Fig. 3.
A substantial group of secretome proteins are also derived from FBS. (A) Venn diagrams of two breast cancer cell lines: MCF7 and MDA-MB-231, showing the overlap of proteins between the secretome data searched against both human and “other mammal” databases (mammal database that does not contain human proteins). Numbers in black represent proteins, numbers in gray represent unique peptides. Between 5–10% of the secretome proteins come from the FBS, and around 20% of the measured proteins could be either coming from tumor cells or from serum. (B) Graph representing the number of proteins measured in the secretome of MCF7 and MDA-MB-231 cells labeled with SILAC media. The results shown come from three biological replicates, each of them containing three technical replicates. The first column represents both labeled and unlabeled proteins (All, 623 proteins), the second column contains only labeled proteins (Silac-Labeled, 598 proteins). The third column (non-labeled proteins) is split between proteins that are both labeled and not labeled (104) and proteins with no labeled peptides (25). The right side of figure 3b shows the SpC levels for some of the proteins that are both SILAC labeled and unlabeled in secretomes of MCF7 and MDA-MB-231 cells. (C) Venn diagram showing the significant proteins different between two cell lines (MCF7 and MDA-MB-231), when comparing the dataset containing the labeled plus unlabeled data (All), and the one with only labeled data (SILAC). A dataset containing three biological replicates with three technical replicates for each cell line each was used to generate the Venn diagram. The statistical test used is GLM Poisson test. The lists of unique significant proteins for both the whole dataset (right) or the dataset with only labeled proteins (right) are shown.