Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany; Graduate School for Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität Munich, Munich, Germany.
Biomedical Center, Protein Analysis Unit, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
Mol Cell Proteomics. 2022 Jun;21(6):100242. doi: 10.1016/j.mcpro.2022.100242. Epub 2022 May 13.
Imaging mass spectrometry (IMS) has developed into a powerful tool allowing label-free detection of numerous biomolecules in situ. In contrast to shotgun proteomics, proteins/peptides can be detected directly from biological tissues and correlated to its morphology leading to a gain of crucial clinical information. However, direct identification of the detected molecules is currently challenging for MALDI-IMS, thereby compelling researchers to use complementary techniques and resource intensive experimental setups. Despite these strategies, sufficient information could not be extracted because of lack of an optimum data combination strategy/software. Here, we introduce a new open-source software ImShot that aims at identifying peptides obtained in MALDI-IMS. This is achieved by combining information from IMS and shotgun proteomics (LC-MS) measurements of serial sections of the same tissue. The software takes advantage of a two-group comparison to determine the search space of IMS masses after deisotoping the corresponding spectra. Ambiguity in annotations of IMS peptides is eliminated by introduction of a novel scoring system that identifies the most likely parent protein of a detected peptide in the corresponding IMS dataset. Thanks to its modular structure, the software can also handle LC-MS data separately and display interactive enrichment plots and enriched Gene Ontology terms or cellular pathways. The software has been built as a desktop application with a conveniently designed graphic user interface to provide users with a seamless experience in data analysis. ImShot can run on all the three major desktop operating systems and is freely available under Massachusetts Institute of Technology license.
成像质谱 (IMS) 已发展成为一种强大的工具，可实现对原位大量生物分子的无标记检测。与鸟枪法蛋白质组学相比，蛋白质/肽可直接从生物组织中检测，并与其形态相关联，从而获得重要的临床信息。然而，MALDI-IMS 目前难以直接鉴定所检测到的分子，这迫使研究人员使用互补技术和资源密集型实验设置。尽管采用了这些策略，但由于缺乏最佳的数据组合策略/软件，仍然无法提取足够的信息。在这里，我们介绍了一种新的开源软件 ImShot，该软件旨在鉴定 MALDI-IMS 获得的肽。这是通过结合 IMS 和 shotgun 蛋白质组学（LC-MS）对同一组织的连续切片测量的信息来实现的。该软件利用两组比较来确定去同位素化相应光谱后 IMS 质量的搜索空间。通过引入一种新的评分系统，消除了 IMS 肽注释的歧义，该系统可在相应的 IMS 数据集中识别出检测到的肽的最可能的母蛋白。由于其模块化结构，该软件还可以单独处理 LC-MS 数据，并显示交互式富集图和富集的基因本体论术语或细胞途径。该软件已作为桌面应用程序构建，并具有方便设计的图形用户界面，为用户提供无缝的数据分析体验。ImShot 可在所有三个主要的桌面操作系统上运行，并根据麻省理工学院的许可证免费提供。
