Cells are the basic structural and functional units in biology that plays important roles in living organisms. It can be affected by several factors that influence their proliferation, differentiation, and metabolic activities and consequently causing the wide heterogeneity among each cell within the same individual. It has been noted that the chemical composition and concentration found in two homogeneous cells are also different. Therefore, accurate cell morphology and composition can be obtained by studying at the single-cell level in a particular microenvironment. Nucleic acids, proteins, trace elements, and small molecule metabolites are the important chemicals present in cells and play key roles in cellular processes. Various analytic techniques such as flow cytometry, fluorescence microscopy, Raman microscopy, and mass spectrometry are used for single-cell analysis. Each technique has own advantages and disadvantages. Among them, mass spectrometry (MS) technique has received a considerable amount of attention owing to its high susceptibility and superior potential for the