Peptide sequence and molecular weight calculator
Type or paste a sequence to get its molecular formula, average and monoisotopic mass, the ions a mass spectrometer would see, net charge, isoelectric point, extinction coefficient and hydropathy. Masses are computed from the elemental formula, so they can be checked against any certificate of analysis. It describes a molecule; it is not a dosing tool.
Accepted: one-letter codes; hyphenated three-letter codes; Ac- and H- N-termini; -NH2 and -OH C-termini; D- prefixes; Nle, Orn, Aib, Abu, Hyp, Cit, Sar, β-Ala and pGlu. Lipid chains, PEG, other metals and unusual linkers are not supported. Atomic weights IUPAC 2021; pKa EMBOSS; extinction Pace 1995; hydropathy Kyte-Doolittle 1982.
Checked against our encyclopedia
The calculator was run on ten encyclopedia entries and compared with the formula and molecular weight each entry records. 6 of 10 agree; the others are logged as data to correct, not hidden. Where the formula matches but the weight does not, the recorded weight is inconsistent with its own formula.
| Entry | Calculated formula | Calculated mass | Recorded formula | Recorded weight | Result |
|---|---|---|---|---|---|
| angiotensin-ii | C50H71N13O12 | 1046.20 | C50H71N13O12 | 1046.18 | match |
| alpha-msh | C77H109N21O19S | 1664.91 | C77H109N21O19S | 1665.9 | weight differs |
| afamelanotide | C78H111N21O19 | 1646.87 | C78H111N21O19 | 1646.85 | match |
| argireline | C34H60N14O12S | 889.00 | C34H60N14O12S | 888.98 | match |
| bivalirudin | C98H138N24O33 | 2180.32 | C98H138N24O33 | 2180.29 | match |
| beta-endorphin | C158H251N39O46S | 3465.03 | C158H251N39O44S | 3465.0 | formula differs |
| amylin | C165H261N51O55S2 | 3903.33 | C165H261N51O55S2 | 3904.3 | weight differs |
| anp | C127H203N45O39S3 | 3080.48 | C127H203N45O39S3 | 3080.5 | match |
| acetyl-hexapeptide-37 | C22H35N7O8 | 525.56 | C24H38N8O9 | 582.61 | formula differs |
| bpc-157 | C62H98N16O22 | 1419.56 | C62H98N16O22 | 1419.55 | match |
Related: the COA Decoder uses these masses to check a certificate's mass spectrum, and what makes a peptide a peptide explains the 40-amino-acid line.
How the calculator works
Every amino acid in a peptide chain is a residue: the amino acid minus one molecule of water, which is lost when two amino acids join. The calculator stores each residue as a count of carbon, hydrogen, nitrogen, oxygen and sulphur atoms, adds them up, adds back one water for the two ends of the chain, then applies any changes you choose: an acetyl group on the start (Ac-), an amide on the end (-NH2), which swaps an oxygen for a nitrogen and a hydrogen, two hydrogens lost for each disulfide bond, or a copper ion replacing two hydrogens. The result is a molecular formula, and the masses come from that formula, not from a list of residue weights typed in by hand.
The average mass uses standard atomic weights, which reflect the natural mix of isotopes; it is the number to compare with a molecular weight on a label or in a database. The monoisotopic mass uses only the most abundant isotope of each element; it is what a high-resolution mass spectrometer measures for the lightest form of the molecule. The calculator also shows the singly and doubly protonated ions, [M+H]+ and [M+2H]2+, which are the peaks a certificate of analysis usually reports.
Charge, pI, extinction and GRAVY
Net charge at a chosen pH adds up the fraction of each acidic and basic group that carries a charge, using a standard set of pKa values; the isoelectric point is the pH at which that total is zero. These matter for how a peptide dissolves and behaves in solution, and different pKa sets give slightly different answers, so treat them as estimates. The extinction coefficient at 280 nm, built from tryptophan, tyrosine and disulfide contributions, lets a laboratory estimate concentration from absorbance; peptides without tryptophan or tyrosine absorb too little at 280 nm, so 205 or 214 nm methods are used instead. GRAVY, the grand average of hydropathy, is the mean Kyte-Doolittle score of the standard residues: positive values are more hydrophobic.
Salt forms and peptide content
Peptides made by solid-phase synthesis are usually sold as salts. Their positively charged groups pair with counter-ions such as trifluoroacetate (TFA), left over from purification, or acetate, after ion exchange. Those counter-ions add weight, so a vial labelled 10 mg of 'peptide' may contain noticeably less of the peptide itself. Choose a salt and the number of counter-ions per molecule (often the number of basic groups: the free N-terminus, lysines, arginines and histidines) and the calculator shows the salt-form weight and the share of it that is peptide. A genuine certificate of analysis should state the salt form and, ideally, the net peptide content measured by amino acid analysis or nitrogen content.
How we checked it
The browser calculator and the Python engine that builds this page share one set of element tables, and every build runs thirteen test sequences through both and refuses to publish if any result differs. We also ran ten encyclopedia entries through it and compared the result with the formula and molecular weight each entry records: 6 of 10 agree. The disagreements are listed on the page and logged for correction rather than hidden. Two are weights that do not match the entry's own formula; the others are a formula that does not match its sequence and a sequence that appears to be missing a residue.
The copper option assumes copper(II) binds by displacing two protons, the usual way peptide-copper complexes are written; some databases record GHK-Cu with one more hydrogen, so its weight here differs from our entry by about one unit.
What it does not do
It does not handle lipid chains (such as semaglutide's fatty-acid side chain), polyethylene glycol, metals other than copper, unusual linkers, or cyclisations other than disulfides; for those, use the formula in our encyclopedia entry. It describes a molecule's composition and properties; it does not tell you what is in a vial, how pure it is, or how much of anything to take. For checking a certificate's mass spectrum against these numbers, see the COA Decoder.
Sources
This explainer describes how the tool works and what its numbers rest on. It is not medical advice and does not recommend any dose or product.