Clinical Proteomics Research Group, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road Manchester, Manchester, UK.
Stoller Biomarker Discovery Centre, Division of Molecular and Clinical Cancer Sciences, NIHR Biomedical Research Centre, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road Manchester, Manchester, UK.
Sci Data. 2021 Apr 26;8(1):118. doi: 10.1038/s41597-021-00896-w.
Murine models are amongst the most widely used systems to study biology and pathology. Targeted quantitative proteomic analysis is a relatively new tool to interrogate such systems. Recently the need for relative quantification on hundreds to thousands of samples has driven the development of Data Independent Acquisition methods. One such technique is SWATH-MS, which in the main requires prior acquisition of mass spectra to generate an assay reference library. In stem cell research, it has been shown pluripotency can be induced starting with a fibroblast population. In so doing major changes in expressed proteins is inevitable. Here we have created a reference library to underpin such studies. This is inclusive of an extensively documented script to enable replication of library generation from the raw data. The documented script facilitates reuse of data and adaptation of the library to novel applications. The resulting library provides deep coverage of the mouse proteome. The library covers 29519 proteins (53% of the proteome) of which 7435 (13%) are supported by a proteotypic peptide.
鼠类模型是研究生物学和病理学最广泛使用的系统之一。靶向定量蛋白质组学分析是一种相对较新的工具，可以用于研究此类系统。最近，需要对数百到数千个样本进行相对定量分析，这推动了数据非依赖性采集方法的发展。其中一种技术是 SWATH-MS，它主要需要预先采集质谱来生成分析物参考文库。在干细胞研究中，已经表明可以从成纤维细胞群开始诱导多能性。在这样做的过程中，表达蛋白的重大变化是不可避免的。在这里，我们创建了一个参考文库来支持此类研究。其中包括一个经过充分记录的脚本，可从原始数据中复制文库的生成。该记录脚本方便了数据的重复使用和对文库的改编以适应新的应用。生成的文库提供了对小鼠蛋白质组的深度覆盖。该文库涵盖了 29519 种蛋白质（蛋白质组的 53%），其中 7435 种（13%）由特征肽支持。
