Peptide molecular weight calculator: mass and formula

By Peptide Care Index · Updated October 2026

Use this peptide molecular weight calculator to turn an amino-acid sequence into average mass, monoisotopic mass, formula, and protonated-ion m/z. Choose the termini and bonds to match the molecule. Peptide Care Index’s reference pack provides 36 calculated cases with the formulas and constants needed to reproduce each result.

What should you check first?

• For linear GG with free termini, the calculated neutral mass is 132.11792 Da average or 132.05349 Da monoisotopic. The formula is C4H8N2O3; NIST lists the same formula and an average value of 132.1179.Copy stat, source and link
• A linear residue sum needs one water molecule: +18.01056 Da monoisotopic. This follows the ExPASy mass calculation rule and the NIST constants listed below.Copy stat, source and link
• One intramolecular disulfide removes two hydrogen atoms: −2.01565 Da monoisotopic, calculated from Unimod’s half-bridge composition. It is a different change from joining the two backbone ends.Copy stat, source and link

How do I use the peptide molecular weight calculator?

Enter the sequence, choose one-letter or three-letter notation, and set the known chemistry. The default is a linear chain with free termini and no disulfide bonds. The result is a theoretical mass for the molecule you describe.

One-letter example: PEPTIDE means Pro–Glu–Pro–Thr–Ile–Asp–Glu. Three-letter example: enter Pro-Glu-Pro-Thr-Ile-Asp-Glu in three-letter mode. Enter modifications with the controls, rather than typing them into the sequence.

How is peptide molecular weight calculated from a sequence?

For an unmodified linear peptide, add the residue masses and then add one water molecule. If you start with whole free amino acids instead, subtract one water molecule for each backbone peptide bond. Both routes give the same formula.1

A residue is an amino acid’s contribution inside the chain. The table below gives residue formulas, each equal to the free amino-acid formula minus H2O. Adding one H2O after summing those formulas supplies the free linear termini.

For a sequence with n residues:

Linear mass = sum of residue masses + mass of H2O

Or:

Linear mass = sum of free amino-acid masses − (n − 1) × mass of H2O

What does that look like for two glycines?

Two free glycines have the combined formula C4H10N2O4. Forming one peptide bond removes H2O, leaving GG = C4H8N2O3. Using the constants on this page gives 132.05349 Da monoisotopic, or 132.11792 Da average.

That formula and the rounded average value agree with the NIST glycylglycine record. Adding water to whole amino-acid masses would count the termini twice.

What is the difference between average and monoisotopic mass?

Average mass uses fixed atomic weights that account for naturally occurring isotopes. Monoisotopic mass uses one specified isotope of each element: 12C, 1H, 14N, 16O and 32S here. The two outputs describe different mass conventions, so they need not match.2

For free linear PEPTIDE, this model gives 799.82252 Da average and 799.35996 Da monoisotopic. Both use C34H53N7O15. The formula has not changed; the atomic constants have.

Atomic constants used in version PCI-PMASS-1.0

Sources: NIST isotope tables for C, H, N, O and S; Unimod’s fixed average constants. Checked October 14, 2026. Constants are published to reproduce calculations, not to promise that many digits of sample accuracy.

Why can another database show a slightly different average mass?

Check the formula and constant set before treating a difference as an error. For KPV, ChEBI lists C16H30N4O4 and 342.22671 Da monoisotopic, which match this calculation to five decimal places. It lists average mass 342.440, while this fixed average convention gives 342.43380.

That is a difference between reported average values with the same formula. This page publishes its constants so the result can be reproduced; it does not claim that every database uses them.

How do terminal changes and disulfide bonds affect peptide mass?

The selected chemical change alters the formula before the mass is calculated. N-terminal acetylation adds C2H2O; C-terminal amidation adds H and N and removes O. Each intramolecular disulfide removes two H atoms.3 4 5

Formula and mass changes relative to a free linear peptide

Sources: Unimod modification accessions 1, 2 and 374; head-to-tail change derived from one additional backbone condensation and the linear water rule. All masses recalculated using this page’s constants, October 14, 2026. The terminal water addition used to build the free linear formula is not a modification in this table.

Adding both terminal changes to PEPTIDE changes its formula from C34H53N7O15 to C36H56N8O15. Its monoisotopic neutral mass changes from 799.35996 to 840.38651 Da.

Does every cyclic peptide lose a water molecule?

No. The −18.01056 Da change here applies to joining a free N terminus to a free C terminus through an additional backbone amide bond. A disulfide ring uses the −2.01565 Da per bridge change instead. Other ring chemistries need their own atom changes.

For example, oxytocin has a C1–C6 disulfide and a C-terminal amide. Its ChEBI structure and formula are represented here by CYIQNCPLG, one disulfide and an amidated C terminus. Do not select head-to-tail cyclization for that structure.

Is peptide molecular mass the same as m/z?

No. Neutral molecular mass describes the molecule before protonation. For the protonated ion [M + zH]ᶻ⁺, add z proton masses to the neutral monoisotopic mass, then divide by the positive charge count z. These theoretical values do not predict which ions an instrument will observe.

m/z = (neutral monoisotopic mass + z × proton mass) ÷ z

The proton mass used here is 1.0072764665789 Da, from the 2022 CODATA table published by NIST. A proton is not a neutral hydrogen atom. Do not use 1.00782503223 in its place.

Theoretical protonated ions for free linear PEPTIDE

Source: Peptide Care Index calculation from C34H53N7O15, NIST isotope constants and the 2022 CODATA proton mass; October 14, 2026. These values exclude sodium, potassium and other adducts, fragments and isotope-envelope peaks.

What are the masses of the 20 standard amino-acid residues?

These are residue masses, not whole free amino-acid masses. Use them with the one-water rule for a free linear chain. Leucine and isoleucine have the same residue formula and mass; mass alone cannot distinguish them.

Standard amino-acid residue formulas and calculated masses

Source: residue formulas from the official Unimod XML, documented on its downloads page. Masses recalculated by Peptide Care Index using the constants above; checked October 14, 2026. Keep full constants for calculation rather than summing these rounded table values.

What reference examples can I use to check a calculation?

The download contains 36 calculated cases: 20 single free amino acids and 16 sequence or chemistry examples. The single-residue rows check the boundary case; they are amino acids, not peptides. Every case states the formula, termini, topology, disulfide count and mass convention.

Selected cases from the Peptide Care Index reference pack

Source: Peptide Care Index theoretical calculations, version PCI-PMASS-1.0, October 14, 2026; underlying formula and adjustment sources are listed in each CSV row. “Free” means a free N terminus and free C-terminal acid. GAG with a head-to-tail bond is a defined hypothetical structure, not a claim that it has been made or can be made readily.

Which outputs were checked against another reference?

• Glycine: formula C2H5NO2 and average 75.0666 match the NIST record.
• Glycylglycine: formula C4H8N2O3 and average 132.1179, rounded to four places, match NIST.
• KPV: formula C16H30N4O4 and monoisotopic 342.22671, rounded to five places, match ChEBI.
• Oxytocin: formula C43H66N12O12S2 and monoisotopic 1006.43646, rounded to five places, match ChEBI.

ChEBI reports average oxytocin mass 1007.207; this calculator’s fixed average constants give 1007.18734. As with KPV, compare the constant sets before comparing the average outputs. These are reference cross-checks, not laboratory tests or a clinical review.

Does the result include acetate, TFA, water or product purity?

No. The output covers the neutral peptide formula and the selected supported changes. It excludes counterions such as acetate and trifluoroacetate, water of hydration and other material in a sample. A sequence alone does not tell you their amounts.

It also excludes isotope labels, nonstandard residues, side-chain modifications, lipids, glycans, metal complexes, intermolecular disulfides and ring chemistries other than the supported intramolecular disulfides or head-to-tail backbone bond. A modified drug or a product name may need more information than its base amino-acid sequence.

The calculated mass does not establish a sample’s identity, sequence order, purity, peptide content, effect or safety. Two different sequences can have the same elemental formula. The number also does not give a dose or tell you how to use a product.

If you are checking an advertised service, use the provider and formulation questions to clarify the exact product. For payment terms, the published provider comparison answers a separate question from molecular mass.

How was this reference pack built?

We extracted the 20 supported residue formulas from the official Unimod XML and read its modification records. We calculated each final molecular formula, then applied the NIST isotope constants and the fixed Unimod average weights shown above. The reference pack was prepared and the sources were checked on October 14, 2026.

For linear molecules we added H2O once to the residue sum. We applied caps and disulfides as atom changes, and treated head-to-tail cyclization separately. Protonated-ion calculations used the 2022 CODATA proton mass. We kept full precision until formatting the outputs.

To reproduce a row, sum its sequence’s residue atom counts, apply the stated chemistry, and multiply the final counts by the appropriate atomic constants. The CSV includes the final atom counts and both mass outputs, so the sequence route and the final-formula route can be checked separately.

All 36 mass cases were recomputed by both routes. The four independent reference checks above cover selected formulas and rounded outputs; they do not independently validate every case. The 24 input fixtures define required calculator behavior. They do not represent completed browser tests.

AI tools assisted with source retrieval, drafting, calculations and editorial checks. No named chemist or clinical reviewer is credited for this release. Our editorial standards explain authorship and corrections.

Version 1.0 — October 14, 2026: First reference pack: 20 residues, 36 calculation cases and 24 input-validation fixtures, with fixed constants and explicit chemistry.

How can I cite the calculator or a result?

Use the page title, model version, check date and permanent URL. For a particular result, also record the sequence, termini, topology, disulfides and whether the number is average mass, monoisotopic mass or m/z.

Reference citation

Peptide Care Index. Peptide molecular weight calculator: mass and formula. Calculation reference version PCI-PMASS-1.0; sources checked October 14, 2026. https://peptidecareindex.com/research/peptide-molecular-weight-calculator/

Example methods sentence

“Theoretical neutral monoisotopic mass for PEPTIDE with free linear termini and no disulfides was calculated as 799.35996 Da using Peptide Care Index’s PCI-PMASS-1.0 reference model and its stated NIST isotope constants.”

You may reuse Peptide Care Index’s original calculations and explanatory text with credit to Peptide Care Index; underlying source material remains subject to its source attribution and terms.

Can I download the formulas and reference results?

Yes. The files are free to download, with no account or email gate. They keep source URLs, check dates and the model version beside the data. The reference values are calculated targets, not measurements from peptide samples.

• 36 formula and mass reference cases
• 20 amino-acid residue formulas and masses
• Atomic constants
• Proton constant
• Terminal, disulfide and backbone adjustments
• 24 input-validation fixtures

For evidence about what a peptide has been studied for, use the peptide comparison chart. A calculated mass and evidence of an effect answer different questions.

What else should I know before using a peptide mass result?

Can I paste one-letter codes, three-letter codes or FASTA?

Yes: choose the matching notation mode. GG and Gly-Gly describe the same sequence in their respective modes. A single FASTA record works in one-letter mode; multiple records are rejected so separate chains are not joined by mistake.

Why does ALA give a different answer from Ala?

In one-letter mode, ALA means three residues: alanine–leucine–alanine. In three-letter mode, Ala means one alanine. The calculator shows the normalized sequence and count so you can check which molecule you entered.

Can I enter B, X, Z, U, O or an unusual amino acid?

This version supports the 20 residues in the table. It rejects ambiguous codes and unsupported residues rather than guessing their masses or deleting them. Use a tool that explicitly supports the required structure for selenocysteine, pyrrolysine, labels or other unusual residues.

Can the calculator infer disulfide bonds from cysteine count?

No. Two cysteines allow at most one intramolecular disulfide in this model, but they do not prove that the bond is present. Enter the known count; an impossible count produces an error. Bond placement requires structural information beyond a count.

Does a matching mass prove that a peptide is genuine?

No. Leucine and isoleucine have the same formula and mass, and changing sequence order can leave the elemental formula unchanged. This tool calculates from a supplied description; it does not test a sample or establish its identity or purity.

Which sources support the formulas and constants?

Sources checked October 14, 2026. Database entries and constant sets are named so later versions can be compared.

1. SIB ExPASy. Compute pI/Mw documentation. Residue-mass sum plus one water molecule; modification limits of that tool.
2. Unimod. Symbols and mass values, downloads documentation and original XML. Residue formulas, fixed average constants and mass conventions.
3. Unimod accession 1. Acetylation. Formula delta C2H2O.
4. Unimod accession 2. Amidation. Formula delta H +N −O.
5. Unimod accession 374. Half of a disulfide bridge. One H removed per cysteine half-bridge; two per intact bridge.
6. NIST. Atomic Weights and Isotopic Compositions: hydrogen, carbon, nitrogen, oxygen, sulfur.
7. NIST. 2022 CODATA complete constants table. Proton mass in unified atomic mass units.
8. NIST Chemistry WebBook. Glycine and N-glycylglycine. Independent formula and rounded average checks.
9. EMBL-EBI ChEBI. Lys-Pro-Val, CHEBI:160254. Formula and monoisotopic check; separate reported average value.
10. EMBL-EBI ChEBI. Oxytocin, CHEBI:7872. Structure, formula and monoisotopic check; separate reported average value.

Peptide Care Index Research is the research and reference section of peptidecareindex.com.