A comprehensive understanding of molecular patterns of health and disease is needed to pave the way for personalized medicine and tissue regeneration. One barrier to predictive, personalized medicine is the lack of a comprehensive molecular understanding at the tissue level. As we grasp the astonishing complexity of biological systems (whether single cells or whole organisms), it becomes more and more evident that within this complexity lies the information needed to provide insight in the origin, progression and treatment of various diseases. The best way to capture disease complexity is to chart and connect multilevel molecular information within a tissue using mass spectrometry and data algorithms. It is the realm of big molecular data for disease classification. Charting this territory through the generation of molecular maps from cells and tissue has become reality through the clinical implementation of imaging mass spectrometry complemented with high throughput peptidomics and proteomics approaches. We have demonstrated how new MS based chemical microscopes target biomedical tissue analysis in various diseases as well as other chemically complex surfaces. In concert they elucidate the way in which local environments can influence molecular signaling pathways on various scales. State-of-the-Art molecular imaging with mass spectrometry now enables high resolution tissue screening that provides direct insight into tissue metabolism. Applications have penetrated various research domains from drug metabolism to visualize molecular signaling pathways in cancer. This lecture will highlight innovations in translational imaging mass spectrometry and showcase how mass spectrometry based multimodal molecular imaging can be used to reveal the phenotypes in complex, heterogeneous biological systems from cells to organs.