Interdisciplinary strategy enabling in vivo subcellular proteo-metabolomic systems biology with demonstrated compatibility for cell-, neurodevelopmental, and behavioral biology using Xenopus laevis as the biological model. As an example, the left dorsal-animal (L-D1) and left ventral-animal (L-V1) cells were identified and the content of each cell rapidly microsampled twice using clean capillaries each time. The collected protein and metabolite samples were analyzed using custom-built ultrasensitive capillary electrophoresis (CE) nano/micro-flow electrospray ionization (ESI) high-resolution orbitrap and time-of-flight (TOF) mass spectrometry (HRMS). The tadpoles developing from the embryos were characterized for survival, anatomy, and behavior. Scale bars = 250 μm (black), 1 mm (white)