title: Information quality in proteomics.
abstract: Proteomics, the study of the protein complement of a biological system, is generating increasing quantities of data from rapidly developing technologies employed in a variety of different experimental workflows. Experimental processes, e.g. for comparative 2D gel studies or LC-MS/MS analyses of complex protein mixtures, involve a number of steps: from experimental design, through wet and dry lab operations, to publication of data in repositories and finally to data annotation and maintenance. The presence of inaccuracies throughout the processing pipeline, however, results in data that can be untrustworthy, thus offsetting the benefits of high-throughput technology. While researchers and practitioners are generally aware of some of the information quality issues associated with public proteomics data, there are few accepted criteria and guidelines for dealing with them. In this article, we highlight factors that impact on the quality of experimental data and review current approaches to information quality management in proteomics. Data quality issues are considered throughout the lifecycle of a proteomics experiment, from experiment design and technique selection, through data analysis, to archiving and sharing.
authors.affiliation: School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK. d.stead@abdn.ac.uk
authors.forename: David A
authors.initials: DA
authors.lastname: Stead
authors.forename: Norman W
authors.initials: NW
authors.lastname: Paton
authors.forename: Paolo
authors.initials: P
authors.lastname: Missier
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Embury
authors.forename: Cornelia
authors.initials: C
authors.lastname: Hedeler
authors.forename: Binling
authors.initials: B
authors.lastname: Jin
authors.forename: Alistair J P
authors.initials: AJ
authors.lastname: Brown
authors.forename: Alun
authors.initials: A
authors.lastname: Preece
mesh_terms: D003628:Database Management Systems; D015180:Electrophoresis, Gel, Two-Dimensional; D016247:Information Storage and Retrieval / Q000379:methods / Q000592:standards; D013058:Mass Spectrometry; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000295:instrumentation / Q000379:methods / Q000592:standards; D011786:Quality Control; D012984:Software
chemical_list: D011506:Proteins