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Figure S1. Correlation plots of normalized protein intensities of quantified proteins (NI; a.u.: arbitrary units) for biological replicates (average of two technical replicates) between samples of the control group.

Figure S2. Correlation plots of normalized protein intensities of quantified proteins (NI; a.u.: arbitrary units) for biological replicates (average of two technical replicates) between samples of the LPS/ATP group.

Figure S3. Correlation plots of normalized protein intensities of quantified proteins (NI; a.u.: arbitrary units) for biological replicates (average of two technical replicates) between samples of the LPS/MDP group.

Figure S4. Correlation plots of normalized peptide intensities of quantified peptides (NI; a.u.: arbitrary units) for technical replicates between samples of the control group (Con, first row, n = 4082), LPS/ATP group, (second row, ATP, n = 5508), and LPS/MDP group (third row, MDP, n = 4560).

Figure S5. Correlation plots of normalized peptide intensities of quantified peptides (NI; a.u.: arbitrary units) for biological replicates (average of two technical replicates) between samples of the control group (Con, first row, n = 4082), LPS/ATP group, (second row, ATP, n = 5508), and LPS/MDP group (third row, MDP, n = 4560).

Figure S6. Correlation plots of normalized protein intensities of quantified proteins (NI; a.u.: arbitrary units) for technical replicates between samples of the control group (Con, first row, n = 561), LPS/ATP group, (second row, ATP, n = 724), and LPS/MDP group (third row, MDP, n = 635).

Table S1. Recovery of selected cytokines after ultrafiltration determined by CBA assay

Table S2. Settings used for ionization and MS detection (Triversa Nanomate and Orbitrap LTQ Velos)

Table S3. Mascot settings

Table S4. Settings used for peptide validation and protein assembly in the Transproteomic Pipeline

Table S6. DanteR workflow

Table S7. Peptides with corresponding m/z values used for quantification of selected cytokines

Table S8. Concentration of selected cytokines in supernatants of cells cultured with supplementation of 10% FCS or under serum-free conditions (determined by CBA assay; all values in pg/mL)

Table S9. Total protein contents of different sample groups (n = 3) determined by BCA assay

pmic7192-sup-0001-tableS1.xls2634KTable S10. List of proteins increased upon stimulation and list of all quantified proteins
pmic7192-sup-0002-tableS2.xls70KTable S11. List of protein groups according to figure 5 and figure 6

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