LC-MS/MS Untargeted Metabolomics

Q: What is the difference between untargeted and targeted metabolomics?

Targeted metabolomics: Focuses on the quantitative analysis of specific metabolites or metabolic pathways, usually calibrated using known metabolite standards. Untargeted metabolomics: Comprehensively detects all metabolites in a sample, not relying on a pre-defined list of metabolites.

Q: Are biological replicates recommended?

It is recommended to have 6 to 10 biological replicates per group (to reduce the impact of individual differences).

Q: How to ensure quality control in LC-MS/MS non-targeted metabolomics experiments?

QC samples: Use pooled QC samples to monitor variation during the experiment. Regular calibration: Inject QC samples at the beginning and end of the experiment and after every 10 samples to calibrate the system.

Q: Should I choose positive ion mode (ESI+) or negative ion mode (ESI-) for LC-MS/MS?

ESI+: Detects alkaline/neutral metabolites (such as amino acids, choline). ESI-: Detects acidic metabolites (such as organic acids, fatty acids). Suggestion: Switch between positive and negative modes or run in two times.

Q: How to verify non-targeted results?

Targeted verification: Quantify key metabolites using MRM (multiple reaction monitoring) mode. Standard comparison: Use the standards to verify retention time and MS/MS spectra.

Creative proteomics offers comprehensive metabolomics services designed to unlock the full potential of your biological samples. For LC-MS/MS untargeted metabolomics, our state-of-the-art technology and expertise enable the unbiased detection and analysis of a wide range of metabolites, providing valuable insights into disease mechanisms, biomarker discovery, and therapeutic efficacy. Enrich and progress your metabolomics research.

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LC-MS/MS Untargeted Metabolomics

Untargeted metabolomics is a technical method for comprehensive and unbiased analysis of all small molecule metabolites (usually with a molecular weight <1000 Da) in biological samples. The core goal is to "panoramic scan" metabolite composition and reveal changes in the metabolic state of biological systems. It is widely used in disease mechanisms, drug development, nutrition and other fields.

There are mainstream platforms for untargeted metabolomics:

LC-MS/MS (liquid chromatography-mass spectrometry): Suitable for polar/non-polar metabolites.

GC-MS/MS (gas chromatography-mass spectrometry): Suitable for volatile/derivatized metabolites.

LC-MS/MS can provide a more comprehensive metabolic profile compare with GC-MS/MS, which shows higher sensitivity and resolution, detect even trace amounts of metabolites, with detection limits down to ppb level.

Data analysis:

Peak extraction (such as XCMS, MS-DIAL).

Metabolite annotation (based on databases such as HMDB, METLIN, etc.).

Multivariate statistics (PCA, PLS-DA) to screen differential metabolites.

General Workflow

LC-MS/MS Untargeted Metabolomics Figure 1. The targeted and untargeted workflow for LC-MS based metabolomics ^[1]

Applications

Basic medicine, clinical diagnosis: biomarker, disease mechanism, disease typing, personalized treatment, etc.

Biomedicine: drug mechanism of action, drug efficacy evaluation, drug development, etc.

Microbiology: pathogenesis, drug resistance mechanism, pathogen-host interaction research, etc.

Marine aquaculture: fishery resources, mariculture, fishery environment and aquatic product safety, etc.

Bioenergy and environmental science: fermentation process optimization, biofuel production, environmental risk assessment, etc.

Plant and agricultural Sciences: plant stress resistance mechanism, crop quality improvement, plant growth and development research.

Food nutrition: food storage and processing conditions optimization, food components and quality identification, functional food development, food safety monitoring and testing, etc.

Our Advantages

Detect up to 3000+ metabolites

Equipped with high-resolution, high-sensitivity mass spectrometry platform

Flexibility ion source choosing

Powerful database support

Advanced software tools and automated analysis

Platform:

Thermo Scientific Orbitrap Exploris 240, Thermo Scientific Q ExactiveTM HF-X MS, TripleTOF^® 6600 System, Sciex

Sample Requirements

Our LC-MS/MS untargeted metabolomics platforms can offer broad coverage of sample type. For other sample types, please inquire us.

Sample type	Minimum amount
Serum, plasma, urine, saliva, cerebrospinal fluid, etc.	200 μL
Brain, lung, kidney, liver, etc.	200 mg
Cell supernatant, cell pellet, cell lysates, etc.	200 μL, 10^{^7} cells
Roots, stems, leaves, fruits, seeds, etc.	200 mg
Feces, bacteria, fungi, etc.	200 mg

FAQs

What is the difference between untargeted and targeted metabolomics?

Targeted metabolomics: Focuses on the quantitative analysis of specific metabolites or metabolic pathways, usually calibrated using known metabolite standards.

Untargeted metabolomics: Comprehensively detects all metabolites in a sample, not relying on a pre-defined list of metabolites.

Are biological replicates recommended?

It is recommended to have 6 to 10 biological replicates per group (to reduce the impact of individual differences).

How to ensure quality control in LC-MS/MS non-targeted metabolomics experiments?

QC samples: Use pooled QC samples to monitor variation during the experiment.

Regular calibration: Inject QC samples at the beginning and end of the experiment and after every 10 samples to calibrate the system.

Should I choose positive ion mode (ESI+) or negative ion mode (ESI-) for LC-MS/MS?

ESI+: Detects alkaline/neutral metabolites (such as amino acids, choline).

ESI-: Detects acidic metabolites (such as organic acids, fatty acids).

Suggestion: Switch between positive and negative modes or run in two times.

How to verify non-targeted results?

Targeted verification: Quantify key metabolites using MRM (multiple reaction monitoring) mode.

Standard comparison: Use the standards to verify retention time and MS/MS spectra.

Learn about other Q&A about other technologies.

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LC-MS/MS Untargeted Metabolomics Case Study

Article

LC-MS/MS Untargeted Metabolomics

Publications

Here are some publications in Metabolomics research from our clients:

Characterization of CYCLOPHILLIN38 shows that a photosynthesis-derived systemic signal controls lateral root emergence. 2021. https://doi.org/10.1093/plphys/kiaa032
A non-probiotic fermented soy product reduces total and ldl cholesterol: A randomized controlled crossover trial. 2021. https://doi.org/10.3390/nu13020535
Pan-lysyl oxidase inhibition disrupts fibroinflammatory tumor stroma, rendering cholangiocarcinoma susceptible to chemotherapy. 2024. https://doi.org/10.1097/HC9.0000000000000502
Untargeted metabolomics reveal sex-specific and non-specific redox-modulating metabolites in kidneys following binge drinking. 2023. https://doi.org/10.1530/REM-23-0005
WI12 Rhg1 interacts with DELLAs and mediates soybean cyst nematode resistance through hormone pathways. 2022. https://doi.org/10.1111/pbi.13709

More Publications

Reference

Jacob M.; et al. Metabolomics toward personalized medicine. Mass Spectrom Rev. 2019, 38(3):221-238 https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21548

Metabolomics Sample Submission Guidelines

Download our Metabolomics Sample Preparation Guide for essential instructions on proper sample collection, storage, and transport for optimal experimental results. The guide covers various sample types, including tissues, serum, urine, and cells, along with quantity requirements for untargeted and targeted metabolomics.

Download

Metabolomics Sample Submission Guidelines

* For Research Use Only. Not for use in diagnostic procedures.

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From Our Clients

"I recently used their proteomics service for a project analyzing protein interactions in yeast models. The team was very responsive and helped clarify the methodology they employed, which made me feel confident in the results. The data quality was solid, with clear identification of several key proteins involved in our study. Their thorough analysis enabled me to pinpoint specific interactions that I hadn't considered before, which significantly improved the direction of my research. I appreciate their professionalism and support throughout the process."

Sarah Thompson, University of California, Berkeley

"Our lab collaborated with them on a project studying cancer biomarkers. The proteomics analysis provided was detailed and focused, specifically highlighting the differential expression of proteins between healthy and tumor samples. Their clear explanations of the data helped my team understand the biological implications. I also appreciated their willingness to revise the reports based on our feedback, ensuring that we had everything we needed for our publication. This collaborative spirit was invaluable."

Emily Rodriguez, Stanford University

"Our lab worked with them on a project studying the effects of diet on gut microbiota using proteomics. They used a label-free quantification method to analyze proteins in fecal samples before and after dietary intervention. The results showed significant changes in protein expression linked to microbial activity. This was pivotal for our hypothesis about diet-microbiota interactions. The clarity of their data presentation made it easy for our team to integrate these findings into our ongoing research."

Dr. Lisa Wong, University of Toronto

"My experience with Creative Proteomics during the mass spectrometry analysis was excellent. We sent in human saliva and mouse brain tissue samples, which they expertly analyzed using both LC-MS and GC-MS techniques. The results were invaluable, revealing key metabolites in the saliva and identifying biomarkers linked to brain function in the brain tissue."

Dr. Emily Carter, Senior Research Scientist

"The overall service from Creative Proteomics was outstanding. They made the entire process seamless and efficient, allowing us to focus on our research. We worked with leaf and root samples from various Arabidopsis genotypes for targeted metabolomics analysis. Their thorough profiling of primary and secondary metabolites gave us important insights into how the plants respond metabolically to environmental stress."

Dr. Laura Henderson, Plant Physiologist

"We had a pleasant collaboration with Creative Proteomics on mass spectrometry analysis of lipids. They conducted a detailed analysis of lipid species, providing us with important insights into lipid metabolism and its relationship with metabolic syndrome disease states."

Dr. Sarah Mitchell, Research Scientist

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