Identification and understanding the structures, interactions and functions of all of a cell’s proteins is one of the major goals of the postgenome era. The genome project has produced a wealth of information that is greatly expounding the genetic basis of cancer. However, it falls short in not allowing for accurate prediction of what is happening at the protein level in a cancer cell or a body fluid proteome. It is the hope that, by deciphering the alterations in the cancer proteome, biomarkers and patterns of biomarkers will be found that will lead to improvements in early detection, diagnosis and treatment monitoring. To achieve this goal, rapid high-throughput proteomic technologies will be required. The SELDI ProteinChip Biomarker mass spectrometry system appears to have potential in this effort, both for biomarker discovery and as a potential clinical diagnostic assay platform.