Five things a purity figure cannot tell you

The reason it matters is that co-elution is the failure mode a single method cannot detect. A chromatogram showing one sharp, symmetrical peak and a purity of 99.3 per cent is consistent with a clean preparation and equally consistent with a preparation in which a related species elutes under the parent. Peak-purity assessment from a diode-array detector helps and is not conclusive. A second separation on a different principle is the practical answer, and it is cheap: the sample is already in the vial, the second run costs instrument time.

Mobile phase, additive and the ion-pairing question

The standard peptide mobile phase is water and acetonitrile with an acidic additive, and the choice of additive has consequences beyond pH. Trifluoroacetic acid at around a tenth of a per cent is the classical choice because it is an effective ion-pairing agent: it associates with basic residues, masks their charge, and produces markedly sharper and better-retained peaks than a simple pH adjustment achieves. For a difficult peptide separation the improvement is substantial.

It has two costs. Trifluoroacetate suppresses ionisation in electrospray mass spectrometry, which means a method optimised for chromatographic performance is frequently unsuitable for identity confirmation on the same run; formic acid is the usual compromise, giving worse peak shape and a usable mass spectrum. And residual trifluoroacetate from purification persists as a counter-ion, contributing mass to the vial and confounding content calculations, which is a manufacturing rather than an analytical issue but originates in the same chemistry.

Acetonitrile is preferred over methanol for peptide work on two grounds: lower viscosity, which means lower backpressure at a given flow, and lower ultraviolet absorbance at the short wavelengths peptide detection requires. Methanol’s absorbance in that region raises the baseline and degrades the signal-to-noise ratio exactly where the small impurity peaks are. A method reading at two hundred and fourteen nanometres in a methanol gradient is fighting its own solvent.

Equal area is not equal mass

Area per cent contains an assumption that is almost never stated: that each species contributes detector signal in proportion to its mass, at the same rate as the parent. In ultraviolet detection that requires equal absorptivity per unit mass, and peptide impurities frequently do not oblige. A truncated fragment missing several amide bonds absorbs less at two hundred and fourteen nanometres per unit mass than the parent; a fragment missing a tryptophan absorbs dramatically less at two hundred and eighty. An oxidation product may absorb slightly more.

The direction of the resulting error is not fixed, which is what makes it awkward. Where impurities under-respond, area per cent overstates purity. Where they over-respond, it understates it. Regulated pharmaceutical practice addresses this by determining relative response factors for known impurities and applying correction factors, or by using an alternative detection principle with a more nearly uniform response — charged aerosol detection and mass-based approaches both aim at this.

Nothing in this market applies correction factors, and it would be unreasonable to expect it, since doing so requires isolated impurity standards. What is reasonable is that the assumption be visible. A purity figure is an area ratio, area ratios approximate mass ratios, and the approximation has not been quantified for the sample in question. Two sentences on a certificate would say so, and would make the number more useful rather than less.¹

Reference standards, and what a retention time proves

A reference standard is material of established identity, purity and content against which an analysis is calibrated. Compendial standards are characterised by collaborative study and supplied with a certificate stating their assigned content. In-house standards are qualified against a compendial standard where one exists, or characterised by a battery of orthogonal methods where one does not. For most research peptides there is no compendial standard, which means every claim of identity or assay in this market ultimately rests on somebody’s in-house material.

What a matched retention time supports is worth stating precisely: it supports the inference that the sample and the standard behave identically in this separation. That is real evidence of consistency between two materials. It is not identification, because retention time is not unique — deletion sequences, epimers and unrelated compounds of similar hydrophobicity can share a retention window, and the peak width of a peptide separation is wide enough to hide a great deal.

Two consequences follow for reading a certificate. A report stating that identity was confirmed by comparison of retention time with a reference standard has told you about consistency, not identity. And a purity figure quoted as an assay — a percentage of label claim — requires a quantitative standard of known content, which is a much stronger claim than area per cent and should be labelled differently. The two are routinely printed in the same field.²

Mass spectrometry, and the limits of a matching mass

Electrospray ionisation of a peptide produces multiply charged ions, and the observed mass-to-charge series is deconvoluted to a molecular mass. Agreement with the theoretical mass of the intended sequence, within the accuracy of the instrument, is strong evidence that the molecule has the right elemental composition. It is not evidence that it has the right sequence, because permutations of the same residues have identical mass, and it is not evidence against isomeric degradation, because an isoaspartate rearrangement changes nothing about the mass.

Fragmentation closes most of that gap. Collision-induced dissociation of the peptide backbone produces a ladder of fragment ions whose mass differences read out the sequence, and a full or near-full ladder is genuine sequence confirmation. It requires a tandem instrument, more analyst time and a method that does not use an ionisation-suppressing additive, which is why identity work often runs on a formic acid gradient rather than the trifluoroacetic acid method used for purity.

The practical reading of a certificate follows. Identity confirmed by mass means the elemental composition matches. Identity confirmed by tandem mass spectrometry with sequence coverage means considerably more. Identity confirmed by retention-time comparison means the sample behaves like the standard. Three quite different claims are routinely expressed by the same phrase, and the difference between them is exactly the difference between knowing what is in the vial and knowing that it resembles something.³

The second method, and what makes it orthogonal

Orthogonality is not a synonym for repetition. Two runs of the same method differ only in random variation. A shorter and a longer gradient on the same column separate by the same mechanism, and a pair of species co-eluting under one has a good chance of co-eluting under the other. Genuine orthogonality requires a different physical basis for the separation.

For peptides the practical options are well established. Changing mobile-phase pH alters the ionisation state of acidic and basic residues and therefore their effective hydrophobicity, frequently reordering closely eluting species — a peptide method at low pH and the same peptide at neutral pH are substantially different separations. Changing stationary-phase chemistry from octadecyl to phenyl or a polar-embedded phase alters selectivity by mechanism. Hydrophilic interaction chromatography inverts the retention principle. Ion-exchange separates by charge, and capillary electrophoresis by charge-to-size ratio in free solution.

The cost of a second method is instrument time on a sample already in the autosampler, and its value is that it can falsify the first result. Where the two agree, confidence rises substantially. Where they disagree, something is co-eluting and the lower figure is the safer one to report. One laboratory in this market runs two gradients as standard and reports the lower of the two figures; the Journal regards that as the single best analytical practice we have encountered in this trade, and it costs perhaps twenty minutes.⁴

Five things a purity figure cannot tell you

First, how much peptide is in the vial. Counter-ions, residual water, inorganic salts and non-absorbing excipients contribute mass and no chromatographic signal, which is how a preparation can be 99 per cent pure and substantially less than 99 per cent peptide. Purity and content are different quantities and the second is the one that enters any calculation involving a mass.

Second, whether anything is aggregated. Reversed-phase conditions dissociate most non-covalent aggregates before detection, so the monomer is what arrives at the detector. Only a size-based separation reports high molecular weight species.

Third, whether the sequence is correct. Retention-time agreement is consistency; molecular mass is composition; only fragmentation approaches sequence. Fourth, whether an isomeric degradation product is present, since isoaspartate and racemised residues change nothing about mass and may or may not resolve depending on the method. Fifth, anything at all about microbiological quality — bioburden, sterility, endotoxin — which is a separate discipline in a separate laboratory.

Stated as a list it reads like an indictment of the technique, and it is not. Reversed-phase chromatography answers its own question superbly. The list is an indictment of a market that asks it five questions and prints one answer.

A note on method and sourcing

The compendial and regulatory material in this piece is taken from the current general chapters on chromatography and on validation of compendial procedures, from the European Pharmacopoeia chapters on liquid chromatography and on chromatographic separation techniques, and from the harmonised guidelines on analytical validation, on impurities and on specifications for biotechnological products, all read in the original. The separation science is drawn from the chromatography literature, with the peptide-specific behaviour cited where it differs from small-molecule practice.

Where the Journal reports a number it obtained, it states the number of vials, the number of laboratories, whether the vials came from one lot, whether the laboratories knew, and what method parameters were disclosed to us. Where we quote a figure from a certificate we state whether the method was disclosed on it. Where a laboratory or a company answered our questions we distinguish an answer from a refusal and a refusal from a non-response.

Nothing in this department is a recommendation to buy, use or avoid anything. The compounds referred to are sold for research use only and are not approved for human use in any jurisdiction. Corrections and disputes go to standards@compoundjournal.com. Readers with certificates or chromatograms they would like read should write to letters@compoundjournal.com; we do not identify the source of anything sent to us, and we do not publish a reader’s name without permission.

The technique is not on trial here and never was. Reversed-phase chromatography can resolve species differing by a single methyl group, and the laboratories running it for this market are, on the evidence we have gathered, largely competent and entirely willing to describe what they did when somebody asks. What is on trial is a document format that omits the four values needed to compare one figure with another.