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pnl.gov/software/). Enrichment ranking of proteins detected in the phagosome preparations and in immature DCs was performed by sorting proteins on enrichment factors, which are calculated according to Eq.?(2): equation(2) Enrichmentfactor=norm.emPAIphagosomeprep/norm.emPAIimmatureDCs. A total of 6 proteins (FN1, SLC37A2, P2RX4, SCAMP3, HTATIP2) were uniquely present in the phagosome dataset and not detected in immature DC. These proteins could either be highly enriched, differentially expressed in DCs and phagosome donor or finally serum derived; a distinction we cannot make based on the available data and therefore we do not study these proteins any further buy ABT-263 here. The enrichment ranked protein list was evaluated initially by the distribution of manually-curated positive and negative marker sets (for positive and negative markers see Supplementary Table 2). We determined the enrichment factor threshold at the most optimal balance between false positives and false negatives at the enrichment factor t that leads to the highest F1 score (a well-established accuracy test; Eq.? (3)): equation(3) F1=2*precision*recall/(precision+recall)F1=2*precision*recall/precision+recall Endonuclease whereprecision=Pm��t/Pm��t+Nm��t andrecall=Pm��t/Pm��t+Pm?t denotes the number of proteins from the positive marker set that exceeds (��?t) or falls below (EGFR inhibitor the prior knowledge about the fraction of proteome that localizes to the phagosome (Pphagosome) equation(5) cFP=(1�Cspecificity)*(1?Pphagosome)cFP=1�Cspecificity*1?Pphagosomewhere specificity?=? Nm