Different tools for different questions.
Proteomics is one of several powerful methods for understanding fish biology. Here’s how it compares to the others - and when each is the right choice.
No single method sees everything
THE CORE IDEA
Aquaculture R&D has never had more tools. Histology, blood chemistry, targeted biomarker panels, genomics, transcriptomics, metabolomics, and proteomics each answer different questions about fish biology.
At MariHealth, we use proteomics — the large-scale study of proteins, because proteins are what actually do the work in a cell. They carry out metabolism, defend against disease, build tissue, and respond to environment. Measuring thousands of them at once gives a uniquely detailed picture of what's happening inside a fish, right now.
But proteomics isn't the right tool for every question. This page explains what each method does well, where each falls short, and how they work together.
AT A glance
Six methods, compared
| Method | What it measures | Scope | Typical use | Sample needs | Turnaround | Best when you want to… |
|---|---|---|---|---|---|---|
| Histology & histopathology | Tissue structure and cellular changes, visually | Whole tissue, microscopic | Disease diagnosis, gold standard for lesions | Fixed tissue samples | Days to weeks | Confirm a visible disease or tissue-level problem |
| Blood chemistry & haematology | Standard markers — glucose, cortisol, enzymes, cell counts | ~10–30 parameters | Routine health screening, stress indication | Blood, plasma | Hours to days | Spot-check general physiological state |
| Targeted biomarker panels | A pre-selected set of proteins or metabolites | Narrow, focused (5–50 markers) | Routine monitoring of known indicators | Blood, plasma, tissue | Hours to days | Track known markers continuously and act quickly |
| Genomics (SNP / WGS) | DNA sequence — the genetic blueprint | Static, lifelong | Breeding, selection, parentage | Fin clip, blood | Days to weeks | Select broodstock or understand genetic predisposition |
| Transcriptomics (RNA-seq) | Gene expression — which genes are switched on | Whole genome, dynamic | Research, mechanistic studies | Tissue (cold chain critical) | Weeks | Understand which genes are being activated |
| Proteomics | Proteins — the molecules doing the work | Thousands per sample, unbiased | R&D, discovery, deep phenotyping | Tissue, blood, plasma, mucus — no cold chain | 2–10 business days | Understand what's actually happening biologically, including changes you didn't anticipate |
method by method
What each one is actually good at
Histology & histopathology
The examination of tissue sections under a microscope, usually after fixing and staining, to identify disease, lesions, or abnormal structures.
Best for
- Confirming a specific disease diagnosis (e.g. gill pathology, parasitic infection)
- Documenting tissue-level damage
- Regulatory and veterinary reporting
Limits
- Labour-intensive and requires trained pathologists
- Subjective — interpretation varies between readers
- Only shows what's structurally visible; biochemical changes are invisible
Histology tells you what the damage looks like. Proteomics tells you what molecular processes drove it. Used together, they give a complete picture — from pathology to mechanism.
Blood chemistry & haematology
Measurement of standard physiological markers in blood — cell counts, electrolytes, enzymes, hormones like cortisol — using clinical chemistry analysers.
Best for
- Routine, high-throughput health monitoring
- Detecting stress (via cortisol) or general physiological imbalance
- Cheap, fast, and familiar to every fish veterinarian
Limits
- Only 10–30 parameters per panel — a narrow window into biology
- Many conditions don't show up in standard panels until advanced
- Doesn't explain why a marker is elevated, only that it is
Blood chemistry is the front-line triage tool. When something's off but the panel doesn't explain it, proteomics provides the deeper investigation.
Targeted biomarker panels
A pre-selected panel of proteins or metabolites — usually 5 to 50 — measured together to monitor specific, known indicators of health, stress, or disease.
Best for
- Routine, operational decisions (when to feed, when to harvest, when to treat)
- Tracking known biomarkers over time
- Fast, repeatable monitoring at scale
Limits
- You can only measure what the panel was designed to detect — novel changes are invisible
- Panel development requires prior knowledge of which markers matter
- New questions often require new, expensive panel development
Targeted panels are built from prior proteomics discoveries. Proteomics is how new biomarkers are found in the first place; targeted panels are how they're monitored once established. The two sit at opposite ends of the same workflow.
Genomics (SNP panels, whole-genome sequencing)
The study of an organism's DNA — its genetic sequence. In aquaculture, this is used to identify genetic markers for traits like growth, disease resistance, and parentage.
Best for
- Broodstock selection and breeding programmes
- Parentage assignment and pedigree
- Identifying genetic predisposition to traits or disease resistance
Limits
- DNA is static — it tells you about potential, not current state
- A fish's genes don't change with nutrition, stress, or environment; its proteins do
- Doesn't capture the effect of feed, management, or environment
Genomics tells you the genetic potential of a fish. Proteomics tells you how that potential is being expressed under real farming conditions. Genetics + proteomics together bridge breeding and performance.
Transcriptomics (RNA-seq, qPCR)
Measurement of gene expression — the RNA molecules produced when genes are activated. Reveals which genes are being switched on in a tissue at a moment in time.
Best for
- Mechanistic research — understanding which genetic pathways are activated
- Dynamic studies where genes change over time
- Discovery of novel regulatory patterns
Limits
- RNA degrades rapidly — requires strict cold chain (frozen at collection, kept at −80°C)
- Gene activation doesn't always translate to protein activity — mRNA correlates with protein levels only ~40% of the time in fish
- Expensive and computationally intensive
Transcriptomics shows which genes are being activated. Proteomics shows which proteins are actually present and functional. The two together reveal the full flow from gene to biological effect.
Proteomics
The large-scale quantitative analysis of proteins — the molecules that carry out almost every biological function in a cell. Our diaPASEF workflow quantifies over 3,000 proteins per sample in a single run, without needing to know in advance which proteins to look for.
Best for
- Deep phenotyping — understanding the full molecular state of a fish under a given condition
- Discovery — finding novel biomarkers, mechanisms, or responses to new interventions
- Feed trials, disease investigations, stress profiling, smolt readiness assessment
- Research questions where "we don't know what we're looking for"
Limits
- Not a rapid operational decision tool — turnaround is days, not hours
- Requires specialist interpretation (which is why we staff aquaculture proteomics experts)
- Proteins with very low abundance can still be below detection limits
Proteomics sits at the depth end of the spectrum. It's not the tool you reach for to make a harvest decision tomorrow — it's the tool you use when you need to understand why something is happening, or to find markers that don't yet exist.
Where each method sits on the spectrum
There’s always a trade-off between how deeply a method sees into biology and how quickly it delivers answers. Here’s how the common methods compare.
No method sits in the top-left quadrant — the "deep and instant" combination doesn't exist. The art of aquaculture R&D is knowing which trade-off matches the question you're asking.
choosing your tool
which one when?
Choosing the right method for your question
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“We need to decide whether to treat this pen this week.”
Blood chemistry or a targeted biomarker panel. You need a fast, known answer, not a deep investigation.
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“We want to understand why our new feed improves growth.”
Proteomics. The mechanism is unknown; you need to see which biological pathways are changing.
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“We're selecting broodstock for disease resistance.”
Genomics. You're looking for genetic predisposition, not current state.
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“Fish are dying and we don't know why.”
Histology first, then proteomics if the cause remains unclear. Rule out visible pathology first; if nothing is structurally obvious, investigate at the molecular level.
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“We want to validate that our ingredient works as claimed.”
Proteomics. You need to demonstrate a specific biological mechanism, not just an outcome.
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“We need to monitor smolt readiness across our hatchery continuously.”
A targeted biomarker panel — built from proteomics discovery work. A panel is operationally practical; proteomics is how you know which markers to include.
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“We want to understand which genes are activated during a stress response.”
Transcriptomics, with proteomics confirmation. Genes activate first; confirm which of those activations produced functional proteins.
our role
We don’t replace these methods. We complete the picture.
We built MariHealth Solutions because aquaculture R&D deserves a proteomics service that's been designed, from the ground up, for fish. Not a repurposed human diagnostics platform. Not a generalist omics provider.
Our role isn't to replace histology, blood chemistry, genomics, or targeted biomarker panels. Each of those methods does something proteomics can't. Our role is to bring proteomics, the deepest molecular view currently available, into the aquaculture toolkit, interpreted by people who understand what fish biology actually looks like.
When you've exhausted what a targeted panel can tell you, or when you need to understand why something is happening rather than just that it is, proteomics is the method. And it's what we do, every day.
faqs
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No. Proteomics adds a layer of depth that other methods can't access, but your existing tools remain essential for fast operational decisions, regulatory reporting, and routine monitoring. Proteomics is best used alongside (not instead of) your current workflow.
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Targeted panels are built for speed and repeatability — they're the right choice for operational, repeat monitoring of known markers. Proteomics is the method you use to discover which markers matter in the first place, or to investigate when a panel doesn't explain what you're seeing.
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When you need an answer in hours, when the question is narrow enough for a targeted panel to answer, or when the issue is visibly structural (a tumour, a lesion, a parasitic load) and histology will confirm it faster and more cheaply. We'll tell you honestly if proteomics isn't the right fit.
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Genomics tells you about genetic potential; transcriptomics tells you which genes are being activated. But the relationship between RNA and protein is imperfect — in fish, only about 40% of protein levels can be predicted from RNA. Proteomics measures what's actually present and functional in the cell.
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No. Proteins are much more stable than RNA. MariHealth accepts samples shipped at ambient or chilled temperatures — no dry ice, no -80°C freezing required. This is a significant operational advantage over RNA-based methods.
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Not exactly — it's different. Histology shows visible pathology; proteomics shows molecular changes, often earlier and in more detail. For diseases with clear histological signatures, histology remains the gold standard. For complex, multi-factor conditions, proteomics often reveals what histology can't see.
next steps
Think proteomics might be right for you?
Book a 20-minute discovery call, or request a sample report to see what the data actually looks like.