Phung Wilson, Bakalarski Corey E, Hinkle Trent B, Sandoval Wendy, Marty Michael T
Microchemistry, Proteomics, and Lipidomics Department, Genentech, Inc., South San Francisco, California 94080, United States.
Department of Chemistry and Biochemistry and the Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States.
Anal Chem. 2023 Aug 1;95(30):11491-11498. doi: 10.1021/acs.analchem.3c02010. Epub 2023 Jul 21.
Recent advances in native mass spectrometry (MS) and denatured intact protein MS have made these techniques essential for biotherapeutic characterization. As MS analysis has increased in throughput and scale, new data analysis workflows are needed to provide rapid quantitation from large datasets. Here, we describe the UniDec processing pipeline (UPP) for the analysis of batched biotherapeutic intact MS data. UPP is built into the UniDec software package, which provides fast processing, deconvolution, and peak detection. The user and programming interfaces for UPP read a spreadsheet that contains the data file names, deconvolution parameters, and quantitation settings. After iterating through the spreadsheet and analyzing each file, it returns a spreadsheet of results and HTML reports. We demonstrate the use of UPP to measure the correct pairing percentage on a set of bispecific antibody data and to measure drug-to-antibody ratios from antibody-drug conjugates. Moreover, because the software is free and open-source, users can easily build on this platform to create customized workflows and calculations. Thus, UPP provides a flexible workflow that can be deployed in diverse settings and for a wide range of biotherapeutic applications.
天然质谱（MS）和变性完整蛋白质质谱的最新进展使这些技术成为生物治疗表征的关键手段。随着质谱分析通量和规模的增加，需要新的数据分析工作流程来从大型数据集中提供快速定量。在此，我们描述了用于分析批量生物治疗完整质谱数据的UniDec处理管道（UPP）。UPP内置于UniDec软件包中，该软件包提供快速处理、去卷积和峰检测功能。UPP的用户界面和编程接口读取一个电子表格，其中包含数据文件名、去卷积参数和定量设置。在遍历电子表格并分析每个文件后，它会返回一个结果电子表格和HTML报告。我们展示了使用UPP来测量一组双特异性抗体数据上的正确配对百分比，以及测量抗体药物偶联物的药物与抗体比率。此外，由于该软件是免费且开源的，用户可以轻松地在此平台上进行扩展，以创建定制的工作流程和计算。因此，UPP提供了一种灵活的工作流程，可部署在各种环境中，并适用于广泛的生物治疗应用。
