An Integrated Approach to Metabolomics Studies: Discovery to Quantitation on a Single Platform

Goal

Demonstrate a comprehensive metabolomics profiling research strategy, with the integration of three mainstream approaches of untargeted component profiling and differential analysis, targeted screening, and targeted quantitation analysis performed on a single MS platform.

Introduction

Cellular metabolomics is an important area of study providing valuable insights into changes associated with biochemical reactions and metabolic pathways. Analyzing the metabolic activities of cells has allowed better understanding of intricate cellular processes involved in cancer progression and drug responses. Therefore, the characterization of cancer cell-specific metabolome signatures would provide beneficial information for early diagnosis of cancer and therapeutic cancer research.

Mass spectrometry (MS)-based metabolomics has proven to be advantageous in investigating the metabolic profiles of cancer cells. A wealth of information, including the biochemical phenotypes, molecular mechanisms of cancer development, response, and resistance against drug therapy, can all be obtained using mass spectrometry.

Mass spectrometry-based strategies for metabolomics provide both qualitative and quantitative information. This not only enables identification of the metabolite structures in a biological system but also allows the monitoring of changes that occur within a system.

Traditionally, MS-based metabolomics studies can be classified into two primary strategies—a discovery-driven untargeted profiling approach using high-resolution, accurate mass (HRAM) mass spectrometry followed by a hypothesis-driven targeted approach using a triple quadrupole mass spectrometer. The discovery stage detects and identifies potential metabolites that are biologically significant, while the targeted validation stage can confirm and quantify these metabolites across large sample populations to enable functional understanding.

Unfortunately, adopting such a comprehensive metabolomics workflow requires the tedious transfer of methods across different mass spectrometers. The use of a single mass spectrometer that performs both stages of analysis, coupled with intuitive software tools, would be far more attractive than conventional analytical strategies. In this application note, the metabolomics research paradigm shift is demonstrated, with utilization of a hybrid quadrupole-Orbitrap mass spectrometer to achieve both discovery and validation in one instrument. The HRAM qualitative capabilities and triple-quadrupole-like quantitative abilities of the Thermo Scientific™ Q Exactive™ mass spectrometer enables untargeted profiling, targeted profiling, and targeted quantitation to be performed on a single instrument. To showcase this capability, the metabolic profiles of the human pancreatic cancer cell line Panc-1 were investigated and the steps involved are outlined in this application note (Figure 1). The power of the discovery workflow will be enhanced with the use of differential analysis software that provides unbiased differential results followed by targeted profiling and targeted quantitation workflow with the use of routine quantitation software.

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