Proteomics has shown great promise as a key tool in the analysis of living systems, providing high-throughput views on the expression and translation of genes into proteins, their abundances, and their modifications. Yet the rapid advances in the field have led to an emphasis on the development of novel methodologies, at the cost of establishing clear quality control metrics and acceptable operational parameters for many of these methods. Since proteomics is ultimately an analytical science however, it is essential for the future of the field to invest in quality control and quality assurance strategies for existing approaches as well. With the support of the European Science Foundation's Frontiers in Functional Genomics programme, a workshop was therefore held in Cambridge, UK from 25 until 27 November 2009 that focused on Quality Control in Proteomics. A report on this workshop is provided here.