5-Methylnonane is primarily used as a reference compound in analytical chemistry for gas chromatography and mass spectrometry. It serves as a standard for identifying and quantifying hydrocarbons in complex mixtures, particularly in petroleum and environmental samples. Its well-defined structure and volatility make it suitable for calibrating instruments and validating analytical methods. Additionally, it is employed in research studies to investigate the behavior of branched alkanes in various chemical processes, such as fuel combustion and atmospheric reactions.