Polyacrylamide gel electrophoresis is an extremely powerful tool for separating and analyzing protein associated with different diseases and has been invaluable in the identification and analysis of proteins associated with characteristics unique to tumor cells. This study presents data demonstrating the application of conventional sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis and substrate-incorporated SDS-polyacrylamide gel electrophoresis (zymography) to obtain information about the proteins and catalytically active (or activatable) proteases associated with the process of tumor cell invasion using established human melanoma and breast carcinoma cell lines. Conventional SDS-polyacrylamide gel electrophoresis was used to show that cells sequentially selected from a low invasive human melanoma cell line on the basis of their ability to invade in vitro have an increase and/or addition of six unique proteins on their cell surface. In a different application of SDS-polyacrylamide gel electrophoresis, zymography was used to demonstrate that there is an increase in the levels of gelatinase A in the conditioned medium from three differently invasive human melanoma cell lines coincident with their ability to invade in vitro. Furthermore, the conditioned medium from the most invasive melanoma cell line demonstrated the greatest amount of gelatinase B activity. While the conditioned medium from three human breast carcinoma cell lines contained low levels of both gelatinase A and B, one breast cell line also contained activity associated with stromelysin(s) not seen in the melanoma cell lines.(ABSTRACT TRUNCATED AT 250 WORDS)