This work presents two novel methods for the analysis of two important plant metabolites free proteinaceous amino acids and phytosiderophores in root exudates. Introductory, tasks and challenges of metabolomics in general and plant metabolomics in particular are described including definitions of relevant terms and the classification of these research areas within systems biology. In this context an overview of the analytical strategies and techniques is given comparing different sample preparation methodologies, various GC-MS and LC-MS instrumental set-ups and NMR as well as data evaluation and statistical approaches. Emphasis is devoted to hydrophilic interaction chromatography (HILIC) and inductively coupled plasma mass spectrometry (ICP-MS), since the methods of choice of the presented publications rely partly on these special techniques. In order to characterize the nature of the investigated samples, an introduction to the topic of root exudates and its putative functions in the rhizosphere is presented. Publication I deals with the development of an LC-MS method for the analysis of underivatized, free proteinaceous amino acids. Prefatory, challenges and the state of the art of amino acid analysis in general are outlined. Subsequently the developed separation of 16 amino acids via HILIC and their detection using either a triple quadrupole mass analyzer in multiple reaction monitoring mode or an ion trap mass analyzer are described and various analytical figures of merit of the presented method are discussed. Moreover, an enrichment procedure based on solid phase extraction for amino acids in nutrient solutions is evaluated. Finally, the application of the proposed method to the analysis of tyrosine in samples obtained from soil adsorption experiments is illustrated.. Publication II presents a novel capillary electrophoretic separation of different phytosiderophores and their complexes with various metals employing a mass spectrometry-compatible background electrolyte. The detection via ESI-MS and ICP-MS for the free ligands and the metal complexes, respectively, is described and the applicability of the CE-ICP-MS method to quantitative analysis is discussed. In addition, the determination of relative complex stability constants using this method is explained.