Abstract
Ambiguous reports in the literature exist regarding the use and usefulness of formalin-fixed paraffin-embedded (FFPE) tissues in mass spectrometry imaging (MSI). Especially for the study of endogenous (non-tryptic) peptides, several studies have concluded that MSI on archived FFPE tissue bank samples is virtually impossible. We here illustrate that by employing a variant of MSI, called mass spectrometry histochemistry (MSHC), biomolecular tissue localization data are obtained that unequivocally comprise endogenous peptides. We here discuss different informatics steps in a data analysis workflow to help filter peptide-related features out of large and complex datasets generated by atmospheric pressure matrix-assisted laser desorption/ionization high-resolution (Orbitrap mass analyzer) MSHC. These include, in addition to accurate mass measurements, Kendrick mass defect filtering and isotopic distribution scrutiny.
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Acknowledgements
The authors gratefully acknowledge the kind gift of the late Prof. F. Vandesande’s vasopressin and oxytocin antisera by Prof. L. Arckens of the Laboratory for Neuroplasticity and Neuroproteomics of the University of Leuven (Belgium). ProteoFormiX is indebted to Flanders Innovation & Entrepreneurship (VLAIO) grant HBC.2019.2796 and imec.istart and BlueHealth Innovation Fund for financial support. Dr. Yury Tsybin is wholeheartedly thanked for a critical review of the manuscript.
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Supplemental Data 1
Average spectrum of neurohypophysis ROI, illustrating relative intensities of vasopressin- and oxytocin-derived ions (TIF 39 kb)
Supplemental Data 2
Heme MSHC data. On-tissue mass accuracy before (left) and after recalibration (right) (TIF 339 kb)
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Bhattacharya, N., Nagornov, K., Verheggen, K., Verhaert, M., Sciot, R., Verhaert, P. (2023). MS1-Based Data Analysis Approaches for FFPE Tissue Imaging of Endogenous Peptide Ions by Mass Spectrometry Histochemistry (MSHC). In: Cole, L.M., Clench, M.R. (eds) Imaging Mass Spectrometry. Methods in Molecular Biology, vol 2688. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3319-9_16
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DOI: https://doi.org/10.1007/978-1-0716-3319-9_16
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