Cell surface proteins are excellent targets for diagnostic and therapeutic interventions. By using bioinformatics tools, we generated a catalog of 3,702 transmembrane proteins located at the surface of human cells (human cell surfaceome). We explored the genetic diversity of the human cell surfaceome at different levels, including the distribution of polymorphisms, conservation among eukaryotic species, and patterns of gene expression. By integrating expression information from a variety of sources, we were able to identify surfaceome genes with a restricted expression in normal tissues and/or differential expression in tumors, important characteristics for putative tumor targets. A high-throughput and efficient quantitative real-time PCR approach was used to validate 593 surfaceome genes selected on the basis of their expression pattern in normal and tumor samples. A number of candidates were identified as potential diagnostic and therapeutic targets for colorectal tumors and glioblastoma. Several candidate genes were also identified as coding for cell surface cancer/testis antigens. The human cell surfaceome will serve as a reference for further studies aimed at characterizing tumor targets at the surface of human cells.colorectal tumors ͉ CT antigens ͉ glioblastoma ͉ transmembrane ͉ tumor cell surface antigens W ith the availability of the human genome sequence, an important goal of current biological research is a more specific and accurate annotation of human genes. One critical property is the subcellular localization of gene products, because this affects their use as potential diagnostic and therapeutic targets. In this respect, the identification of cell surface proteins is of particular interest (1-3) because these proteins represent ideal therapeutic targets. Indeed, cell surface proteins have proved to be relevant to many areas of medicine, and a number of monoclonal antibodies against them are approved for therapeutic applications by the Food and Drug Administration, particularly in cancer therapy. Furthermore, cell surface proteins are also excellent targets for diagnostic assays, especially in biological fluids. On the other hand, there are several issues that make cell surface proteins difficult to manipulate biochemically. First, their hydrophobic transmembrane (TM) domain makes them insoluble. Second, several posttranslational modifications are not executed in commonly used expression systems. Finally, interactions involving cell surface proteins usually have an extremely short half-life (on the order of milliseconds), which has an effect on the development of purification protocols. Despite these limitations, decades of intensive research of cell surface proteins have generated a significant information base. Ideally, this information should be analyzed in a genome-wide context.We generated here a catalog of more than 3,700 genes believed to encode proteins located at the surface of human cells. For the sake of simplicity, we will call this catalog the ''human cell surfaceome.'' An integrated ...