What Is a Peptide Mass Calculator?
A peptide mass calculator helps researchers, chemists, and biologists determine the molecular weight of a peptide based on its amino acid sequence. By inputting a protein or peptide sequence (using single-letter amino acid codes), you'll get precise mass values that support experimental planning for mass spectrometry, HPLC prep, or synthetic peptide design.
You can also estimate the isoelectric point (pI), identify fragment masses from enzyme digests (like Trypsin), and factor in PTMs like oxidation, phosphorylation, or acetylation. Note that pI calculations are simplified estimates - for precise values, consider using specialized pI calculators.
Features
Monoisotopic & Average Mass Calculation
Choose between highly accurate monoisotopic mass or the average mass for broader calculations. Includes pI estimation based on amino acid composition.
Enzymatic Digestion Simulation
Select an enzyme (Trypsin, Chymotrypsin, etc.) to simulate digestion and view fragment peptide masses.
Supports Post-Translational Modifications (PTMs)
Add modifications like phosphorylation, acetylation, methylation, and oxidation directly into your sequence (e.g., M(Oxidation)).
Custom Sequence Input
Paste any sequence in single-letter code or use a UniProtKB ID (e.g., ALBU_HUMAN or P04406) to auto-load known protein data.
Charge State Simulation
View m/z values for peptides in different ionization states ([M+H]+, [M+2H]2+, [M+3H]3+, etc). Also provides pI estimation.
Internal Modifications and Cysteine Handling
Choose between free cysteines, CAM modifications, or acrylamide adducts. Control methionine oxidation settings too.
Common Use Cases
- Mass spectrometry sample prep
- Peptide synthesis validation
- Protein digestion planning
- Post-translational modification tracking
- Academic and pharma research
Whether you're checking the mass of a short peptide or mapping fragments from a full-length protein, this tool gives you everything you need in seconds.
Frequently Asked Questions
Q: What's the difference between monoisotopic and average mass?
A: Monoisotopic mass uses the exact mass of the most common isotopes. Average mass uses the weighted average of all isotopes — it's more generalized but less precise for MS.
Q: Can I simulate Trypsin digestion on a UniProt protein?
A: Yes, just enter the UniProt ID (like P04406), select Trypsin, and click calculate.
Q: Can I use oxidized methionines or modified cysteines?
A: Absolutely. You can define changes to the sequence manually or by enabling toggles in the modification settings section.
Q: What format should I use for PTMs?
A: Use single-letter code with the modification in parentheses, for example S(Phospho) or C(CAM). Common abbreviations are supported: M(Ox) for oxidation, S(P) for phosphorylation, K(Ac) for acetylation, K(Me) for methylation.
