Details up front: hydrolysis · minus 80 °C.
I can predict the outcome but I cannot explain it, which means I will get the next case wrong.
I would like to know how confident the field actually is about this.
Can someone derive this rather than assert it?
Because temperature enters the rate constant through an exponential, so equal steps in temperature multiply the rate instead of adding to it. Arrhenius puts the rate proportional to exp(−Ea/RT); the working approximation is a doubling per 10 K, which takes 5, 15, 25 and 35 °C to multipliers of 1, 2, 4 and 8. The steps in temperature are equal and the steps in rate are not, and that is the whole of the observation. At minus 80 °C the same rule gives no useful multiplier at all, because below freezing the reaction is no longer happening in bulk solution. Backbone amide bonds cleave, so every product is shorter than the parent and the mass ladder they leave behind is the evidence that it happened. Ea differs by route, so the ranking of routes changes with temperature too — which is why accelerated data extrapolates badly and why nobody should read a 40 °C study as a fast version of a 5 °C one.
Asparagine and glutamine are the deamidation risk, and methionine is the oxidation risk.
Hydrolysis cleaves the backbone, most readily at aspartate-proline and aspartate-glycine sequences, and is acid-catalysed. In a dry solid it barely proceeds at all.
A mass spectrum resolves most of this: minus eighteen is dehydration or succinimide, plus one is deamidation, plus sixteen is oxidation, and an unchanged mass with a shifted retention time is an isomer.
Deamidation via the succinimide intermediate is well characterised, with sequence-dependent rates highest for asparagine-glycine motifs.
The caveat is that none of these pathways can be seen by looking at a vial, and a clear solution can be substantially degraded.
Cold, dry, dark, still. Those four words cover most of the mitigation.
Analytical standards and reagents with traceable certificates. Every quantitative result you read inherits the accuracy of the standard behind it.
Shop standardsThe relevant point is that a mass shift of plus one dalton is deamidation and plus sixteen is oxidation, so degradation is often visible in a mass spectrum if anyone looks.
Adsorption onto glass and plastic is significant at low concentrations — micrograms per millilitre — and negligible at milligrams per millilitre. It is the usual explanation for an apparent loss in a dilute preparation.
Oxidation targets methionine, cysteine and tryptophan, adding sixteen daltons per oxygen. It is catalysed by trace metals and promoted by dissolved oxygen and by light.
Apparent loss in a dilute preparation is usually adsorption rather than degradation and is worth ruling out first.
Swirl, never shake. Aggregation is a handling problem more than a time problem.
edited 22 Jul 2024 by marta_okonkwo — tightened the wording; no substantive change
Answer first: the degradation pathways worth knowing are hydrolysis, deamidation, oxidation, aggregation and adsorption, and each has a different trigger and a different mitigation.
Light exposure matters for tryptophan-containing sequences and for anything with a chromophore. Amber vials and a closed box are free mitigations.
Aggregation is physical: peptides unfold at air-liquid interfaces and associate. Shaking maximises that interface, which is why swirling and shaking produce visibly different outcomes on the same vial.
Aggregation at air-liquid interfaces is established from surface-tension and particle-count studies and is the basis for anti-agitation handling guidance.
At dilute concentrations, suspect adsorption before you suspect chemistry.
Aggregation is a physical process and is the one most often caused by handling rather than by time.
Deamidation converts asparagine or glutamine to the corresponding acid via a succinimide intermediate, adding one dalton. It is base-catalysed, accelerates above neutral pH and is the dominant aqueous pathway for many peptides.
Sequence determines which pathways apply, so general statements are general.
Sequence decides which pathways are even available. Check the residues.
Ask PeptideStack is a static archive. Posting is closed, but the norms are worth stating: answer the question that was asked, show your working, cite the trial or the certificate, and say plainly where the evidence runs out.