GUIDE FOR CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY DATA PROCESSING

In this work, a discussed and step-wise tutorial for LC-MS and GC-MS data processing using the open-access software MZMine2 is presented and discussed. The rationale behind each step was demonstrated to enable the readers to go through their own data and process it accordingly. The main lesson to be learned is that each parameter must be chosen in light of the raw data and no guidelines should suggest a predetermined value. Still, it is worth mentioning that ideal values for each parameter do not exist, and that the user might end up investing too much time futilely optimizing values. Our suggestion is to process your data in light of the raw data (and the study design) following the preview figure result and the resulting feature list generated in each processing step, interpret your data, and go back to process it again to tune the detection of important features.

本文呈现并探讨了一套基于开源软件MZMine2的液相色谱-质谱联用（LC-MS）与气相色谱-质谱联用（GC-MS）数据处理分步教程。本教程对每一步操作的理论依据进行了演示说明，以便读者能够针对自身的原始数据完成对应的数据处理流程。本教程的核心要点在于：所有参数的选取均需结合原始数据而定，不存在普适性的预设参数值。需特别说明的是，不存在适配所有场景的最优参数值，使用者可能会徒劳地耗费大量时间进行参数优化。我们建议：结合原始数据（及研究设计方案），参考每一步处理后生成的预览图结果与特征列表完成数据处理，对数据进行解读后，可回溯调整处理流程，以优化关键特征的检出效果。