The core technologies in the rapidly expanding field of proteomics have matured to the point where quantitative measurements of thousands of proteins can be conducted, enabling truly global measurements of protein expression. This advent has brought with it the hope of discovering novel biomarkers that promise a renaissance in clinical medicine. To meet this need, many proteomic studies have focused on the identification and subsequent comparative analysis of the thousands of proteins that populate complex biological systems such as serum and tissues. A novel application of mass spectrometry has been in proteomic pattern analysis, which has emerged as an effective method for the early diagnosis of diseases. In stark contrast to 'classical' proteomics, proteomic pattern analysis relies on the pattern of proteins observed, rather than on the discrete identification of a protein. Proteomic pattern technology allows hundreds of clinical samples to be analyzed per day and promises to be a novel, highly sensitive predictive clinical tool to improve diagnostic and prognostic medicine.