5 | Issue 10 | e13133