title: Problems inherent to a meta-analysis of proteomics data: a case study on the plants' response to Cd in different cultivation conditions.
abstract: This meta-analysis focuses on plant-proteome responses to cadmium (Cd) stress. Initially, some general topics related to a proteomics meta-analysis are discussed: (1) obstacles encountered during data analysis, (2) a consensus in proteomic research, (3) validation and good reporting practices for protein identification and (4) guidelines for statistical analysis of differentially abundant proteins. In a second part, the Cd responses in leaves and roots obtained from a proteomics meta-analysis are discussed in (1) a time comparison (short versus long term exposure), and (2) a culture comparison (hydroponics versus soil cultivation). Data of the meta-analysis confirmed the existence of an initial alarm phase upon Cd exposure. Whereas no metabolic equilibrium is established in hydroponically exposed plants, an equilibrium seems to be manifested in roots of plants grown in Cd-contaminated soil after long term exposure. In leaves, the carbohydrate metabolism is primarily affected independent of the exposure time and the cultivation method. In addition, a metabolic shift from CO2-fixation towards respiration is manifested, independent of the cultivation system. Finally, some ideas for the improvement of proteomics setups and for comparisons between studies are discussed.
  
  
  CONCLUSIONS
  This meta-analysis focuses on the plant responses to Cd stress in leaves and roots at the proteome level. This meta-analysis points out the encountered obstacles when performing a proteomics meta-analysis related to inherent technologies, but also related to experimental setups. Furthermore, the question is addressed whether an extrapolation of results obtained in hydroponic cultivation towards soil-grown plants is possible.
authors.affiliation: Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium. Electronic address: joke.dupae@uhasselt.be.
authors.forename: Joke
authors.initials: J
authors.lastname: Dupae
authors.affiliation: Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium. Electronic address: sacha.bohler@uhasselt.be.
authors.forename: Sacha
authors.initials: S
authors.lastname: Bohler
authors.affiliation: Biomedical Institute, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium. Electronic address: jeanpaul.noben@uhasselt.be.
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Noben
authors.affiliation: Afdeling Plantenbiotechniek, Catholic University Leuven, Willem de Croylaan 42 - bus 2455, 3001 Leuven, Belgium. Electronic address: sebastien.carpentier@biw.kuleuven.be.
authors.forename: Sebastien
authors.initials: S
authors.lastname: Carpentier
authors.affiliation: Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium. Electronic address: jaco.vangronsveld@uhasselt.be.
authors.forename: Jaco
authors.initials: J
authors.lastname: Vangronsveld
authors.affiliation: Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium. Electronic address: ann.cuypers@uhasselt.be.
authors.forename: Ann
authors.initials: A
authors.lastname: Cuypers
mesh_terms: D002104:Cadmium / Q000633:toxicity*; D002245:Carbon Dioxide / Q000378:metabolism; D010101:Oxygen Consumption / Q000187:drug effects; D018515:Plant Leaves / Q000378:metabolism*; D010940:Plant Proteins / Q000378:metabolism*; D018517:Plant Roots / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D013312:Stress, Physiological / Q000187:drug effects*
chemical_list: D010940:Plant Proteins; D002104:Cadmium; D002245:Carbon Dioxide
keywords: Cadmium; Meta-analysis; Plant proteome