One of the first steps in the analysis of adherent cells on a flow cytometer is their detachment from the substrate and obtaining a cell suspension, however this procedure can affect the composition and integrity of the molecules expressed on the cell surface. To avoid this, we decided to examine the effect of trypsin and EDTA solutions on the expression of certain proteins, given the incubation time. Proteins whose levels were monitored are the molecules MHC I, m04 and CD80, the expression of which is influenced by murine cytomegalovirus (MCMV) to avoid recognition by immune system cells, and their regulation and expression is the subject of intensive research at the Center for Proteomics. Levels of these molecules were studied on MEF, B12, DC 2.4, and Raw264.7 cells with and without MCMV infection. The results obtained by flow cytometer analysis showed that the expression of MHC I and m04 was significantly reduced only on infected RAW264.7 cells after treatment with EDTA solution for 10 minutes, and CD80 levels on uninfected and infected DC2.4 cells after treatment with trypsin solution for 10 minutes. The obtained results indicate that it is important to stop the action of trypsin and EDTA solutions on time in order to obtain accurate and reliable results in future experiments. In addition, the level of these molecules on the cells was compared and a higher level of MHC I and m04 was shown on RAW264.7 and DC 2.4 cells, which indicates that the expression of virus altered MHC I on their surface is probably higher than on MEF and B12 cells. What effect this phenomenon has on the immune system remains to be investigated.