Two-dimensional electrophoresis (2-DE) was previously established for analysis of plasma protein adsorption patterns on particulate carriers for intravenous drug targeting. This study addresses a possible effect of polymeric particles on protein separation in the first dimension, e.g., hindrance of protein entry into the gel or interaction of particles with the gel matrix. Polystyrene beads of mean diameter 100, 200 and 1000 nm were used as model carriers. Two different separation techniques were performed in the first dimension of 2-DE to study possible interactions of the beads with the different gel matrices, i.e., carrier ampholytes (CA) and immobilized pH gradients (IPGs). Comparison of gels obtained from samples including the particles from samples separated from the polystyrene beads showed no noteworthy differences. Therefore, a negative effect of the particles can be excluded, and particle separation from the sample is not necessary. Another goal of this study was the transfer of analytical protocols for isoelectric focusing from CA to IPGs with regard to enhanced reproducibility, faster sample processing, and easier handling. Transfer from CA to IPGs was carried out successfully and showed improved resolution of basic proteins. In contrast to that, lower amounts of a few high molecular mass proteins were detected, especially when sample application cups were employed. A qualitative change in the obtained protein pattern was not observed. Increased entry of high molecular weight proteins was achieved by in-sample rehydration instead of using sample cups.