Proteomics involves measuring and possibly discovering a large number of proteins in a biological sample, and comparative proteomics includes comparing two or more biological samples to identify differences. The ability to conduct comparative proteomics in complex biological samples such as serum or plasma could revolutionize medical and biological research, especially for identifying diagnostic biomarkers that can differ healthy and diseased individuals. Recent technological advances in biotechnology -- liquid chromatography/mass spectrometry -- now makes it feasible to survey and quantify large numbers of proteins in complex samples, but these technologies are highly data intensive, often producing more than a gigabyte of raw data for each measurement. Problems of signal extraction, quantification, and clustering these data remain open problems in need of novel quantitative methods research. In this talk I will describe class of mass spectrometry technologies that are now being used for biomarker discovery. I will present the data and introduce a few important research questions that need to be solved to help move the field forward. Some sample data presented in the talk will be made available to interested parties.