This thesis focuses on the development of new analytical platforms for molecular mass spectrometry imaging and their applications in plant biology and forensic toxicology. So far, in drug metabolism or forensic toxicology, liquid chromatography with mass spectrometric detection is the technique of choice for analyzing drugs and metabolites in complex biological samples. LC-MS remains however challenging, because the development of appropriate sample preparation requires complex and time-consuming multiple-steps, increasing dramatically the overall analysis throughput and degrading samples. This thesis proposes alternative approaches, combining straightforward sample preparation, and direct, fast, sensitive and selective MS/MS analyses, using triple quadrupole linear ion trap MS platforms. They allow for profiling and monitoring drugs and their metabolites in single intact hair samples, postmortem human tissues and plant leaves. This thesis highlights the importance of multimodality imaging to answer a particular analytical question, and address some issues related to absolute quantification in tissue by MS imaging.