Fourier transform mass spectrometry (FTMS) applications require accurate analysis of extremely complex mixtures of species in wide mass and charge state ranges. To optimize the related FTMS data analysis accuracy, parameters for data acquisition and the allied data processing should be selected rationally, and their influence on the data analysis outcome is to be understood. To facilitate this selection process and to guide the experiment design and data processing workflows, we implemented the underlying algorithms in a software tool with a graphical user interface, FTMS Isotopic Simulator. This tool computes FTMS data via time-domain data (transient) simulations for user-defined molecular species of interest and FTMS instruments, including diverse Orbitrap FTMS models, followed by user-specified FT processing steps. Herein, we describe implementation and benchmarking of this tool for analysis of a wide range of compounds as well as compare simulated and experimentally generated FTMS data. In particular, we discuss the use of this simulation tool for narrowband, broadband, and low- and high-resolution analysis of small molecules, peptides, and proteins, up to the level of their isotopic fine structures. By demonstrating the allied FT processing artifacts, we raise awareness of a proper selection of FT processing parameters for modern applications of FTMS, including intact mass analysis of proteoforms and top-down proteomics. Overall, the described transient-mediated approach to simulate FTMS data has proven useful for supporting contemporary FTMS applications. We also find its utility in fundamental FTMS studies and creating didactic materials for FTMS teaching.

中文翻译：

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FTMS同位素分布和质谱的瞬态中介模拟，可指导实验设计和数据分析。

傅里叶变换质谱（FTMS）应用需要对宽质量和电荷状态范围内的极复杂物种混合物进行准确分析。为了优化相关的FTMS数据分析精度，应合理选择数据采集和相关数据处理的参数，并了解它们对数据分析结果的影响。为了简化选择过程并指导实验设计和数据处理工作流程，我们在具有图形用户界面FTMS同位素模拟器的软件工具中实现了基础算法。该工具通过时域数据（瞬态）仿真计算FTMS数据，以仿真用户定义的感兴趣分子种类和FTMS仪器，包括各种Orbitrap FTMS模型，然后是用户指定的FT处理步骤。在这里 我们描述了该工具的实现和基准测试，可用于分析各种化合物以及比较模拟和实验生成的FTMS数据。特别是，我们讨论了使用此仿真工具进行小分子，肽和蛋白质的窄带，宽带以及低分辨率和高分辨率分析，直至达到其同位素精细结构的水平。通过演示相关的FT处理工件，我们提高了对FTMS现代应用正确选择FT处理参数的认识，包括完整的蛋白质形式质量分析和自上而下的蛋白质组学。总体而言，事实证明，所描述的瞬态介导的模拟FTMS数据的方法可用于支持现代FTMS应用。我们还发现它在FTMS基础研究和为FTMS教学创建教学材料方面具有实用性。