iMet-Q: A User-Friendly Tool for Label-Free Metabolomics Quantitation Using Dynamic Peak-Width Determination

Efficient and accurate quantitation of metabolites from LC-MS data has become an important topic. Here we present an automated tool, called iMet-Q (intelligent Metabolomic Quantitation), for label-free metabolomics quantitation from high-throughput MS1 data. By performing peak detection and peak alignment, iMet-Q provides a summary of quantitation results and reports ion abundance at both replicate level and sample level. Furthermore, it gives the charge states and isotope ratios of detected metabolite peaks to facilitate metabolite identification. An in-house standard mixture and a public Arabidopsis metabolome data set were analyzed by iMet-Q. Three public quantitation tools, including XCMS, MetAlign, and MZmine 2, were used for performance comparison. From the mixture data set, seven standard metabolites were detected by the four quantitation tools, for which iMet-Q had a smaller quantitation error of 12% in both profile and centroid data sets. Our tool also correctly determined the charge states of seven standard metabolites. By searching the mass values for those standard metabolites against Human Metabolome Database, we obtained a total of 183 metabolite candidates. With the isotope ratios calculated by iMet-Q, 49% (89 out of 183) metabolite candidates were filtered out. From the public Arabidopsis data set reported with two internal standards and 167 elucidated metabolites, iMet-Q detected all of the peaks corresponding to the internal standards and 167 metabolites. Meanwhile, our tool had small abundance variation (≤0.19) when quantifying the two internal standards and had higher abundance correlation (≥0.92) when quantifying the 167 metabolites. iMet-Q provides user-friendly interfaces and is publicly available for download at http://ms.iis.sinica.edu.tw/comics/Software_iMet-Q.html.

从液相色谱-质谱（LC-MS）数据中实现代谢物的高效准确定量，已成为当前的重要研究方向。本研究推出一款自动化分析工具iMet-Q（智能代谢组定量工具，intelligent Metabolomic Quantitation），用于基于高通量一级质谱（MS1）数据的无标记代谢组定量分析。通过执行峰检测与峰对齐流程，iMet-Q可输出定量结果汇总，并分别在生物学重复水平与样本水平报告离子丰度。此外，该工具还可输出已检测代谢物峰的电荷态与同位素比值，以辅助代谢物鉴定工作。研究团队采用iMet-Q分析了一套内部标准品混合数据集与一套公开的拟南芥（Arabidopsis）代谢组数据集。选取XCMS、MetAlign与MZmine 2三款公开定量工具作为对照，用于性能对比评估。在标准品混合数据集的分析中，四款定量工具均检出7种标准代谢物，其中iMet-Q在轮廓模式（profile）与质心模式（centroid）两类数据集中的定量误差均仅为12%，为四款工具中最低。同时，该工具可准确判定7种标准代谢物的电荷态。通过将7种标准代谢物的质荷比信息与人类代谢组数据库（Human Metabolome Database）进行匹配，共得到183个代谢物候选物。借助iMet-Q计算得到的同位素比值，可过滤掉其中49%（183个中的89个）的候选物。在公开的拟南芥代谢组数据集（该数据集标注了2种内标与167种已鉴定代谢物）中，iMet-Q成功检出了对应2种内标与167种代谢物的全部峰信号。同时，在对2种内标进行定量时，该工具的丰度变异系数≤0.19，表现出良好的重复性；在对167种代谢物进行定量时，其丰度相关系数≥0.92，相关性优异。iMet-Q搭载了友好的用户交互界面，可通过网址http://ms.iis.sinica.edu.tw/comics/Software_iMet-Q.html免费下载使用。