A Strong Neutrophil Elastase Proteolytic Fingerprint Marks the Carcinoma Tumor Proteome

Supplemental Data

• Supplemental Figures and Tables legend (.docx, 17 KB) - Supplemental Figures and Tables legend
• Supplemental Figure 1 (.pdf, 1.3 MB) - Exemplary MS/MS spectra, corresponding to 48 selected peptides cleaved according to VIATC consensus.
• Supplemental Figure 2 (.doc, 44 KB) - Exemplary iTRAQ reporter signal regions for keratin 18 peptide LLEDGEDFNLGDALDSSNSMTIQK (upper panels) and the two ????????????????daughter??????????????? peptides LLE..NLG (middle panel) and DAL???????????????IQK (lower panel) resulting from non-tryptic cleavage of the Gly-Asp bond.
• Supplemental Figure 3 (.doc, 83 KB) - Exemplary iTRAQ reporter signal regions for keratin 19 peptide ASDGLAGNEK resulting from cleavage of the Thr-Ala bond.
• Supplemental Table 1 (.xls, 226 KB) - List of Dataset 1 peptides cleaved at the VIATC consensus at P1 and characterized by FC>4 in adenocarcinoma tissue and in nuclear fraction of adenocarcinoma tissue.
• Supplemental Table 2 (.docx, 27 KB) - Fragments of sequences of 22 RRM containing RNPs from Table S1 aligned using COBALT.
• Supplemental Table 3 (.xls, 96 KB) - List of Dataset 1 peptides cleaved at non-tryptic sites other than the VIATC consensus and their abundance ratios.
• Supplemental Table 4 (.xlsx, 21.5 MB) - List of peptides and proteins identified in all four datasets.
• Supplemental Table 5A (.xls, 69 KB) - The 250 Dataset 3 proteins for which the fraction of queries identifying VIATC peptides out of the total number of queries assigned to this protein (qVIATC/qTotal) is at least two-times larger in AC than controls in the PRIDE dataset.
• Supplemental Table 5B (.xls, 37 KB) - The 49 proteins preferentially VIATC-cleaved in disease in both the iTRAQ-based (Dataset 1) and PRIDE AC Dataset 3, but not the UC Dataset 4.