Effect of Sampling Rate and Data Pretreatment for Targeted and Nontargeted Analysis by Means of Liquid Chromatography Coupled to Drift Time Ion Mobility Quadruple Time-of-Flight Mass Spectrometry

Ion mobility as an
additional separation dimension can help to
resolve and annotate metabolite and lipid biomarkers and provides
important information about the components in a sample. Identifying
relevant information in the resulting data is challenging because
of the complexity of the data and data evaluation strategies for both
targeted or nontargeted workflows. Frequently, feature analysis is
used as a first step to search for differences between samples in
discovery workflows. However, follow-up experimentation often leads
to more targeted data extraction methods. In both cases, optimizing
data sets for data extraction can make an important contribution to
the overall results. In this work, we evaluate the effect of experimental
conditions including acquisition sampling rate and data pretreatment
on lipid standards and lipid extracts as examples of complex biological
samples analyzed by liquid chromatography coupled to drift time ion
mobility quadrupole time-of-flight mass spectrometry. The results
show that a reduction of both peak variation and background noise
can be achieved by optimizing the sampling rate. The use of data pretreatment
including data smoothing, intensity thresholding, and spike removal
also play an important role in improving detection and annotation
of analytes from complex biological samples, whereas nonoptimal data
sampling rates and preprocessing can lead to adverse effects including
the loss or alternation of small, or closely eluting, low-abundant
peaks.

离子迁移率作为额外的分离维度，有助于解析和注释代谢物和脂质生物标志物，并提供了有关样本中成分的重要信息。由于数据的复杂性和针对目标或非目标工作流程的数据评估策略，识别结果数据中的相关信息具有挑战性。通常，在发现工作流程中，特征分析被用作第一步，以寻找样本之间的差异。然而，后续实验往往导致更针对性的数据提取方法。在两种情况下，优化数据集以进行数据提取对于整体结果都具有重要意义。在本研究中，我们评估了包括采集采样率和数据预处理在内的实验条件对脂质标准品和脂质提取物的影响，这些标准品和提取物是利用液相色谱联用漂移时间离子迁移率四极杆飞行时间质谱分析的复杂生物样本的实例。结果表明，通过优化采样率可以实现峰变和背景噪声的降低。使用包括数据平滑、强度阈值设置和峰去除在内的数据预处理方法，在提高复杂生物样本中分析物的检测和注释方面也发挥着重要作用，而不优化的数据采样率和预处理可能导致不利影响，包括小峰或紧密洗脱的低丰度峰的丢失或改变。