The effects of plasma preparation methods on the status of human plasma proteins were analyzed by non-denaturing micro-2-DE followed with polypeptide assignment with MALDI-TOF MS and PMF. In order to facilitate the separation of high-molecular-mass plasma proteins (up to ca. 2 x 10(3) kDa) in short separation time, agarose micro-IEF gels were employed. The comparisons of the 2-DE patterns between EDTA-plasma (1.0 mg EDTA/mL blood) and heparin-plasma (0.025 mg heparin/mL blood) revealed the differences in protein distribution around pI 5.4-6.5 and apparent molecular mass of ca. 1 x 10(3) kDa, which were mainly attributed to the presence of the complexes of complement C4b and C4b-binding protein in heparin-plasma and their absence in EDTA-plasma. The distribution of several spots around pI 5.0-5.6 and apparent molecular mass 1.2-1.5 x 10(2) kDa was also found to be different; the fragments of complement C3 and C4 were detected in heparin-plasma but not in EDTA-plasma. The 2-DE pattern of high-heparin-plasma (0.50 mg heparin/mL blood) showed pI changes of three plasma proteins, fibronectin, complement factor B, and pre-alpha-inhibitor when compared with that of heparin-plasma, suggesting the interactions between heparin and the proteins. These results demonstrated that subtle changes in plasma proteins, caused by the different plasma preparation procedures, can be analyzed by non-denaturing agarose-IEF/micro-2-DE followed by MALDI-MS and PMF.