Abstract
Mass spectrometry imaging (MSI) has emerged as a cornerstone of modern biomedical analysis, enabling the spatial mapping of chemical species within tissues while preserving their histological context. This article reviews the methodology and challenges associated with the quantitative variant of this technique – qMSI (quantitative Mass Spectrometry Imaging). Particular attention is given to the distinction between relative and absolute quantification, with a focus on three principal calibration strategies: off-tissue, on-tissue, and biomimetic tissue homogenates. The limitations imposed by matrix effects and tissue heterogeneity – both of which compromise signal linearity and necessitate advanced normalization strategies – are critically discussed.
References
Korber, A., Anthony, I. G., & Heeren, R. M. (2025). Mass spectrometry imaging. Analytical chemistry, 97(29), 15517-15549.
Holbrook, J. H., Kemper, G. E., & Hummon, A. B. (2024). Quantitative mass spectrometry imaging: therapeutics & biomolecules. Chemical Communications, 60(16), 2137-2151.
Lietz, C. B., Gemperline, E., & Li, L. (2013). Qualitative and quantitative mass spectrometry imaging of drugs and metabolites. Advanced drug delivery reviews, 65(8), 1074-1085.
Zhao, C., & Cai, Z. (2022). Three‐dimensional quantitative mass spectrometry imaging in complex system: From subcellular to whole organism. Mass spectrometry reviews, 41(3), 469-487.
Kibbe, R. R., & Muddiman, D. C. (2024). Quantitative mass spectrometry imaging (qMSI): A tutorial. Journal of Mass Spectrometry, 59(4), e5009.
Shariatgorji, R., Niehues, M., Nilsson, A., Angerer, T., Stroth, N., Paslawski, W., ... & Andrén, P. E. (2025). Quantitative Mass Spectrometry Imaging Protocols for Spatially Heterogeneous Samples. Analytical Chemistry, 97(21), 10957-10961.
Wang, Q., Ding, S. L., Li, Y., Royall, J., Feng, D., Lesnar, P., ... & Ng, L. (2020). The Allen mouse brain common coordinate framework: a 3D reference atlas. Cell, 181(4), 936-953.
Dreisewerd, K. (2014). Recent methodological advances in MALDI mass spectrometry. Analytical and bioanalytical chemistry, 406(9), 2261-2278.
Mellinger, A. L., Kibbe, R. R., Rabbani, Z. N., Meritet, D., Muddiman, D. C., & Gamcsik, M. P. (2022). Mapping glycine uptake and its metabolic conversion to glutathione in mouse mammary tumors using functional mass spectrometry imaging. Free Radical Biology and Medicine, 193, 677-684.
Zelows, M. M., Cady, C., Dharanipragada, N., Mead, A. E., Kipp, Z. A., Bates, E. A., ... & Helsley, R. N. (2023). Loss of carnitine palmitoyltransferase 1a reduces docosahexaenoic acid-containing phospholipids and drives sexually dimorphic liver disease in mice. Molecular Metabolism, 78, 101815.
Zhang, Q., Li, Y., Sui, P., Sun, X. H., Gao, Y., & Wang, C. Y. (2024). MALDI mass spectrometry imaging discloses the decline of sulfoglycosphingolipid and glycerophosphoinositol species in the brain regions related to cognition in a mouse model of Alzheimer's disease. Talanta, 266, 125022.
Bagley, M. C., Stepanova, A. N., Ekelöf, M., Alonso, J. M., & Muddiman, D. C. (2020). Development of a relative quantification method for infrared matrix‐assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings. Rapid Communications in Mass Spectrometry, 34(6), e8616.
Stoeckli, M., Staab, D., & Schweitzer, A. (2007). Compound and metabolite distribution measured by MALDI mass spectrometric imaging in whole-body tissue sections. International Journal of Mass Spectrometry, 260(2-3), 195-202.
Palmer, A., Phapale, P., Chernyavsky, I., Lavigne, R., Fay, D., Tarasov, A., ... & Alexandrov, T. (2017). FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry. Nature methods, 14(1), 57-60.
Groseclose, M. R., & Castellino, S. (2013). A mimetic tissue model for the quantification of drug distributions by MALDI imaging mass spectrometry. Analytical chemistry, 85(21), 10099-10106.
Barry, J. A., Groseclose, M. R., Fraser, D. D., & Castellino, S. (2018). Revised preparation of a mimetic tissue model for quantitative imaging mass spectrometry.
Barry, J. A., Groseclose, M. R., & Castellino, S. (2019). Quantification and assessment of detection capability in imaging mass spectrometry using a revised mimetic tissue model. Bioanalysis, 11(11), 1099-1116.
Clemis, E. J., Smith, D. S., Camenzind, A. G., Danell, R. M., Parker, C. E., & Borchers, C. H. (2012). Quantitation of spatially-localized proteins in tissue samples using MALDI-MRM imaging. Analytical chemistry, 84(8), 3514-3522.
Signor, L., Varesio, E., Staack, R. F., Starke, V., Richter, W. F., & Hopfgartner, G. (2007). Analysis of erlotinib and its metabolites in rat tissue sections by MALDI quadrupole time‐of‐flight mass spectrometry. Journal of mass spectrometry, 42(7), 900-909.
Hu, J. B., Chen, Y. C., & Urban, P. L. (2013). Coffee-ring effects in laser desorption/ionization mass spectrometry. Analytica chimica acta, 766, 77-82.
Nazari, M., Bokhart, M. T., Loziuk, P. L., & Muddiman, D. C. (2018). Quantitative mass spectrometry imaging of glutathione in healthy and cancerous hen ovarian tissue sections by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI). Analyst, 143(3), 654-661.
Bokhart, M. T., Rosen, E., Thompson, C., Sykes, C., Kashuba, A. D., & Muddiman, D. C. (2015). Quantitative mass spectrometry imaging of emtricitabine in cervical tissue model using infrared matrix-assisted laser desorption electrospray ionization. Analytical and bioanalytical chemistry, 407(8), 2073-2084.
Ellis, S. R., Bruinen, A. L., & Heeren, R. M. (2014). A critical evaluation of the current state-of-the-art in quantitative imaging mass spectrometry. Analytical and bioanalytical chemistry, 406(5), 1275-1289.
Gao, L., Zhang, Z., Wu, W., Deng, Y., Zhi, H., Long, H., ... & Guo, D. A. (2022). Quantitative imaging of natural products in fine brain regions using desorption electrospray ionization mass spectrometry imaging (DESI-MSI): Uncaria alkaloids as a case study. Analytical and bioanalytical chemistry, 414(17), 4999-5007.
Lanekoff, I., Stevens, S. L., Stenzel-Poore, M. P., & Laskin, J. (2014). Matrix effects in biological mass spectrometry imaging: identification and compensation. Analyst, 139(14), 3528-3532.
Hankin, J. A., & Murphy, R. C. (2010). Relationship between MALDI IMS intensity and measured quantity of selected phospholipids in rat brain sections. Analytical chemistry, 82(20), 8476-8484.
Taylor, A. J., Dexter, A., & Bunch, J. (2018). Exploring ion suppression in mass spectrometry imaging of a heterogeneous tissue. Analytical chemistry, 90(9), 5637-5645.
Deininger, S. O., Cornett, D. S., Paape, R., Becker, M., Pineau, C., Rauser, S., ... & Wolski, E. (2011). Normalization in MALDI-TOF imaging datasets of proteins: practical considerations. Analytical and bioanalytical chemistry, 401(1), 167-181.
Tu, A., & Muddiman, D. C. (2019). Systematic evaluation of repeatability of IR-MALDESI-MS and normalization strategies for correcting the analytical variation and improving image quality. Analytical and bioanalytical chemistry, 411(22), 5729-5743.
Hamm, G., Bonnel, D., Legouffe, R., Pamelard, F., Delbos, J. M., Bouzom, F., & Stauber, J. (2012). Quantitative mass spectrometry imaging of propranolol and olanzapine using tissue extinction calculation as normalization factor. Journal of proteomics, 75(16), 4952-4961.
Bergman, H. M., Lundin, E., Andersson, M., & Lanekoff, I. (2016). Quantitative mass spectrometry imaging of small-molecule neurotransmitters in rat brain tissue sections using nanospray desorption electrospray ionization. Analyst, 141(12), 3686-3695.
Pirman, D. A., Reich, R. F., Kiss, A., Heeren, R. M., & Yost, R. A. (2013). Quantitative MALDI tandem mass spectrometric imaging of cocaine from brain tissue with a deuterated internal standard. Analytical chemistry, 85(2), 1081-1089.
Lanekoff, I., Thomas, M., Carson, J. P., Smith, J. N., Timchalk, C., & Laskin, J. (2013). Imaging nicotine in rat brain tissue by use of nanospray desorption electrospray ionization mass spectrometry. Analytical chemistry, 85(2), 882-889.
Zhang, H., Zhang, J., Yuan, C., Zhang, D., Lu, D., Chen, S., ... & Wu, C. (2024). Recent advances in mass spectrometry imaging combined with artificial intelligence for spatially clarifying molecular profiles: Toward biomedical applications. TrAC Trends in Analytical Chemistry, 178, 117834.
Alexandrov, T. (2020). Spatial metabolomics and imaging mass spectrometry in the age of artificial intelligence. Annual review of biomedical data science, 3(1), 61-87.
Jamzad, A., Warren, J., Syeda, A., Kaufmann, M., Iaboni, N., Nicol, C. J., ... & Mousavi, P. (2025). MassVision: An Open-Source End-to-End Platform for AI-Driven Mass Spectrometry Imaging Analysis. Analytical Chemistry, 97(39), 21588-21597.
Watanabe, K., Takayama, S., Yamada, T., Hashimoto, M., Tadano, J., Nakagawa, T., ... & Shimma, S. (2024). Novel mimetic tissue standards for precise quantitative mass spectrometry imaging of drug and neurotransmitter concentrations in rat brain tissues. Analytical and Bioanalytical Chemistry, 416(26), 5579-5593.
Ghafari, N., & Sleno, L. (2024). Challenges and recent advances in quantitative mass spectrometry‐based metabolomics. Analytical science advances, 5(5-6), e2400007.

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