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Combining imaging mass spectrometry with diverse of microscopy techniques for the same sample on the same holder enables complex analysis of the sample morphology and chemical composition. A new sample preparation protocol was developed allowing complex analysis of germinal vesicles mice oocytes minimizing cellular chemistry redistribution and cell structure distortion. Mammalian oocytes can contain nucleolus-like body (NLB) units which were investigated. A domain structure of densely packed granules inside NLBs was revealed. Mass spectrometry shows increased amino acids and phosphate ions signal from the granules compared to cytoplasm area.