Proteomic Profiling of Ascitic Fluid

Silver-stained 2D gels were scanned in a GS-800 densitometer (Bio-Rad, Hercules, CA). Digital images were compared using the Melanie 7.0 software (GE Healthcare). Each of the 50 ascitic fluid samples was run three times. The electrophoretic entities of interest were excised, alkylated, reduced, digested in a Proteineer line (Bruker Daltonics, Bremen) with the aid of a DP Chemicals 96 gel digestion kit (Bruker Daltonics) and processed by a MALDI-TOF Autoflex (Bruker Daltonics) to obtain a peptide mass fingerprint. Peak lists of the tryptic peptide masses were generated using FlexAnalysis1.2vSD1 Patch 2 (Bruker Daltonics) [21 (link)]. The search engine MASCOT server 2.0 was used to compare the fingerprints against human taxonomy with the following parameters: one missed cleavage allowed, carbamidomethyl cysteine as the fixed modification and oxidation of methionine as the variable modification. Proteins with scores greater than 50 and a p < 0.05 were accepted.