Stow Sarah M, Gibbons Bryson C, Rorrer Iii Leonard C, Royer Lauren, Glaskin Rebecca S, Slysz Gordon W, Kurulugama Ruwan T, Fjeldsted John C, DeBord Daniel, Bilbao Aivett
Agilent Technologies, Santa Clara, California 95051, United States.
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.
J Am Soc Mass Spectrom. 2024 Aug 7;35(8):1991-2001. doi: 10.1021/jasms.4c00220. Epub 2024 Jul 26.
Ion mobility (IM) is often combined with LC-MS experiments to provide an additional dimension of separation for complex sample analysis. While highly complex samples are better characterized by the full dimensionality of LC-IM-MS experiments to uncover new information, downstream data analysis workflows are often not equipped to properly mine the additional IM dimension. For many samples the data acquisition benefits of including IM separations are all that is necessary to uncover sample information and the full dimensionality of the data is not required for data analysis. Postacquisition reduction and adaptation of the dimensions of LC-IM-MS and IM-MS experiments into an LC-MS format opens the possibility to use a plethora of existing software tools. In this work, we developed data file conversion tools to reduce the complexity of IM data analysis. Three data file transformations are introduced in the PNNL PreProcessor software: (1) mapping the IM axis to the LC axis for IM-MS data, (2) converting the drift time vs / space to CCS/z vs / space, and (3) transforming All Ions IM/MS mobility aligned fragmentation data to a standard LC-MS DDA data file format. These new data file conversions are demonstrated with corresponding lipidomics and proteomics workflows that leverage existing LC-MS data analysis software to highlight the benefits of the data transformations.
离子淌度（IM）通常与液相色谱-质谱（LC-MS）实验相结合，为复杂样品分析提供额外的分离维度。虽然高度复杂的样品通过LC-IM-MS实验的全维度能更好地表征，以揭示新信息，但下游数据分析工作流程往往没有能力充分挖掘额外的IM维度。对于许多样品，包含IM分离的数据采集优势对于揭示样品信息来说就足够了，数据分析并不需要数据的全维度。采集后将LC-IM-MS和IM-MS实验的维度进行缩减和调整，转换为LC-MS格式，这使得使用大量现有软件工具成为可能。在这项工作中，我们开发了数据文件转换工具，以降低IM数据分析的复杂性。太平洋西北国家实验室预处理软件（PNNL PreProcessor）引入了三种数据文件转换方式：（1）将IM-MS数据的IM轴映射到LC轴；（2）将漂移时间对/空间转换为碰撞截面/电荷对/空间；（3）将所有离子IM/MS淌度对齐的碎裂数据转换为标准的LC-MS数据依赖采集（DDA）数据文件格式。通过相应的脂质组学和蛋白质组学工作流程展示了这些新的数据文件转换方式，这些工作流程利用现有的LC-MS数据分析软件来突出数据转换的优势。
