Mass Calculator

Enter peptide sequences under Peptide Sequences (raw or FASTA), one sequence per line. Lines starting with > (FASTA headers) are skipped.

Choose Mass Type:

• Average — average isotopic mass
• Monoisotopic — monoisotopic mass

Optionally tick one or more entries under Select PTMs or Alternative Amino Acids. MassCalc calculates the base peptide mass plus every combination of the PTMs you select (for example, choosing two PTMs yields unmodified, each PTM alone, and both together).

Click Compute Masses to run the calculation. Results appear in a table with sequence, applied PTMs (or None), and total mass.

Use Download CSV to export the table. The CSV can be uploaded on the MS Analysis (Peptide Mass Matcher) page to match masses against the database.

Use Refresh to clear the form and start over.

Input limits (enforced on submit):

• Up to 50 sequences per request
• Each sequence: 2–500 residues; standard amino acid letters (X allowed)
• Up to 12 PTMs selected; every combination is computed per sequence
• At most 10000 result rows per request (reduce sequences or PTMs if you hit this limit)
• PTMs without a mass difference for the selected mass type are skipped (you will see a warning)