HP-CIL Metabolomics (Targeted and Untargeted) by High-Performance CIL LC-MS

Description

Overview

This HP-CIL LC–MS platform provides a hybrid approach to metabolomics, enabling both broad untargeted profiling and targeted analysis of specific metabolites and pathways within a single workflow. By combining extensive metabolome coverage with accurate relative quantification, it offers a flexible, cost-effective solution for both discovery-driven and hypothesis-driven studies.

Technology

To achieve high metabolome coverage with accurate quantification, we use a High-Performance Chemical Isotope Labeling (HP-CIL) Metabolomics platform (Zhao et al., 2019; Zhao et al., 2020). This approach analyzes the metabolome by combining multiple chemical-group-based submetabolomes, including amine/phenol, carboxyl, carbonyl, and hydroxyl channels. By integrating results from these four complementary channels, the platform can cover approximately 85%–95% of the metabolome chemical space. Depending on study goals and budget, users can select one or more channels to balance coverage and cost. Using a single-channel analysis, the platform enables detection and accurate relative quantification of up to ~2,500 metabolites (not features) across diverse sample types, including urine, blood, plant extracts, and cell extracts. Expanding to multi-channel analysis (up to four channels) increases coverage to approximately 7,000–10,000 metabolites per sample (sample dependent).

The workflow includes 1) Sample preparation and metabolite extraction, 2) Chemical isotope labeling, 3) LC–MS analysis, 4) Data processing and metabolite identification, and 5) Statistical analysis (e.g., PCA, PLS-DA, volcano plots).

Results are delivered as a comprehensive report along with Excel data files containing detected metabolites, confident and putative identifications, and accurate relative quantification data. These outputs are ready for downstream analysis, including pathway and statistical analysis using tools such as MetaboAnalyst.

References: Shuang Zhao, Hao Li, Wei Han, Wan Chan and Liang Li, “Metabolomic Coverage of Chemical-Group-Submetabolome Analysis: Group Classification and 4-Channel Chemical Isotope Labeling LC-MS”, Anal. Chem. 2019, 91, 12108-12115. Shuang Zhao and Liang Li, “Chemical Derivatization in LC-MS-Based Metabolomics Study”, Trends in Analytical Chemistry (TrAC), 2020, 131, 115988.

Untargeted Analysis Using HP-CIL LC-MS

The untargeted analysis capability of the HP-CIL LC–MS platform enables comprehensive detection and relative quantification of a large number of metabolites, including both known and unknown compounds. By leveraging multi-channel labeling strategies, this approach provides broad metabolome coverage with high sensitivity and reproducibility. The scalable design allows users to begin with a cost-effective single-channel analysis and expand to multi-channel analysis for deeper coverage as needed.

Targeted Analysis Using HP-CIL LC–MS

In addition to untargeted profiling, the HP-CIL LC–MS platform supports targeted analysis of metabolites across multiple pathways and panels within the same high-coverage framework. Compared to conventional targeted LC–MS methods, this approach enables analysis of a larger number of metabolites simultaneously, providing a more comprehensive view of pathway-level changes. Users can select metabolites of interest from predefined panels or customize their target lists based on specific research questions.

Integration with FOCUS Targeted Metabolomics and Global Lipidomics

The HP-CIL LC–MS platform can be seamlessly integrated with FOCUS targeted metabolomics assays to provide a comprehensive and flexible analytical strategy. While HP-CIL LC–MS enables high-coverage metabolome profiling for discovery, FOCUS assays offer targeted measurement of selected metabolites, including those not captured by CIL-based approaches. This combined strategy enhances overall metabolome coverage and supports targeted validation of discovery findings.

In addition, integration with the Global Lipidomics platform further expands analytical coverage, enabling simultaneous investigation of both metabolites and lipids for a more complete systems-level understanding.

For more information on available options and levels of metabolome coverage, please contact us (info@metabolomicscentre.ca) to discuss your specific needs and request detailed assay information.

Service Workflow

Untargeted Analysis Using HP-CIL LC–MS

TMIC’s Li Node employs a flexible, staged analysis strategy designed to maximize results while minimizing upfront investment. For discovery studies, where outcomes may be uncertain, we offer a cost-effective one-channel analysis as an entry point.

This single-channel CIL metabolomics analysis enables detection and accurate relative quantification of approximately 2,000–3,000 metabolites (not features) at $126 CAD per sample (≥20 samples). The results include metabolite identification, relative quantification, and basic statistical analysis, providing valuable insights for guiding further study design.

A typical workflow includes:

• Receipt of raw samples (e.g., urine, plasma, serum, tissue, cells)
• Sample aliquoting based on the number of channels and optional lipidomics analysis and/or FOCUS analysis
• Initial one-channel analysis for cost-effective metabolome profiling
• Delivery of results and consultation to discuss findings
• Decision on next steps:
  • Expand coverage by adding additional channels (Elevated or Comprehensive analysis) and/or lipidomics and/or FOCUS analysis
  • Stop after initial analysis, with no further cost beyond the first stage

This staged approach allows users to start small and scale up, reducing risk while enabling informed decision-making.

Targeted Analysis Using HP-CIL LC–MS

For pathway-focused or hypothesis-driven studies, targeted analysis using the CIL LC–MS platform enables measurement of metabolites across multiple pathways and panels within a single workflow. By selecting pathways or metabolite panels of interest, users can design customized targeted analyses. This approach allows simultaneous measurement of a large number of metabolites in a cost-effective manner, providing broader coverage than conventional targeted LC–MS methods. For metabolites not covered by HP-CIL LC–MS, the FOCUS Targeted Metabolomics platform can be used as a complementary solution.

Platform Strengths

High-coverage metabolite profiling with accurate relative quantification, enabling simultaneous analysis of multiple pathways for both discovery and targeted metabolomics applications.

Metabolite Identification

Metabolite identification is performed using a three-tiered approach:

Tier 1 (or Level 1): High-confidence identification using the CIL Library, based on accurate mass, retention time (RT), and isotope peak pairs

Tier 2 (or Level 2): High-confidence putative identification (~90% accuracy) using the Linked Identity (LI) Library, based on accurate mass and predicted RT

Tier 3 (or Level 3): Mass-based annotation using the MyCompoundID database

 

Example Results (Human Serum*)

Basic Analysis

~2,051 metabolites detected and relatively quantified

532 identified with high confidence (Tier 1 & 2)

1,313 mass-matched (Tier 3)

206 unidentified

 

Elevated Analysis

~4,196 metabolites detected and relatively quantified

937 identified with high confidence (Tier 1 & 2)

2,809 mass-matched (Tier 3)

450 unidentified

 

Comprehensive Analysis

~8,196 metabolites detected and relatively quantified

1,483 identified with high confidence (Tier 1 & 2)

5,523 mass-matched (Tier 3)

1,190 unidentified

 

*Results are sample-dependent; similar performance is expected across different biological sample types.

For detailed lists of metabolite identifications from basic, elevated, or comprehensive analyses, as well as targeted metabolite panels, please contact us at info@metabolomicscentre.ca.

 

Statistical Analysis

Basic statistics included. 

Pricing

Untargeted Analysis Using HP-CIL LC–MS

Academic / Government

Basic (1 channel): $126 per sample

Elevated (2 channels): $224 per sample

Comprehensive (4 channels): $420 per sample

Flexible option:

$126 per sample for the first channel

$98 per sample for each additional channel

Example: 3 channels = $126 + (2 × $98) = $322 per sample

 

Notes:

Prices apply to ≥20 samples

For <20 samples, add $400 per channel

A $200 flat fee per project applies for sample handling

Industry:

Add 30% university overhead to the above prices

 

Targeted Multi-Pathway Profiling Using HP-CIL LC–MS

Users can design customized targeted analyses by selecting pathways or metabolite panels. Pricing is calculated based on the selected metabolites and scope of analysis. For a quote, please contact us at info@metabolomicscentre.ca.

Compounds

We continuously expand our coverage of identifiable metabolites across diverse sample types. For more information, please contact us at info@metabolomicscentre.ca.