Crude, Desalted and >95%: Only One Is a Purity Specification

“Crude”, “desalted” and “>95%” describe three different things, and only one of them is a purity specification. Reading them as points on a single scale is the most common misunderstanding about how peptides are supplied.

What comes off the resin

At the end of a synthesis, cleavage releases the peptide from the solid support and strips its protecting groups in one operation. What is recovered is a mixture: the target sequence, plus deletion and truncation sequences from every coupling that did not go to completion, plus incompletely deprotected species, plus oxidation products, plus the scavengers and their adducts, plus the cleavage acid.

The proportion of target in that mixture depends almost entirely on length. A short sequence assembled cleanly can emerge at 70–90%. A long or difficult one can emerge below 50%. The arithmetic behind that is in the solid-phase synthesis cycle.

Crude

Crude peptide is that mixture, precipitated and dried, with no chromatographic purification. It is the cheapest form and the fastest to produce.

The critical point: **crude is a process description, not a purity figure.** Two crude preparations of two different sequences can differ by forty percentage points in actual purity, and neither is mislabelled. A crude preparation should still carry a measured purity figure; without one, the word tells you only what was *not* done to it.

Desalted

Desalting passes the crude material through a short column, or a solid-phase extraction cartridge, to remove salts, scavengers and small-molecule reaction residues. It is a separation by size and gross polarity, not a purification of the peptide from its own related impurities.

**A desalted peptide is not a purified peptide.** Deletion sequences, truncations and oxidised species are chemically very similar to the target and travel with it through a desalting step. What changes is the removal of things that are not peptide at all.

The value is real but narrow: cleaner handling, less interference in downstream measurements, a more accurate mass on the balance. The purity figure barely moves.

Purified to a stated percentage

This is the one that is a specification. The crude material is separated by preparative reversed-phase chromatography, fractions are collected, the ones meeting the target are pooled, and the pool is lyophilised.

Common grades are >95% and >98%, and occasionally >99%. Each step up costs disproportionately more, for a straightforward reason: the impurities hardest to remove are the ones closest to the target in the separation — a single deletion, an oxidation, an isomer — so the final few percent requires either a much shallower gradient, a second orthogonal purification, or the acceptance of a much lower yield.

The yield arithmetic, which is what drives the price

Purification discards material. Fractions at the edges of the peak contain the target mixed with the species eluting nearest to it, and collecting them raises yield while lowering purity. Narrowing the collection window raises purity and lowers yield.

So a >98% preparation is not simply a >95% preparation with an extra step. It is frequently a preparation where a substantially larger fraction of the synthesised material was thrown away. That, rather than machine time, is the dominant cost difference between the grades.

The specification is incomplete without its method

A grade of >95% means 95% by some measurement, and that measurement has a wavelength, a gradient, a column and a run length. The same material can carry different figures under different methods without anyone being wrong, for the reasons set out in what “98% by HPLC” is a percentage of and why certificates disagree on purity.

A grade with no method behind it is a claim about a number, not a measurement.

What none of the grades tell you

All three describe **chromatographic** purity, which is the proportion of the eluting, absorbing material that is the target. None of them addresses:

• Net peptide content — how much of the weighed solid is peptide rather than counter-ion and water. A 98% pure peptide can be 75% peptide by mass.
• Stereochemistry — a D-for-L substitution is invisible to the separation and to the mass.
• Co-eluting species — anything hiding under the main peak is counted as main peak.
• Elemental impurities, residual solvents, endotoxin — outside the measurement entirely.

Choosing a grade honestly

The correct grade is the one the intended measurement requires, and higher is not automatically better value. A structural or analytical comparison against a reference standard needs a high-purity preparation because impurities interfere directly. A method-development exercise, or work where the peptide is a reagent rather than the subject, is often perfectly served by crude or desalted material at a fraction of the cost.

What matters in every case is that the document states which of the three it is, and — for the third — reports the measured figure with the method that produced it.