Metabolomics 101
Reading the body's chemistry — your blood carries thousands of small molecules, and non-targeted metabolomics is the science of measuring them all at once.
When most of us picture a blood test, we picture a single number: a cholesterol value, a glucose reading, a thyroid level. Each one answers one pre-set question. But your blood holds far more than a handful of numbers. At any moment it carries thousands of small molecules—the working materials and by-products of your living cells—and together they form a remarkably detailed picture of how your body is functioning right now.
Reading that fuller picture is the job of metabolomics. And one approach in particular—non-targeted (also called untargeted or global) metabolomics—tries to measure as many of those molecules as possible in a single analysis, rather than checking a short, predefined list.1 Here's what that means, how it works, and—just as importantly—what it can and can't tell you.
01What is non-targeted metabolomics?
Start with the word at its center: the metabolome. It's the complete set of small molecules—called metabolites—found in a biological sample like blood, urine, or tissue. Metabolites are the substrates and products of metabolism: the sugars, fats, amino acids, vitamins, and countless other compounds that drive essential cellular activities such as producing and storing energy and sending signals between cells.2
Crucially, metabolites don't come only from your own cells. They also arrive from your gut microbes, from your diet, and from other outside sources like medications and environmental compounds.2 Your metabolome, in other words, is where your genetics and your daily life meet.
The reference catalog of human metabolites keeps growing as analytical tools improve: the Human Metabolome Database now lists more than 217,000 metabolite entries.3 The distinction between the two main ways of measuring them is simple:
Measures a short, predefined list of known molecules with high precision.
Casts a wide net, measuring thousands of molecules in one analysis to map the whole picture.
Metabolomics studies the metabolome—the thousands of small molecules in a sample. Non-targeted metabolomics measures as many of them as possible at once, instead of checking a short, predefined list.
02Why measure thousands of molecules at once?
Because of where metabolites sit in the chain of biology. Your genes set out instructions; proteins carry them out; metabolites are largely the result—the molecules left behind as all of that activity happens. That makes the metabolome the layer of biology closest to your actual physiology, and researchers describe it as a direct, functional readout of biochemical activity that can be correlated with the traits and states we can observe.1
A single-target test is like reading one word on a page. A broad metabolomic profile is closer to reading the sentence. And because the approach is sensitive, it can pick up subtle shifts across whole biological pathways rather than just one isolated value.2 That breadth is what makes non-targeted metabolomics such a powerful research tool across fields from nutrition to metabolic health to the biology of aging.
Your metabolome is where your genetics and your daily life meet—a real-time snapshot of your biochemistry.
Metabolites are largely the downstream result of your genes, proteins, diet, and environment in action—so a broad profile offers a sensitive, real-time readout of how your biology is functioning.
03How does it actually work?
The everyday part is familiar: it begins with a standard sample, most often blood serum. What follows is where the technology earns its keep. The sample is carefully extracted to pull out its small molecules, and the extract is analyzed with mass spectrometry—an instrument that sorts molecules by their precise mass.
Thanks to modern mass spectrometry, thousands of metabolites can now be measured from a very small amount of biological material.1 For each molecule the instrument reports two things: an accurate mass, which helps identify what it is, and an intensity, which reflects how much is present. Stitched together, those readings become a detailed biochemical profile—the raw material that software and scientists then work to interpret.
Sample
A standard blood serum sample is collected.
Extract
Small molecules are separated out for analysis.
Measure
Mass spectrometry sorts molecules by exact mass.
Profile
The result is a broad biochemical profile.
A blood sample is extracted and analyzed by mass spectrometry, which records each molecule's mass and relative amount—producing a broad biochemical profile from a small sample.
04What can your metabolome reveal?
Because it changes in real time, the metabolome reflects your current biochemistry—not a fixed, lifelong value. That sensitivity is precisely what makes it interesting. In research settings, broad metabolite profiling has been used to study metabolic health, nutrition and diet, and the molecular changes that accompany aging, and to detect subtle pathway-level shifts that single tests can miss.2
One especially well-studied category is lipids—the fats and fat-like molecules that, among other roles, build the membranes around every cell. Within that category sits a class of molecules central to this brand's work: plasmalogens.
The metabolome is a dynamic snapshot of your current biochemistry. Researchers use broad profiling to study areas like metabolic health, nutrition, and aging—and lipids are one of the most informative molecule classes it captures.
05A closer look: plasmalogens
Plasmalogens are a distinctive class of membrane phospholipids. Their defining feature is an unusual chemical link—a vinyl-ether bond—at one position on the glycerol backbone, paired with polyunsaturated fatty acids at another.4 They make up a meaningful share of the body's phospholipids (up to roughly 20% of total phospholipid mass) and are especially abundant in tissues with high demands, including the brain, heart, and immune cells.4
That unusual bond also makes plasmalogens chemically reactive in a useful way: research suggests they may help protect other molecules from oxidative damage, acting as a kind of built-in antioxidant within the membrane.4 Their precise physiological roles are still being worked out and appear to differ across tissues and life stages.4
Plasmalogens are also of interest in the study of aging. Levels tend to decline with age, and in research, lower ethanolamine plasmalogen levels have been observed in association with the severity of dementia.5 It's important to read that carefully: these are observed associations reported in scientific studies.
Plasmalogens are membrane phospholipids defined by a vinyl-ether bond, abundant in the brain and heart, and studied for a possible antioxidant role. Levels tend to fall with age, and research has reported associations with cognitive decline—associations only, not proof of cause or treatment.
06What a metabolomic baseline can—and can't—tell you
Here's where honesty matters, and where the science world is refreshingly candid. A broad metabolomic profile is powerful, but it is not a diagnostic test. It does not name a disease, and a single snapshot can be influenced by ordinary things—what you ate, how you slept, your activity, the time of day.
That variability is actually the case for measuring it well. The most useful comparison is usually you-to-you over time. By establishing a personal baseline—a clear picture of where your biochemistry sits today—and then re-measuring later, you can see what's changing and put any future result in context. It's the same principle behind knowing your own "normal" so you can notice when something shifts.
This is the role of metabolomics- and lipidomics-based assessments like ProdromeScan™ and PlasmalogenScan™: to measure a broad panel of these molecules and help establish your personal biochemical baseline for educational and research purposes—a starting point you can understand and track, not a diagnosis.
A metabolomic profile is a baseline, not a diagnosis. Because the metabolome shifts day to day, its real value is comparing you to yourself over time—so you can establish a starting point and track change.
07How to think about supporting your biology
Whatever a baseline shows, the fundamentals of supporting your body's chemistry are familiar and well within your control. A balanced, plant-forward diet, regular movement, quality sleep, and managing stress all shape your metabolism—and therefore your metabolome—day in and day out. The goal of measurement isn't to replace those basics; it's to give you objective information alongside them, and to work from data rather than guesswork.
And the most important partner in interpreting any result is a qualified healthcare professional who knows your history and can put the numbers in the context of your whole health.
Diet, movement, sleep, and stress management remain the foundation of metabolic health. Measurement adds objective context—but results are best interpreted with a qualified healthcare professional.
Frequently asked questions
What's the difference between targeted and non-targeted metabolomics?
Targeted metabolomics measures a short, predefined list of known molecules. Non-targeted (untargeted) metabolomics tries to measure as many molecules as possible at once, which can reveal broad patterns rather than answering a single pre-set question.1
Is a metabolomic test the same as a genetic test?
No. A genetic test reads the instructions you were born with. A metabolomic profile reflects what your body is doing right now—shaped by your genes and your diet, environment, lifestyle, and gut microbes.2 It changes over time; your genome largely doesn't.
Can metabolomics diagnose a disease?
A broad metabolomic profile is a research and educational tool for establishing a biochemical baseline. It is not designed to diagnose, treat, cure, or prevent any disease. Diagnosis is the role of a qualified healthcare professional.
Why measure plasmalogens?
Plasmalogens are an abundant, chemically distinctive class of membrane lipids—concentrated in the brain and heart—whose levels tend to change with age. That makes them an informative part of a lipid baseline.4
A single number answers one question; your metabolome tells a fuller story. Non-targeted metabolomics reads thousands of molecules at once to capture how your biology is functioning today—giving you an objective baseline to understand and to track over time.
Curious about your own baseline?
BioAssess™ uses ProdromeScan™ and PlasmalogenScan™ to help establish your personal biochemical baseline for educational and research purposes.
Explore BioAssess™The editorial team translates the science behind Dr. Goodenowe Perpetual Health into clear, accurate explainers for a general audience.
This explainer draws on the metabolomics research of Dr. Dayan Goodenowe — a neuroscientist and biochemist (PhD, Medical Science, 1993) who, in 1999, invented the ion cyclotron resonance mass spectrometry technology behind comprehensive biochemical profiling. He is a research scientist and educator, not a licensed physician.
References
- Patti, G. J., Yanes, O., & Siuzdak, G. (2012). Metabolomics: the apogee of the omics trilogy. Nature Reviews Molecular Cell Biology, 13(4), 263–269. https://doi.org/10.1038/nrm3314
- Johnson, C. H., Ivanisevic, J., & Siuzdak, G. (2016). Metabolomics: beyond biomarkers and towards mechanisms. Nature Reviews Molecular Cell Biology, 17(7), 451–459. https://doi.org/10.1038/nrm.2016.25
- Wishart, D. S., Guo, A., Oler, E., Wang, F., Anjum, A., Peters, H., et al. (2022). HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Research, 50(D1), D622–D631. https://doi.org/10.1093/nar/gkab1062
- Braverman, N. E., & Moser, A. B. (2012). Functions of plasmalogen lipids in health and disease. Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease, 1822(9), 1442–1452. https://doi.org/10.1016/j.bbadis.2012.05.008
- Goodenowe, D. B., Cook, L. L., Liu, J., Lu, Y., Jayasinghe, D. A., Ahiahonu, P. W. K., et al. (2007). Peripheral ethanolamine plasmalogen deficiency: a logical causative factor in Alzheimer's disease and dementia. Journal of Lipid Research, 48(11), 2485–2498. https://doi.org/10.1194/jlr.P700023-JLR200
Dr. Goodenowe Perpetual Health operates as a self-directed research model and is not a medical facility. The information provided here is for educational and research purposes only and is not intended to diagnose, treat, cure, or prevent any disease or medical condition.
Participation is voluntary, and individuals assume full responsibility for their own health and well-being. Always consult a qualified healthcare professional regarding your individual health needs and before making changes to your health routine. Results are not guaranteed and will vary from person to person.
These statements have not been evaluated by the Food and Drug Administration. ProdromeScan™, PlasmalogenScan™, BioAssess™, and any related products or services are not intended to diagnose, treat, cure, or prevent any disease.
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What Your Blood Can Tell You