Poids moléculaire des acides aminés - Réconcilier les terminaisons, Modifications et conventions de masse
Argireline Instant Peptide A sequence can be copied correctly while its calculated mass is wrong. The missing information is often at the ends: a free amino group or an acetylated nitrogen, a free carboxyl group or a terminal amide. For a student comparing a calculator result with a supplier certificate, these are structural differences that must be resolved before judging the arithmetic. An amino acid molecular weight table alone does not define the complete peptide.
This tutorial compares two accounting methods for the same neutral, linear peptide. Both assume ordinary peptide bonds, free amino and carboxyl termini, and no additional modifications unless specified. The teaching example is H-Gly-Ala-Lys-OH, abbreviated H-GAK-OH, with L configuration at its chiral amino acid centers. La glycine est achirale. H and OH here describe terminal groups; they are not extra histidine or sequence residues.
The result is a theoretical molecular mass, not a measurement of the material in a vial. Contre-ions, eau, solvant résiduel, impuretés, and incomplete dissolution require separate consideration when preparing a concentration. A correct calculation therefore answers a narrower question: what mass corresponds to this specified molecular composition?
Choose a mass definition before choosing the arithmetic
Monoisotopic mass uses specified isotopes, conventionally the most abundant isotope of each element for these common peptide compositions. Average mass uses isotope abundance weighted atomic masses. These conventions produce different numbers for the same molecule. Neither becomes correct merely because a spreadsheet displays more decimal places.
Mass in daltons describes a molecule. Molar mass in grams per mole describes an amount of substance and has essentially the same numerical value at the precision used here. Strictly, relative molecular mass is dimensionless, although “molecular weight” is often used informally for these related quantities. State which quantity and convention the number represents.
The residue inputs below come from the ExPASy FindMod mass table. Use its residue entries for G, A and K, rather than masses copied from free-amino-acid reagent labels. Keep the water term from the same table. A spreadsheet that combines free-amino-acid values with a residue-summation formula will count atoms twice even when every addition is numerically correct.
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| Composant | Monoisotopic mass, Et | Average mass, Et |
|---|---|---|
| Gly residue, G | 57.02146 | 57.0519 |
| Ala residue, UN | 71.03711 | 71.0788 |
| Lys residue, K | 128.09496 | 128.1741 |
| Water accounting term | 18.01056 | 18.01524 |
These are rounded tabulated inputs. The extra digits retained below make the calculation reproducible; they do not create additional physical precision. Use one consistent table and convention throughout, especially when comparing older calculators that may use slightly different atomic mass constants.
Two methods that must agree for the same free-ended peptide
Method one: sum residue masses and add one water. For the hypothetical H-GAK-OH molecule, the monoisotopic calculation is 57.02146 + 71.03711 + 128.09496 + 18.01056 = 274.16409 Et. The final water accounts for the atoms needed to complete the two free termini of this linear chain.
The average calculation is 57.0519 + 71.0788 + 128.1741 + 18.01524 = 274.32004 Et. The corresponding average molar mass is Palmitoyl Tripeptide 1 environ 274.32004 g/mol using these inputs. Adding a water for every residue would count terminal atoms repeatedly.
Method two: sum free amino acid masses and subtract bond waters. Derive each free amino acid mass from the same residue table by adding one water. The monoisotopic values are therefore 75.03202, 89.04767, et 146.10552 Et. Three free amino acids form two conventional peptide bonds, giving 310.18521 − 2 × 18.01056 = 274.16409 Et.
The average counterpart is 75.06714 + 89.09404 + 146.18934 − 2 × 18.01524 = 274.32004 Et. This is composition bookkeeping, not a claim that a particular synthetic reaction literally releases free water at every coupling step. Protected building blocks and activated intermediates have different reaction chemistry.
| Avantage | Limitation | Conditions applicables | Méthode de vérification |
|---|---|---|---|
| Residue summation gives a compact calculation with one terminal water term. | Fails if free amino acid values are mistaken for residue values or terminal chemistry is omitted. | A fully specified linear sequence with known modifications and a stated mass convention. | Recalculate using free amino acids and explicit bond accounting; inspect every terminal adjustment. |
| Free amino acid summation makes the number of condensation equivalents visible. | Requires correct bond counting and cannot treat branches or rings as an ordinary linear chain without changes. | The same free-ended target and same mass constants used by the residue method. | Confirm three residues, two backbone bonds, and agreement with the residue calculation. |
The two methods are complementary checks, not independent experimental evidence. They can agree while sharing the same wrongly transcribed sequence. Verify the molecular specification before celebrating matching totals.
Apply terminal modifications to a declared reference structure
Le Unimod acetyl record specifies a +42.010565 Da monoisotopic increment; c'est amidation record specifies −0.984016 Da. These are changes relative to a defined starting structure. Here the acetyl group is on the N-terminal nitrogen, leaving the lysine side-chain amino group unchanged, and amidation replaces the C-terminal free acid with a carboxamide. Specify those sites before using the increments. Biotinoyl Tripeptide 1
| Hypothetical target | Change from H-GAK-OH | Neutral monoisotopic mass, Et |
|---|---|---|
| H-GAK-OH | No modification | 274.16409 |
| Ac-GAK-OH | Acétylation N-terminale | 316.17466 |
| H-GAK-NH2 | Amidification C-terminale | 273.18007 |
| Ac-GAK-NH2 | Both specified terminal changes | 315.19064 |
The displayed results are rounded to five decimal places after adding the recorded increments. Average mass calculations require average increments, not these monoisotopic values. A mixed-convention total is inconsistent even if it happens to resemble a reported peak.
Separate a rounding difference from a structural difference. If a hypothetical deconvoluted neutral result were 274.16500 Et, its difference from the rounded GAK calculation would be 0.00091 Et, ou environ 3.32 parts per million of the calculated value. That arithmetic describes a relative discrepancy; it is not an acceptance limit. Whether the result supports an assignment depends on calibration, incertitude, peak selection and the analytical method.
Do not round each residue to an integer before summation and then assess the final answer at five decimal places. Information discarded in an early step cannot be restored by formatting the total. Inversement, disagreement in the last displayed digit can reflect different retained constants rather than a different molecule. Save unrounded working values when available and round once for the intended report.
A discrepancy table can list distinct hypotheses alongside their predicted effect: wrong terminal group, mixed mass convention, different ion charge, or an incomplete sequence. Eliminate them using the specification and spectrum metadata, rather than repeatedly changing calculator defaults until one number happens to match. A numerical match obtained through an unjustified assumption leaves the original identity question unresolved. Peptide Manufacturers Usa
Acetylation at the lysine side chain instead of the N terminus would give the same composition increment for one acetyl group. Intact mass alone cannot establish its location. De la même manière, changing an L residue to its D counterpart does not change elemental composition. A mass match cannot establish stereochemical identity.
For a cyclic or branched peptide, rebuild the accounting around the actual bonds and terminal groups. Do not apply the free-ended formula and then attach an informal “cyclic” label. The structural specification must identify what is connected to what, including whether cyclization consumes the termini or involves side chains.
Resolve a discrepancy before using the number
A useful discrepancy review starts with the reported quantity. Is the certificate listing neutral monoisotopic mass, average molecular mass, or a particular ion? Comparing an average neutral value directly with an isolated monoisotopic mass-to-charge peak introduces two differences at once. Resolve the convention and ion assignment before interpreting a residual difference as a chemical impurity.
Worked ion comparison. Assume, for arithmetic only, that H-GAK-OH produces a doubly protonated ion without other adducts. With the rounded ExPASy proton mass of 1.00728 Et, its predicted mass-to-charge ratio is (274.16409 + 2 × 1.00728) / 2 = 138.089325. The singly protonated alternative is 275.17137. Neither result means that a neutral peptide acquired an extra residue; the added protons and division by charge explain the difference.
For the corresponding doubly protonated amide, the prediction becomes (273.180074 + 2 × 1.00728) / 2 = 137.597317. Thus the acid-to-amide separation is about 0.492008 in mass-to-charge units at charge two, plutôt que 0.984016. A reviewer who applies the neutral increment directly to every charged peak can reject the correct structure. This example assumes the same charge and adduct type for both assignments; an unknown charge cannot be fixed by guessing the modification.
After assigning the ion, compare the written structures. For this tripeptide, verify three residues, the two terminal groups, and whether lysine is modified. An unexplained difference close to a known increment is a candidate explanation, not a site assignment. A positional acetyl isomer can have the same calculated mass while placing the group on a different nitrogen.
To close the discrepancy, state which explanation was checked against which record. An amended terminal specification resolves a different issue from a corrected ion assignment. Preserve the earlier result and the reason for the correction so that a later reviewer can follow the decision.
There is a different error when the calculated molecular mass is right but a stock concentration is wrong. Suppose a hypothetical powder contains associated counterion and water whose amounts have not been assigned. Entering the correct neutral mass in a concentration calculator does not remove their contribution to the weighed powder. Inversement, measuring peptide content does not resolve an unspecified terminal structure. The calculation and the material amount assignment need separate evidence.
Keep the discrepancy worksheet compact: declared structure, mass convention, neutral result, proposed ion formula, observed value, and remaining difference. Record intermediate numbers before rounding the final display. Another reviewer can then reproduce the comparison and see whether the unresolved issue concerns arithmetic, an ion assignment, or chemistry.
Questions fréquemment posées
Why do I add water when calculating a peptide from residue masses? Residue masses omit the atoms needed to complete the two free termini of a conventional linear peptide. One water restores that composition. Different terminal or ring chemistry requires an explicitly adjusted formula.
Does C-terminal amidation increase peptide mass? Relative to the corresponding free carboxyl terminus, ordinary amidation decreases monoisotopic mass by approximately 0.984016 Et. The reference structure matters; “adding an amide” is not a sufficient calculation instruction.
Can two differently modified peptides have the same mass? Oui. One acetyl group at different eligible sites can produce positional isomers with identical composition. Sequence isomers and stereoisomers can also share a mass. Additional structural evidence is needed.
Which value should I send to a technical team? Send the complete target description together with a clearly labeled neutral monoisotopic mass or average molar mass, as appropriate. Ask the team to confirm terminal groups and the measurement comparison rather than sending an unexplained number.
