Specific molecular markers for various normal and pathogenic cell states and cell types provide knowledge of basic biological systems and have a direct application in targeted therapy. We describe a proteomics method based on the combination of new and improved phage display antibody technologies and mass spectrometry, which allows identification of cell type specific protein markers. The most important features of the method are (i) reduction of experimental noise originating from background binding of phage particles and (ii) isolation of affinity-binders after a single round of selection, which assures a high diversity of binders. The method demonstrates, for the first time, the ability to detect, identify and analyse both secreted and membrane associated extracellular proteins, as well as a variety of different cellular structures including proteins and carbohydrates. The optimised phage display method was applied to analysis of human skin keratinocytes resulting in the isolation of a panel of antibodies. Fourteen of these antibodies were further characterised, half of which predominantly recognised keratinocytes in a screen of a range of different cell types. Three cognate keratinocyte antigens were subsequently identified by mass spectrometry as laminin-5, plectin and fibronectin. The combination of phage display technology with mass spectrometry methods for protein identification is a general and promising approach for proteomics analysis of cell surface complexity.