Iterative calibration algorithms were used to achieve a final, absolute mass accuracy of better than 10 parts per million (p.p.m.) for all peptide ions. These high-accuracy spectra were searched against a human protein database, using MASCOT probability-based scoring in which the fragment ions are matched against the calculated fragments of all tryptic peptides from the human sequences. Additional constraints were set by searches against a reversed human database to minimize false positive protein identifications.

A comprehensive protein inventory of clinical grade immature and cytokine cocktail matured (Il-6, IL-1 beta, TNF alpha, PGE2; 48 hours) monocyte derived human dendritic cells (DC) from a healthy donor has been established. To this aim, iterative calibration algorithms were used to achieve a final, absolute mass accuracy of better than 10 parts per million (p.p.m.) for all peptide ions.