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MS1-Based Data Analysis Approaches for FFPE Tissue Imaging of Endogenous Peptide Ions by Mass Spectrometry Histochemistry (MSHC)

Tijdschriftbijdrage - Tijdschriftartikel

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.

Tijdschrift: Methods in Molecular Biology: In Silico Methods for Predicting Drug Toxicity
Volume: 2688
Pagina's: 187-202
Jaar van publicatie:2023
Trefwoorden:Peptides/chemistry, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods, Diagnostic Imaging, Histocytochemistry, Tissue Fixation/methods, Paraffin Embedding, Formaldehyde/chemistry