Figure 2: Quantitative interaction network.

(a) Quantitative crosslinked peptide interaction network consisting of 1,308 nodes representing unique crosslinked peptides connected by 1,166 edges representing crosslinks between two peptides. Loop edges connecting the same node to itself represent unambiguous homodimer crosslinked peptide pairs. Nodes are grouped in circular clusters according to their protein assignment. A force-directed layout reveals clusters of linked proteins corresponding to general functional class or subcellular localization, which are indicated by coloured shapes encompassing clusters of linked proteins. (b) Distribution of log₂(Resistant/Sensitive; R/S) ratios (average values obtained from analysis of six biological replicates) obtained by traditional SILAC analysis representing relative global protein level changes between the HeLa and HeLa/SN100 cell lines. The histogram is colour coded to match the node colour in the network. Red coloured nodes represent proteins with increased relative expression levels in the chemoresistant cell line versus the sensitive cell line, while green coloured nodes represent proteins with decreased relative expression levels in the chemoresistant cell line versus the sensitive cell line. Black coloured nodes represent proteins that did not have a measureable change between the two cell lines. *Blue nodes represent proteins for which no R/S ratio was obtained. (c) Distribution of log₂(R/S) ratios (average values obtained from analysis of five biological replicates) for the crosslinked peptide pairs quantified between the HeLa and HeLa/SN100 cell lines, colour coded according to match the edge colour in the network. Red, green and black coloured edges correspond to relative changes in crosslinked peptide levels between the resistant and sensitive cell lines with the same colour coding scheme as for the nodes.