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Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data

submitted on 01.09.2020, 12:27 and posted on 02.09.2020, 05:18 by Raphaël La Rocca, Christopher Kune, Mathieu Tiquet, Lachlan Stuart, Theodore Alexandrov, Edwin De Pauw, Loïc Quinton

Mass spectrometry imaging (MSI) is a powerful and convenient method to reveal the spatial chemical composition of different biological samples. The molecular annotation of the detected signals is only possible when high mass accuracy is maintained across the entire image and the m/z range. However, the heterogeneous molecular composition of biological samples could result in fluctuations in the detected m/z-values, called mass shift. Mass shifts impact the interpretability of the detected signals by decreasing the number of annotations and by affecting the spatial consistency and accuracy of ion images. The use of internal calibration is known to offer the best solution to avoid, or at least to reduce, mass shifts. The selection of internal calibrating signals for a global MSI acquisition is not trivial, prone to false positive detection of calibrating signals and therefore to poor recalibration. To fill this gap, this work describes an algorithm that recalibrates each spectrum individually by estimating its mass shift with the help of a list of internal calibrating ions generated automatically in a data-adaptive manner. The method exploits RANSAC (Random Sample Consensus) algorithm, to select, in a robust manner, the experimental signal corresponding to internal calibrating signals by filtering out calibration points with infrequent mass errors and by using the remaining points to estimate a linear model of the mass shifts. We applied the method to a zebrafish whole body section acquired at high mass resolution to demonstrate the impact of mass shift on data analysis and the capacity of our algorithm to recalibrate MSI data. We illustrate the broad applicability of the method by recalibrating 31 different public MSI datasets from METASPACE from various samples and types of MSI and show that our recalibration significantly increases the numbers of METASPACE annotations, especially the high-confident annotations at a low false discovery rate.


Interreg EMR project: EURLIPIDS (R-8598)

European Nework of FT-ICR (Fourier Transform Ion Cyclotron Resonance) Mass spectrometer centers – EU_FT-ICR_MS

Agence Nationale de la Recherche

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European Research Council (agreement 773089)

European Horizon2020 ICT project CloudButton (agreement 825184)


Email Address of Submitting Author


University of Liège ULiège



ORCID For Submitting Author


Declaration of Conflict of Interest

no conflict of interest


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