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Infrared absorption properties of silica nanoparticles were studied. The transverse optical and the longitudinal optical phonon modes from the silica were proved to be the characteristic spectroscopic fingerprint signals. Based on this, a sandwich-structured immunoassay was performed, and the detection of the analyte (human IgG) was achieved by using biofunctional silica nanoparticles as infrared probes. The immunoassay based on Fourier transform infrared reflection absorption spectroscopy of silica nanoparticles shows significant value for potential applications in many areas, such as biomedicine, food safety, and waste treatment.