This commentary article has a brief introduction to matrix-assisted laser desorption/ionization (MALDI), time-of-flight mass spectrometry (TOFMS), and their importance in proteomics, followed by a description of expected improvements in the mass-spectrometry-based proteome analysis achieved by employing a mid-infrared free electron laser (MIR-FEL) which can be a laser light source for a selective vibrational excitation. Our preliminary work for developing “UV/FEL-MALDI”, in which samples containing a dense solubilizing agent added to usual analyte/matrix mixtures are exposed to N₂ laser and MIR-FEL simultaneously, is shown as an example of successfully applying MIR-FEL to mass spectrometry. The experimental result obtained from human hair keratin in 8 M urea solution is an evidence of that UV/FEL-MALDI can bring a novel selectivity on the MALDI process and may facilitate the proteomics of insoluble proteins, which are not amenable to the conventional analytical approach of proteomics.

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Our major goal is to develop advanced analytical techniques for biomedical researches based on the Raman spectroscopic applications of an electronically tuned Ti:sapphire laser and the developments of advanced spectroscopic tools. Three studies are on going in our laboratory: 1) extraction of Raman signals from fluorescent interference, 2) extraction of Raman signals of no-resonant species in the presence of resonant species, 3) development of fiber-optic Raman probes less than 750 μm in diameter. Three new spectroscopic techniques and the development of a micro Raman probe 600 μm in diameter are reviewed in the present paper.

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