Bhattacharya Nivedita, Nagornov Konstantin, Verheggen Kenneth, Verhaert Marthe, Sciot Raf, Verhaert Peter
ProteoFormiX, Beerse, Belgium.
MassTech Inc., Columbia, MD, USA.
Methods Mol Biol. 2023;2688:187-202. doi: 10.1007/978-1-0716-3319-9_16.
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.
关于福尔马林固定石蜡包埋（FFPE）组织在质谱成像（MSI）中的应用及效用，文献中的报道并不明确。特别是对于内源性（非胰蛋白酶消化）肽的研究，多项研究得出结论，对存档的FFPE组织库样本进行MSI几乎是不可能的。我们在此表明，通过采用一种称为质谱组织化学（MSHC）的MSI变体，可以获得明确包含内源性肽的生物分子组织定位数据。我们在此讨论数据分析工作流程中的不同信息学步骤，以帮助从大气压基质辅助激光解吸/电离高分辨率（轨道阱质量分析仪）MSHC生成的大型复杂数据集中筛选出与肽相关的特征。这些步骤除了精确质量测量外，还包括肯德里克质量亏损过滤和同位素分布审查。
