Metabolomic analysis of plants broadens understanding of how plants may benefit humans, animals and the environment, provide sustainable food and energy, and improve current agricultural, pharmacological and medicinal practices in order to bring about healthier and longer life. The quality and amount of the extractible biological information is largely determined by data acquisition, data processing and analysis methodologies of the plant metabolomics studies. This PhD study focused mainly on the development and implementation of new metabolomics methodologies for improved data acquisition and data processing. The study mainly concerned the three most commonly applied analytical techniques in plant metabolomics, GC-MS, LC-MS and NMR. In addition, advanced chemometrics methods e.g. PARAFAC2 and ASCA have been extensively used for development of complex metabolomics data processing and analysis methods. The first study (Journal of Chromatography A, 1266 (2012) 84–94) demonstrated how the application of a multiway decomposition method, PARAFAC2, can help in providing maximum xtraction of metabolite features from the raw LC-MS data obtained from complex plant extracts. The second study (Analytical and Bioanalytical Chemistry, In Press, DOI: 10.1007/s00216-013-7341-z) outlines a novel GC-MS derivatization method using TMSCN for trimethylsilylation for improved analysis of complex biological mixtures . A review paper (Journal of Cereal Science, Accepted) written for the special issue of the Journal of Cereal Science dedicated to the journal’s 30th anniversary comprises current analytical challenges and perspectives of cereal metabolomics with emphasis on new development in the use of multivariate data nalysis methods for exploitation of the full information level in the analytical platforms. A third study (Journal of Experimental Botany, Submitted) combined the knowledge gained from the first and second studies and applied cutting-edge chemometric methods in a real case biological question related to barley breeding. This study revealed several biological questions associated with plant- environment, plant-gene mutation relationships and alterations of the plants’ physiology during their development stages.