Proteomics has recently demonstrated utility for increasing the understanding of cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled with high mass accuracy mass spectrometry for high‐throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC‐FTICR‐MS‐based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced. � 2006 Wiley Periodicals, Inc., Mass Spec Rev 25:450–482, 2006