Educational guides and overviews on research peptides, what they are and how they're studied in the laboratory. For research use only.
Move the acyl group from a serine or threonine alpha-nitrogen onto its side-chain hydroxyl and the backbone loses a hydrogen-bond donor and gains a charge. The ester isomer survives cleavage and reversed-phase purification as its TFA salt; neutralise it and an O-to-N acyl shift restores the native chain. What the switch costs at the acyl donor's stereocentre, when it runs, and how it divides labour with pseudoprolines.
Read moreA branched lysine core multiplies copy number without a carrier protein, and the same near-identical arms that make it useful make the product hard to assay for purity. Divergent versus convergent assembly, the analytical workarounds, and what a multivalent binding number does and does not license.
Read moreWhat the backbone carbonyl stretch licenses you to conclude about a peptide's fold, why a beta component below about 1630 cm-1 reads as aggregation rather than native sheet, and where second-derivative and self-deconvolution treatments stop being trustworthy.
Read moreHow an electrospray charge-state envelope is turned into a mass, why deconvolution algorithms can emit harmonic peaks at half and a third of the true value over too wide a mass window, how sodium, potassium and trifluoroacetate reshape the envelope before the software ever sees it, and what a mass accurate to 1 ppm does and does not establish about a peptide's identity.
Read moreSequence coverage is a statement about your digest before it is a statement about your molecule. How protease choice, missed versus non-specific cleavage, and the deamidation, oxidation and carbamylation your own preparation introduces decide what a peptide map can claim - and why identity confirmation, coverage mapping and modification site assignment are three separate results.
Read moreA fibril has no solution spectrum and no diffraction-quality crystal. What magic-angle spinning and dipolar recoupling put back, how segmental, sparse, diluted and mixed labelling each answer a different question, how parallel in-register is told from antiparallel, and why the structure you obtain belongs to the preparation that produced it.
Read moreThe dye lights up when an aromatic groove holds its rings in the right electronic environment, on fibrils a groove spanning four consecutive beta-strands, which is why species without cross-beta architecture can be absent from the data rather than present at zero and why plateau heights compared across conditions are not a mass comparison. What the lag, growth and plateau phases actually contain, why global fitting across a concentration series is what recovers microscopic rate constants, and how agitation, read interval, surface area, the meniscus and dye concentration move the curve you are comparing.
Read moreDMF and NMP dominate solid-phase peptide synthesis because they swell the resin and dissolve everything else in the vessel. DMF's reprotoxic classification and its restriction under REACH turned that convenience into a liability. How the replacements are judged, and how much of the comparison is still single-laboratory.
Read moreUncaging quantum yields across the o-nitrobenzyl family span 0.1-1% to 0.53 depending on chromophore and leaving group, and the same chromophore lost three- to six-fold in photoconversion quantum yield moving from an amino acid derivative into a peptide. What governs release, what the nitroso by-product does to your readout, and which controls separate photochemistry from photodamage.
Read moreThe alpha-amino group sits about 2.4 pK units below a lysine epsilon-amine in model peptides - enough to bias an acylation, not enough to guarantee one. A working account of pH-controlled acylation, ketenes, PLP transamination, 2-pyridinecarboxaldehyde and the cysteine, serine/threonine, glycine and proline handles, with the proteolytic mapping that has to sit underneath the claim.
Read moreThe temperature ceiling of a freeze-drying cycle belongs to the formulation, not the dryer. What Tg′ and the collapse temperature each mean, why freezing and drying are separate stresses and how sugars are thought to protect against the second, why a crystallising bulking agent stops protecting, and why cake appearance is a weak proxy for what happened to the molecule.
Read moreWhy bioburden recovery has to be validated against the specific material rather than assumed, how a peptide can suppress the count of its own contaminants, what neutralisation must demonstrate, and why bioburden, sterility and endotoxin answer three different questions.
Read moreA computed pI is the root of an equation built from model-compound pKa values, and it carries a spread of a few tenths of a pH unit at best. This guide covers where that spread comes from, what isoelectric focusing and capillary IEF actually license you to conclude, and why the charge at your working pH — not the pI — is the number that bears on solubility, adsorption, ion-exchange retention and the electrospray charge envelope.
Read moreA leakage curve reports dequenching, not mechanism. How ANTS/DPX requenching and single-vesicle imaging separate graded from all-or-none release, why lipid composition and lipid-to-peptide ratio dominate the result, and which osmotic and dye artefacts produce signal with no membrane event behind them.
Read moreA solution SAXS measurement is one dimension of data. This is what Guinier, P(r), Porod and Kratky analysis extract from it, the point at which each stops being valid, and why a single ab initio envelope is a weak claim.
Read moreA digest can rearrange the very bonds it is meant to report. This is the assignment problem: the mass arithmetic that flags a linked peptide pair, the digestion conditions and enzyme choices that decide whether the answer survives sample preparation, the cases where no protease cuts between two cysteines, and the controls that separate a real scrambled species from one the method made.
Read moreResin substitution fixes the nominal batch size and every equivalent downstream of it, and the loading a sequence tolerates is capped by aggregation and other factors rather than by the resin specification. What changes when a solid-phase synthesis scales: substitution measurement, swelling and mass transfer, reagent excess, wash volume, and heat.
Read moreGetting ordered material out of a short, mobile, highly soluble peptide is a different problem from solving the structure. What each drop geometry controls, what a screening hit is, why racemic crystallisation changes the odds, and how to tell a peptide crystal from a salt crystal before beam time.
Read moreQ1B pins the illumination and ultraviolet energy targets and leaves the lamp, the container and the physical form to you. What the 1.2 million lux hour and 200 watt hour per square metre targets do and do not establish, why quinine actinometry is temperature- and position-dependent, how a dark control separates photolysis from thermal change, and which residues give which photoproducts.
Read moreAn extractables inventory lists what a material could release, not what a fill actually receives. This guide separates the forced-extraction measurement from the storage-condition one, works through solvent selection, uncertainty-factor-adjusted reporting thresholds and the GC-MS/LC-MS/ICP-MS split, then traces what elastomer and polymer leachables do to a peptide.
Read moreA de novo assignment claims that one residue order, and no other, explains a fragment spectrum. Which activation method gives which ion series, how a ladder is read and where it breaks, the isobars that survive any resolving power, why a de novo score is not an error rate, and what confirmation against a synthetic standard does and does not settle.
Read moreA MARTINI trajectory answers a narrow question well. What the 4-to-1 mapping buys in reach and costs in chemical detail, why the backbone bead's secondary structure is an input rather than a prediction, how large the encoding choice can make an aggregation score swing, why effective microseconds are not experimental microseconds, the documented over- and under-aggregation biases and the corrections aimed at them, and when a coarse-grained morphology has to be backmapped before it means anything.
Read moreAn immobilised peptide bait recovers weak motif interactions because it is presented at a high local concentration, and that same crowding can supply avidity. This guide covers anchoring direction and spacer, bait density, lysate and wash conditions, the sequence controls a beads-only channel cannot replace, on-bead versus eluted digestion, and the narrow claim an enrichment ratio supports.
Read moreA letter string fixes side chains and their order and nothing else. How IUPAC symbolism, controlled vocabularies and ProForma close the gaps left by direction, configuration, terminal state, cyclisation and disulfide pairing - and which free-text descriptions cannot be recovered.
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