Complete Guide

How to Use the Protocol Builder

What it is, what it is not, how it decides what to recommend — and how to overrule it when you know what you are doing.

What this guide covers

What the Protocol Builder is — and what it is not
Why the book comes first
The core principle: the minimum number of compounds
The order you build in, and why it matters
How the logic engine actually decides
Choosing your experience level
Overriding the recommendations
A worked example, start to finish
Common questions

Section One

What the Protocol Builder is

The Protocol Builder is an implementation tool. It takes the decision framework, compound hierarchy and protocol logic set out in Targeted Peptide Systems and applies them to one specific person: you.

You describe your situation in plain language — “carrying extra weight,” “joint injury,” “poor sleep.” The Builder translates that into the physiological pathways involved, ranks those pathways into a primary and a secondary focus, and assembles a starting protocol that follows the book’s logic. Then it shows you its reasoning at every step, so you can agree with it or change it.

What it is

A structured way to apply the book’s framework to your own situation
A validation engine that checks protocols for redundancy and overlap
A way to organise sequencing, timing windows and monitoring checkpoints
A brake on unnecessary complexity
A starting point for a conversation with a qualified clinician

What it is not

A replacement for the book — it applies knowledge, it does not teach it
Medical advice, diagnosis, or treatment of any kind
Aware of your bloodwork, medications, or medical history
A dosing calculator — amounts come from the book
A substitute for professional supervision

Important. Many compounds referenced in the Builder are research peptides that are not approved for these uses. Nothing the Builder produces is a recommendation to take anything. Always consult a qualified healthcare professional before acting on any protocol.

Section Two

Why the book comes first

The Builder is designed to work with Targeted Peptide Systems, not instead of it. The two are doing different jobs.

The book gives you	The Builder gives you
The scientific foundation	Your situation mapped to specific pathways
The decision framework	That framework applied, automatically
The compound hierarchy and why it exists	A ranked shortlist for your goals
The reasoning behind every recommendation	Redundancy and overlap checking
Progression logic across cycles	Sequencing, timing and monitoring for this cycle
Dosing ranges	Which compounds to look up

You can use the Builder without the book and get something useful. But every time you find yourself asking why did it choose that?, the answer is in the book — and that question is the one worth answering, because it is what turns a protocol you were handed into a protocol you understand.

Where the dosing lives. The Builder tells you which compounds, in what order, on what timing framework, and what to monitor. It does not invent dosing. Amounts come from the book, and the Dosing Upgrade simply displays the book’s own reference ranges inside the app so you do not have to flip back and forth.

Section Three

The principle everything else rests on

“Use the minimum number of compounds necessary to achieve the desired outcome.”

The foundational principle of Targeted Peptide Systems

More compounds do not produce better outcomes. They produce more variables.

That is the whole argument, and it is worth sitting with. Every compound you add is one more thing that could be responsible for a result — and one more thing you cannot separate out afterwards. Run two compounds and get a strong response, and you have learned something you can use for years. Run six and get the same response, and you have learned nothing except that something in there worked.

Why the simpler protocol wins

You can evaluate it. A clear result with few variables is attributable. A clear result with many variables is a coincidence you cannot repeat.
Side effects are traceable. If something feels wrong on a simple protocol, you know where to look. On a complex one you are guessing, and usually the answer is to stop everything and start over.
It is easier and cheaper to actually run. Fewer injections, less to time correctly, less to source, fewer chances to make a mistake.
You build a personal baseline. Knowing how your body responds to a given compound is worth more in the long run than a fast start is worth now.

Add a compound when you have a reason, not a hope. A new compound should be answering a specific question the framework raised. If you cannot say in one sentence what it is there to do, it is not ready to go in the protocol.

How the Builder enforces this

This principle is not a slogan in the Builder — it is wired into the behaviour:

Starting protocols are deliberately small: two compounds for a Beginner, three above that
A simplicity reading updates live as you select, and tells you when a protocol has passed the point where you could interpret its result
Only one compound per receptor family is allowed at a time — one GHRH, one GHRP, one incretin, one IGF
Blends are blocked from running alongside their own component compounds
The final brief explains, in writing, why your protocol is the length it is

None of this is the tool being restrictive. It is the tool refusing to help you build something you would not be able to learn anything from.

Section Four

The order you build in

Protocol design runs in a specific sequence, and each step narrows the one after it. This is why the Builder asks for context before it will name a single compound — a compound chosen before the objective is set is just a guess with a brand name.

Your primary objective. What you actually want to change. Everything downstream is judged against this.
Your desired outcome. What success looks like specifically enough that you would recognise it when it happened.
The target pathway. You do not need to name this — the Builder derives it from the plain-language concerns you tick, then ranks the systems involved into a primary, a secondary, and sometimes a third.
Your experience level. Sets how conservative the defaults start out.
What you are already taking. So the Builder works around your current routine instead of duplicating it.
Established versus newer. Where you want to sit between the longest clinical track record and the newest available options.

Only once those are established does the Builder generate anything. If the Build My Protocol button is greyed out, it is because one of them is still missing — the panel underneath it names exactly which.

The optional step people skip. If you are already running something, add it under Already Using Anything? The Builder then treats that compound’s slot as occupied and will not hand you a second compound doing the same job. Skipping this is the most common way to end up with a redundant stack.

Section Five

How the logic engine decides

The Builder does not populate a list of popular compounds. It scores every compound in the database against your specific inputs, and the order you see is the result.

What goes into the ranking

Pathway match. Does this compound act on the system your concerns pointed at? Anything that does not is excluded outright.
Priority weighting. Compounds serving your top-priority pathway outrank compounds serving your secondary one.
Experience fit. Compounds above your stated level are pushed down — pushed down, never removed.
Evidence preference. Your established-versus-newer setting tilts the order.
Body type. Endomorph, mesomorph and ectomorph each promote and demote different compounds, and this genuinely changes your primary driver.
Safety flags. Anything your own inputs contraindicate is sunk to the bottom and marked. Tick insulin resistance, for example, and GH secretagogues are steered away from automatically.
Established pairings. Combinations with a track record together are favoured over two compounds that merely both look good alone.

Why compounds appear in the order they do

The first compound in your Primary lane is your main driver — the one doing the bulk of the work on your top priority. Directly beneath your protocol you will see a Recommended pairing: the compound that best complements that driver for your level and build, weighted heavily toward combinations that are established together rather than merely compatible.

Everything below those is a genuine alternative, ranked. Nothing in the list is filler, and nothing is there because it is fashionable.

It validates — it does not just populate

This is the part most people miss. As you build, the engine is continuously checking for:

Two compounds hitting the same receptor family
Duplicate pathway targeting — a second compound that adds variables but not effect
A blend that already contains a compound you selected separately
Compounds your inputs flagged as a caution for you personally
Overall complexity, against whether you could still interpret the result

If a compound un-ticks itself when you tick another, that is not a fault. It is the redundancy check enforcing one-per-family. The Builder tells you exactly what it swapped and why, every single time — and you can always re-tick the original if you would rather keep that one. Nothing is lost.

Section Six

Choosing your experience level

Experience using peptides and knowledge about peptides are related — but they are not the same thing.

This is the single most misunderstood setting in the Builder, so it is worth being blunt about it.

You can have never used a peptide in your life and still have read deeply, understood the mechanisms, and worked through the reasoning in the book until it makes sense. If that is you, you are not a Beginner in the sense that matters here, and you should not feel obliged to select it.

Your level is a statement about how confident you are applying the book’s logic — not a count of how many compounds you have run.

Questions that will tell you

Have you previously used peptide protocols?
Do you understand how these compounds work — the mechanism, not just the effect?
Can you follow the reasoning in the book and see why one compound is chosen over another?
Do you prefer established compounds with long-term evidence behind them?
If you are drawn to a newer compound, can you articulate why — beyond it being newer?
If the Builder recommended something and you disagreed, could you say what you disagreed with?

Answer honestly rather than generously. Nobody sees this but you, and a level set too high mostly costs you the safeguards you would have benefited from.

The three levels

Beginner

Learning before optimising

Generally: little or no peptide experience, limited exposure to protocol design, prefers evidence-supported recommendations, wants guidance throughout.

The Builder:

Defaults to the strongest clinical evidence
Starts you with two compounds
Limits stacking and minimises variables
Prioritises safety and proven outcomes

Intermediate

Room to optimise

Generally: understands the compound categories, has used several, understands protocol timing and dose progression, wants moderate customisation.

The Builder:

Allows greater protocol flexibility
Starts you with three compounds
Introduces optimisation options
Still flags redundancy and still prefers the simpler protocol

Advanced

Full customisation

Generally: understands mechanisms of action and pathway manipulation, understands sequencing, comfortable evaluating newer compounds and the tradeoff between evidence and theoretical superiority.

The Builder:

Unlocks full customisation
Surfaces newer compounds readily
Permits overriding every default
Keeps validating and redundancy-checking regardless

Beginner mode is a feature, not a limitation. Simplifying the decision, leaning on clinically established compounds and holding back the complexity is the fastest route to knowing what a compound actually does for your body. That knowledge is the foundation everything else is built on, and there is no shortcut to it.

Advanced mode never turns off validation. It gives you more room inside the framework — not a version of the tool with the thinking removed. The redundancy checking is the part that protects you, and it runs at every level.

Nothing is locked at any level. Every compound in the database is selectable no matter what you select here. Your experience level shapes what the Builder offers first, not what you are permitted to choose.

Section Seven

Overriding the recommendations

Every recommendation the Builder makes is a default, not a rule.

The default recommendation reflects the most established clinical evidence — not necessarily the newest or potentially most effective option.

Those are different things, and conflating them is how people end up either dismissing the tool or following it blindly. Neither is what it is for.

A worked example

For metabolic pathway optimisation, a Beginner default leans toward semaglutide. Not because it is the most powerful option on the market, but because it currently has the longest clinical history and the strongest body of long-term evidence behind it. That is precisely what “default” means here.

An informed user who has read the framework and understands the tradeoff may deliberately choose retatrutide instead — newer, less long-term data, a different mechanism profile, and a genuinely different risk calculus. That is a legitimate decision when it is an informed one. The Builder will accept it, build the protocol around it, and carry on validating everything else.

The difference between those two users is not permission. It is whether they can explain the choice.

How to override in practice

Set your experience level honestly. It shapes what appears first.
Set your evidence preference. The two directions carry equal weight: Established evidence preferred moves the longest-studied compounds up your list, and Open to newer moves the emerging ones up by the same amount. Neither setting removes the other side — a well-evidenced compound is still offered to someone who asked for newer, because it is still frequently the right answer.
Tick whatever you want. Any compound, any lane. Nothing is locked.
Read the flag if one appears. A pick above your stated level is marked as an intentional override and the tradeoff is explained. It does not stop you and it is not an error message.
Keep watching the checks. Redundancy and simplicity checking run on your custom protocol exactly as they do on the default one.

The honest summary. The Builder’s defaults encode what the evidence best supports for someone in your position. Departing from them is a legitimate, sometimes better decision — made by someone who knows what they are departing from, and why.

Section Eight

Start to finish

What actually happens when you use it, in order.

Accept the terms. A one-time acknowledgement that this is educational, not medical advice.
About You. Sex, age, weight, body type, experience level and evidence preference. Body type is not cosmetic — it genuinely shifts which compound becomes your driver.
What’s Going On. Tick every concern that applies, in plain terms. You never have to know which system it belongs to; that translation is the Builder’s job.
Already Using Anything? Optional but valuable. Add your current compounds so the Builder builds around them.
Cycle. Duration and phase. This shapes the timing language in your brief, not the dosing.
Build My Protocol. You get a narrative explaining what it built and why, a sequencing note, a recommended pairing, any safety steers it applied on your behalf, and a pre-ticked starting protocol.
Refine. Ranked alternatives in every lane. Swap, add or remove, watching the simplicity reading as you go.
Confirm & Build Full Protocol Brief. The complete document: primary plan, support, adjuncts, confirmed pairings, timing framework, biomarkers and checkpoints, stop rules, and safety checks.
Save as PDF. A clean printable copy with none of the app furniture — worth taking to your clinician.

Stuck at the Build button? It stays greyed out until the required inputs are filled in. The panel directly beneath it lists exactly what is still missing.

Section Nine

Common questions

Why did a compound disappear when I selected another one?

Because the two occupy the same slot — one GHRH, one GHRP, one incretin, one IGF compound per cycle. The Builder swaps rather than stacking them, and tells you what it swapped and why. Re-tick the original if you would rather keep that one instead. Nothing is lost either way.

Why so few compounds? I expected more.

That is the book’s core principle in action. A short protocol is one you can learn from; a long one gives you a result you cannot attribute. If you want more, add them deliberately — but be able to say what each one is for.

I have never used peptides but I have read a great deal. Which level?

Choose the level that reflects your confidence applying the book’s logic, not your injection history. If you understand the mechanisms and can follow the reasoning, Intermediate or Advanced is a legitimate choice. See Section Six.

Can I use a compound the Builder did not recommend?

Yes. Nothing is locked at any level. If it sits above your stated experience level it will be flagged as an intentional override, with the tradeoff explained — but you will not be blocked. See Section Seven.

Where are the doses?

In the book. The Builder tells you which compounds and in what order; the amounts come from Targeted Peptide Systems. The Dosing Upgrade displays those same reference ranges inside the app, labelled Low / Moderate / High, with the tier matching your experience level highlighted as a starting point.

Does my body type really change anything?

Yes, materially. An endomorph and an ectomorph with identical concerns will often be given different primary drivers, and the Builder names the reason in your recommended-pairing note.

Is my information stored anywhere?

Your inputs stay in your browser. If you save a PDF you will be asked once for an email address, which is used for the newsletter and can be unsubscribed from in one click.

Can I use it on my phone?

Yes, and you can install it. On Android use the Install button; on iPhone or iPad tap Share, then Add to Home Screen. Installing matters on Apple devices: Safari clears stored data after seven days of not visiting a site, which can otherwise wipe a saved unlock code.

Ready

Education before optimisation

Simplicity before complexity. Evidence before novelty. Logic before stacking. The Builder is an intelligent implementation tool built on the educational foundation in the book — use them together.

Open the Protocol Builder Get the Book

Educational use only. The Protocol Builder does not provide medical advice, diagnosis or treatment, and many compounds referenced are research peptides not approved for these uses. Always consult a qualified healthcare professional before acting on any protocol.
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