Scientific lookup tool Peptide Sequence Database

Educational resource

Molecular weight calculations

The molecular weight on each compound record is the value reported by the cited public source — typically the average (chemical) mass of the free-base peptide, not a salt or hydrate. This page explains how that number relates to sequence so you can spot inconsistencies and avoid mixing incompatible conventions.

Unmodified linear peptide

Using average residue masses mi and water ≈ 18.015 g·mol−1:

MW ≈ Σ mi + 18.015

Equivalently: sum the free amino-acid average masses and subtract 18.015 × (n − 1) for the waters lost in forming n − 1 peptide bonds.

Worked outline for a simple free-acid peptide:

  1. Count residues n from the sequence.
  2. Sum residue masses (or free AA masses − waters).
  3. Confirm no disulfide, amide, pyroglutamate, or lipid corrections are required.
  4. Compare to the recorded MW and formula.

C-terminal amide

Relative to the free carboxylic acid, amidation replaces OH with NH2. Average ΔMW ≈ −0.984 Da. Apply this after the linear-peptide sum. Omitting the correction is a common source of ~1 Da discrepancies.

Disulfides

Each cystine bridge is an oxidation that removes two hydrogen atoms: ΔMW ≈ −2.016 Da per disulfide. Insulin has three disulfides; somatostatin-14 has one. Residue count does not change.

N-terminal pyroglutamate

Cyclization of N-terminal Gln loses water (ΔMW ≈ −18.015 Da versus Gln). If the 1-letter sequence already writes a stand-in E/Q, do not subtract water twice. Prefer the recorded formula when display notation shows pGlu.

Lipidation and non-canonical residues

Palmitoyl-γ-Glu on liraglutide, the C18 diacid linker on semaglutide, Aib, MeBmt, ornithine, and amino alcohols have elemental compositions outside the twenty-letter alphabet. They cannot be recovered from a naïve residue-mass table. Use the recorded molecular formula and molecular weight; treat the 1-letter string as an index for search, not as a complete mass-spec calculator input.

Monoisotopic versus average mass

High-resolution proteomics usually reports monoisotopic masses (often as [M+H]+). Pharmacopeial entries and many PubChem compound pages list average mass. Records in this database follow the source’s average mass unless a note says otherwise. Do not expect six-decimal agreement between a monoisotopic calculator and an average-mass record.

Salts, hydrates, and CAS identity

CAS Registry Numbers sometimes refer to acetates, hydrochlorides, or hydrates (for example octreotide acetate or desmopressin acetate). This tool stores the peptide free-base formula unless the title or notes say otherwise. Always open the cited CAS Common Chemistry or PubChem page before using a mass for quantitative analytical work.

Practical verification

  1. Read display notation for termini and adducts.
  2. Count disulfides and apply −2.016 Da each if recalculating.
  3. Decide whether you are comparing average or monoisotopic mass.
  4. Confirm the registry entry matches free base versus salt.