title: Organelle proteomics experimental designs and analysis.
abstract: In biology, localisation is function: knowledge of the localisation of proteins is of paramount importance to assess and study their function. This supports the need for reliable protein sub-cellular localisation assignment. Concomitant with recent technological advances in organelle proteomics, there is a requirement for more rigorous experimental and analysis design planning and description. In this review, we present an overview of current experimental designs in qualitative and quantitative organelle proteomics as well as associated data analysis. We also consider the major benefits associated with careful description and dissemination of the experiment and analysis designs, namely (i) comparison and optimisation of experimental designs and analysis pipelines, (ii) data validation, (iii) reproducible research, (iv) efficient repository submission and retrieval and (v) meta analysis. Formalization of experimental design and analysis work flows is of direct benefit for the organelle proteomics researchers and will result in providing organelle localisation data of highest quality for the wider research community.
authors.affiliation: Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK.
authors.forename: Laurent
authors.initials: L
authors.lastname: Gatto
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Huber
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
mesh_terms: D006801:Humans; D015388:Organelles; D040901:Proteomics / Q000379:methods*; D012107:Research Design