UNCORRECTED PROOF 1 Problems inherent to a meta-analysis of proteomics 2 data: A case study on the plants' response to Cd in 3 different cultivation conditions

13 Article history:14 Received 8 December 201315 Accepted 15 April 20141617 Thismeta-analysis focuses on plant-proteome re sponsestocadmium(Cd) stress. Initially, some18 general topics related to a proteomics meta-anal ysis are discussed: (1) obstacles encountered19 during data analysis, (2) a consensus in proteomic research, (3) validation and good reporting20 practices for protein identificat ion and (4) guidelines for statist ical analysis of differentially21 abundant proteins. In a second part, the Cd responses in leaves and roots obtained from a22 proteomics meta-analysis are discussed in (1) a time comparison (short versus long term23 exposure), and (2) a culture comparison (hydroponics versus soil cultivation). Data of the24 meta-analysis confirmed the existence of an initial alarm phase upon Cd exposure. Whereas no25 metabolic equilibrium is established in hydroponically exposed plants, an equilibrium seems to26 be manifested in roots of plants grown in Cd-con taminated soil after long term exposure. In27 leaves,thecarbohydratemetabolismisprimarilyaffectedindependentoftheexposuretimeand28 the cultivation method. In addition, a metabolic shift from CO

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