Mass shift in mass spectrometry imaging: comprehensive analysis and practical corrective workflow


MALDI mass spectrometry imaging (MSI) allows the mapping and the tentative identification of compounds based on their m/z value. In typical MSI, a spectrum is taken at incremental 2D coordinates (pixels) across a sample surface. Single pixel mass spectra show the resolving power of the mass analyzer. Mass shift, i.e., variations of the m/z of the same ion(s), may occur from one pixel to another. The superposition of shifted masses from individual pixels peaks apparently degrades the resolution and the mass accuracy in the average spectrum. This leads to low confidence annotations and biased localization in the image. Besides the intrinsic performances of the analyzer, the sample properties (local composition, thickness, matrix deposition) and the calibration method are sources of mass shift. Here, we report a critical analysis and recommendations to mitigate these sources of mass shift. Mass shift 2D distributions were mapped to illustrate its effect and explore systematically its origin. Adapting the sample preparation, carefully selecting the data acquisition settings, and wisely applying post-processing methods (i.e., m/z realignment or individual m/z recalibration pixel by pixel) are key factors to lower the mass shift and to improve image quality and annotations. A recommended workflow, resulting from a comprehensive analysis, was successfully applied to several complex samples acquired on both MALDI ToF and MALDI FT-ICR instruments.

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The authors would like to thank the University of Maastricht (The Netherlands) and Dr. S. Ellis for the use of the HTX Sprayer and the HTX Sublimator, Pr. M. Ongena and Dr. A. Argüelles Arias, Microbial Processes and Interactions (MiPI) of Gembloux Agro Biotech (Belgium), for the bacteria samples. D. Van Kruining and Pr. P. Martinez Martinez, Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University (The Netherlands), are kindly acknowledged for providing the mouse brain tissue samples. CAREM platform (University of Liège, Belgium) is thanked for performing electron microscopy acquisition of the crystal samples.


This work was funded by the Excellence Of Science Program, FNRS F.R.S (Rhizoclip EOS30650350), by the European Union Horizon 2020 research and innovation program under grant agreement No. 731077 and by interreg’s EURLIPIDS project (R-8598). The MALDI ToF RapifleX and the MALDI FT-ICR SolariX XR were funded by FEDER BIOMED HUB Technology Support (number 2.2.1/996).

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Correspondence to Christopher Kune.

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All experiments were done with permission of the Committee on Animal Welfare, Maastricht University, according to Dutch governmental rules.

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Andréa McCann and Sophie Rappe are co-first authors of this paper.

Published in the topical collection Mass Spectrometry Imaging 2.0 with guest editors Shane R. Ellis and Tiffany Porta Siegel.

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McCann, A., Rappe, S., La Rocca, R. et al. Mass shift in mass spectrometry imaging: comprehensive analysis and practical corrective workflow. Anal Bioanal Chem 413, 2831–2844 (2021).

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  • Mass spectrometry imaging
  • FT-ICR
  • Mass shift
  • Data recalibration
  • Time of flight
  • Mass accuracy