Storing, searching, and disseminating experimental proteomics data

Abstract

The chapter introduces the challenges of storing, sharing, and querying proteomics data caused by the complexity of the experimental techniques, and the speed with which the techniques evolve. Public proteome databases are difficult to develop and populate because of the range of data types and queries that must be supported, and the quantity of metadata required to validate results. There are several data standards under development that should alleviate some of the challenges, and databases that utilize the standards are becoming more widely supported. The chapter describes a model of a complete proteomics pipeline, including the metadata that should be captured to allow confidence to be placed on the results. Software is also required, which can produce data conforming to the standards and that can be used to query proteomics data repositories. The chapter outlines the requirements for software and presents two exemplars developed at the University of Manchester. Finally, there is a description of the likely future developments in standardization for proteomics. © 2007 Humana Press Inc.