Figure 4. Zoom scan mass spectra of labeled and unlabeled peptide pairs detected for complement C3 and syndecan-4 proteins. Panels A and D show the mass spectra and the relative intensity of labeled and unlabeled peptide pairs detected for complement C3 (A) and for syndecan-4 (D) in TNF-α-treated ARPE-19 cells versus untreated cells. In this case labeled cells were treated with TNF-α (+TNF-α) while unlabeled cells remained untreated (-TNF-α). Panels B and E show the mass spectra obtained for these same set of peptides in the reverse experiment where unlabeled cells were treated with TNF-α (+TNF-α) while labeled cells remained untreated (-TNF-α). Panel C shows the tandem mass spectrum and the fragment ions obtained for the doubly-charged ion m/z=645.2 and confirming the peptide sequence [SGSDEVQVGQQR] of complement C3 protein. Panel F shows the tandem mass spectrum and the fragment ions obtained for the doubly-charged ions m/z=579.3 and confirming the peptide sequence [AGSGSQVPTEPK] of syndecan-4 protein.