نطاق واسع غير المستهدفة التنميط Metabolomic من المصل بواسطة الترا الطيف الأداء اللوني الكتلة السائل (UPLC-MS)

The term “metabolomics” can encompass many things. For example, a metabolomics experiment can be performed using a variety of analytical platforms such as NMR and both gas and/or liquid chromatography coupled with mass spectrometry. Furthermore, metabolomics experiments can be performed in a targeted or non-targeted manner, or a combination of both. A targeted metabolomics experiment will involve directed analysis of a panel of molecules important to the biological question at hand (e.g. small molecules involved in the TCA cycle will allow for accurate quantitation of that pathway). In this situation, the biological hypothesis is dictating the choice of metabolites to be targeted in the analysis and the analytical steps are optimized for the detection of these molecules. Alternatively, a non-targeted metabolomics experiment is hypothesis generating. In this case, the experiment is performed in a broad and unbiased manner to enable detection of as many metabolites as possible. The results from a non-targeted experiment will drive the next step of the research (which in many cases may involve a targeted metabolomics workflow). It is also possible to combine the two approaches, in which case an experiment is performed in a non-targeted manner while concurrently a panel of known molecules are monitored within the data.

The tutorial presented here is focused specifically on non-targeted metabolite profiling of serum. As described above, the non-targeted approach provides an unbiased view of the detectable metabolites, can generate large amounts of information, and ultimately allow for novel discoveries. The use of this approach, specifically employing ultra performance liquid chromatography coupled with mass spectrometry (UPLC-MS), is becoming widespread ^{1, 2, 3} and involves the following steps: (1) experimental design (2) sample collection (3) sample preparation (4) data acquisition by UPLC-MS (5) data pre-processing (peak detection, integration, alignment, and normalization) (6) statistical data analysis (both uni- and multivariate) (7) metabolite identification and (8) biological interpretation.

Currently, there are no established standard methods for UPLC-MS based non-targeted metabolite profiling and subsequent data pre-processing steps. This lack of standardization is due in part to one of the primary analytical challenges of metabolite profiling; the chemical diversity of the metabolome. Because of this diversity, it is impossible for a single extraction method or mass spectrometry acquisition method to provide comprehensive coverage of all metabolites in a single analysis. In concept, metabolite coverage can be maximized by using multiple extractions (e.g. aqueous, methanol, chloroform:methanol, etc.) coupled with various chromatographic conditions (e.g. reverse phase, HILIC, etc.) and various ionization modes (e.g. positive ion, negative ion, chemical ionization, etc.). Often, however, researchers do not have a pre-determined bias for a specific chemical class and thus the expense of performing multiple extractions and instrument acquisitions is not warranted, especially for large-scale experiments. Thus, the video tutorial presented here was designed to provide a general procedure for large scale non-targeted metabolite profiling of serum by UPLC-MS. It will enable new and established laboratories to perform these types of experiments and the building blocks upon which they can expand the approach for various sample types, specific chemical classes, or targeted analysis. Specifically, this protocol will include the steps of: serum sample preparation, sample organization for large scale studies, UPLC-MS data acquisition, quality control (QC) procedures, and metabolite identification. Strategies for data pre-processing and statistical analysis are also presented.

The protocol will not focus on the steps of experimental design, sample collection, or biological data interpretation as it is outside the scope of this tutorial. However, many resources exist in the literature for these topics and the authors encourage researchers new to metabolomics to explore these thoroughly ^{4, 5, 6, 7, 8, 9}. In particular, experimental design is extremely important and is critical to the success of a non-targeted metabolomics experiment. Factors such as appropriate biological replication and consistency in sample collection procedure (e.g. time on bench, storage temperature, storage time, freeze-thaws, etc.) must be considered to ensure a viable study and to facilitate appropriate biological interpretation of the data.