Ordering a custom peptide

Custom synthesis quotations are cheap and fast to obtain, and that is part of the problem: two quotes for the same sequence can differ by a factor of five and both be honest, because they are quoting different products.

The sequence is the beginning, not the specification

“Ac-XXXX-NH₂, 95%, 10 mg” leaves at least a dozen decisions unstated. Each one is a line item in a real quotation, and each one can make the difference between material that works in your assay and material you cannot use.

Field	Why it changes the product	Example of a complete entry
Sequence	One-letter code, N→C direction, unambiguous residues	H-Ala-Gly-Ser-OH, written N to C
Length	Cost rises non-linearly with residues; coupling efficiency falls	State the residue count
N-terminus	Free amine, acetyl, biotin, fluorophore, fatty acid	Acetylated, or free amine
C-terminus	Free acid vs amide — a 1 Da difference that changes charge and stability	C-terminal amide
Non-natural residues	D-amino acids, β-amino acids, N-methylation, stapling	Specify position and stereochemistry
Labelling	FAM, FITC, biotin at a defined position, with or without a linker	Biotin at Lys⁵ via Ahx linker
Disulfides	Which cysteines pair; random oxidation gives a mixture	Cys²–Cys⁷, Cys⁴–Cys¹¹
Cyclisation	Head-to-tail, side-chain-to-side-chain, or lactam bridge	Head-to-tail cyclic
Scale	mg, g; affects purification method and price per mg	50 mg delivered
Purity	By HPLC area percent, with method stated	≥95% by RP-HPLC, 214 nm
Counter-ion	TFA or acetate; changes mass and assay compatibility	Acetate salt
Deliverable	Vial format, fill mass basis, documentation	10 mg × 5 vials, peptide basis stated

The specification annex article covers how to write these as testable limits in a purchase document — see writing a specification annex. This article is about the earlier step: deciding what you actually need.

Sequence features that drive difficulty

Suppliers price difficulty, not just length. The features below are the usual reasons a quote comes back high or with a longer lead time:

Hydrophobic stretches. Long runs of leucine, isoleucine, valine or phenylalanine aggregate on the resin and during cleavage, reducing coupling efficiency and complicating purification.
Multiple cysteines. Each disulfide pairing is a folding problem; four cysteines give three possible pairings, and the desired one may not be favoured.
Arginine-rich sequences. Guanidinium side chains interact strongly with resin and with purification media, and the peptide can be difficult to release from the column.
β-branched and sterically hindered residues (Val, Ile, Thr) slow coupling and increase deletion impurities.
Long proline runs and sequences prone to aspartimide formation during coupling.
Length beyond about 40–50 residues. Stepwise yield compounds: at 99% average coupling, a 50-mer is already at roughly 60% full-length before purification (0.99⁵⁰ ≈ 0.61).

That last arithmetic is worth internalising. It is not a supplier's limitation; it is the reason long sequences are quoted at a different order of magnitude, and why a fragment-condensation or native-ligation route may be proposed instead of straight solid-phase synthesis.

Purity grade: choose by use, not by prestige

Moving from 95% to 98% can double the price because it costs yield, not because the extra 3% is inherently expensive. Whether that trade is worth it depends on what the material is for:

Immunoassay or ELISA coating. Impurities can cross-react or raise background; a high grade is usually cheap insurance relative to the cost of the assay.
Analytical standards and method development. You need a well-characterised main peak and, often, a known impurity profile. Purity grade and full data matter more than mass.
Structural studies. Homogeneity matters; a mixture of diastereomers may not crystallise or may not give interpretable spectra.
Bulk screening or optimisation runs. A lower grade may be adequate if the readout is tolerant and the lot is characterised.

What purity grade cannot do is fix a wrong sequence. Area percent is silent on whether the main peak is the intended molecule; that requires mass confirmation. See mass spectrometry identity for what a mass match does and does not prove.

Scale and fill: the part buyers most often get wrong

“10 mg” is ambiguous in three independent ways:

Fill weight vs peptide content. A vial containing 10 mg of powder at 80% net peptide content contains 8 mg of peptide, and the salt and water make up the rest. If your assay is planned on peptide mass, the shortfall is 20%.
Per vial vs total. Five vials at 10 mg each is 50 mg; five vials totalling 10 mg is not.
Overfill vs exact fill. Some suppliers add a small overfill to compensate for handling loss; if you are calculating molarity from the label, overfill changes the concentration.

The arithmetic of net content is worked through in net peptide content and cost per mg. The practical rule: state the basis explicitly — “10 mg peptide content per vial, peptide basis, net content ≥80%” — and ask for the fill weight and the net content result on the certificate.

What to ask before accepting a quote

Is the quoted price per vial or per mg, and on which basis is the milligram defined?
What is the expected crude purity for this sequence, and what recovery from crude is assumed in the price?
Which counter-ion will be supplied, and is a residual TFA limit reported?
What is the expected lead time, and what part of it is synthesis versus purification versus QC?
Which analytical data accompany the batch — HPLC at which wavelength, MS by which ionisation mode, and are the raw traces included?
If the sequence proves difficult, will the supplier re-quote or deliver at a lower purity, and who decides?
Is the sequence treated as confidential, and is there a written undertaking?

That last item is not paranoia. Custom sequences are often the most valuable thing in the transaction, and a supplier who will not put confidentiality in writing is telling you something about how they handle information.

Red flags in a custom quote

Signal	What it usually means
A quote returned in minutes for a 40-mer with four cysteines	Template pricing, not a feasibility assessment
No question about disulfide pairing or terminus	The order will be made with default assumptions
“Purity 98%” with no method or wavelength	The number is not a measurement
Price far below every other quote with no explanation	Different scale, different grade, or a different (possibly resold) product
Refusal to provide a chromatogram before shipment	You are buying a promise, not a batch
Lead time quoted without a QC stage	Release testing may be nominal

A practical ordering sequence

Write the sequence in one-letter code with explicit N- and C-termini, and check the residue count yourself.
Compute the expected mass from residue masses plus terminal groups, and decide whether you expect the free or salt form. The arithmetic is in sequence notation and molecular weight.
Define the assay first. Concentration, solvent, plate type and readout determine the purity grade, the counter-ion and the quantity you need.
Request quotes with a fixed field list, so that the quotes are comparable.
Order a small qualification lot and test it in your own system before committing to bulk.
Write the acceptance criteria into the purchase order, including what happens if the batch fails.

Steps 1–3 cost an hour and prevent most of the expensive mistakes. The rest is procurement discipline, which the supplier checklist covers in more detail.

For laboratory research use only. This article describes procurement and analytical practice; it makes no claim about any specific compound and does not support administration to humans or animals.

Editor's take

A custom synthesis order is a specification exercise, not a shopping cart. The more precisely you define sequence, purity, salt and documentation, the fewer surprises arrive in the box.

Limitations

This is commercial due diligence guidance, not legal advice. Supplier claims must be verified against batch documents and, where required, an independent audit.