The present invention describes devices and methods for performing protein analysis on laser capture microdissected cells, which permits proteomic analysis on cells of different populations. Particular disclosed examples are analysis of normal versus malignant cells, or a comparison of differential protein expression in cells that are progressing from normal to malignant. The protein content of the microdissected cells may be analyzed using techniques such as immunoassays, 1D and 2D gel electrophoresis characterization, Western blotting, liquid chromatography quadrapole ion trap electrospray (LCQ-MS), Matrix Assisted Laser Desorption Ionization/Time of Flight (MALDI/TOF), and Surface Enhanced Laser Desorption Ionization Spectroscopy (SELDI). In addition to permitting direct comparison of qualitative and quantitative protein content of tumor cells and normal cells from the same tissue sample, the methods also allow for investigation of protein characteristics of tumor cells, such as binding ability and amino acid sequence, and differential expression of proteins in particular cell populations in response to drug treatment. The present methods also provide, through the use of protein fingerprinting, a rapid and reliable way to identify the source tissue of a tumor metastasis.