What this peptide MW calculator does
This peptide molecular weight calculator estimates the mass of a peptide from its one-letter amino acid sequence. It supports both monoisotopic mass and average mass, plus two common terminal modifications: N-terminal acetylation and C-terminal amidation.
If you enter a charge state, the calculator also returns an estimated m/z value using the proton mass. That makes it useful for quick planning in LC-MS workflows, synthetic peptide ordering, and sequence verification tasks.
How peptide molecular weight is calculated
1) Sum the residue masses
Each amino acid contributes a residue mass in a peptide chain. The calculator sums the residues for all amino acids in your sequence.
2) Add terminal water
A peptide with free termini includes one molecule of water equivalent overall, so the formula adds H2O to the summed residue masses.
3) Apply optional modifications
- N-terminal acetylation: adds approximately +42.0106 Da (monoisotopic)
- C-terminal amidation: changes mass by approximately -0.9840 Da (monoisotopic)
4) Convert to m/z if a charge state is provided
For charge state z, m/z is calculated as:
m/z = (M + z × H+) / z
Monoisotopic vs average mass
Use monoisotopic mass when matching high-resolution mass spectrometry peaks. Use average mass for lower-resolution workflows or when comparing with references that report mean isotopic composition.
- Monoisotopic mass uses the lightest isotope of each atom.
- Average mass uses natural isotopic abundance-weighted values.
Input tips for best results
- Use only the 20 standard amino acids in one-letter format.
- Remove non-sequence characters such as numbers and punctuation.
- Double-check whether your experimental peptide includes terminal modifications.
- For MS planning, test expected charge states (1+, 2+, 3+, etc.).
Common use cases
Peptide synthesis and ordering
Confirm target peptide molecular weight before placing custom synthesis orders and before preparing QC acceptance criteria.
Mass spectrometry method setup
Estimate precursor m/z values quickly for targeted methods and expected ion detection windows.
Sequence sanity checks
Compare measured mass against calculated mass to catch sequence errors, truncations, or unexpected modifications.
Limitations to keep in mind
This tool is designed for fast estimation, not full proteomics annotation. It does not automatically account for:
- Non-standard amino acids (e.g., selenocysteine, pyroglutamate conversion)
- Side-chain modifications (phosphorylation, oxidation, glycosylation, etc.)
- Adducts (Na+, K+) and isotope envelope simulation
- Disulfide bond context across multiple chains
Quick example
Sequence: ACDE
Choose monoisotopic mode and charge state 1.
The calculator sums residue masses, adds water, and reports neutral MW plus [M+H]+ m/z.
Toggle terminal mods to see how the mass shifts instantly.
Bottom line
If you need a fast, practical peptide mass calculator for day-to-day lab work, this page gives you exactly that: sequence in, molecular weight out, with useful MS-ready m/z estimates.