What it does
Paste a protein sequence in one-letter codes (or open a FASTA file) and the calculator gives the numbers you need before an experiment:
- Molecular weight, both the average mass (what a balance or SDS-PAGE sees) and the monoisotopic mass (the lightest-isotope peak in mass spectrometry), plus the chemical formula.
- Isoelectric point (pI): the pH where the protein carries no net charge. Proteins are least soluble near their pI, and ion exchange depends on which side of it your buffer is.
- Net charge at any pH, with a curve of charge from pH 0 to 14.
- Extinction coefficient at 280 nm from the tryptophans, tyrosines and cystines, and the absorbance of a 1 mg/mL solution.
- Concentration from A280: type your blank-corrected reading and path length to get mg/mL and µM.
- Composition: how many of each amino acid, and their share.
Options
- pH for the charge: the pH of your buffer.
- Disulfide bonds: how many pairs of cysteines are joined. Each bond takes two hydrogens off the mass, adds to the extinction coefficient and removes two cysteines from the charge. Leave it at 0 for a reduced protein, such as in SDS-PAGE sample buffer with DTT.
- pKa values and extinction coefficients: the values used, which you can change. The default pKa values are fibub’s own rounded values. Every tool uses a slightly different set, so pI values from different tools often differ by 0.1 to 0.5. Type in another tool’s values to match it.
Worked example
Press Use the example. It is a made-up sequence of 120 amino acids (not a real protein). The results are:
- Average mass: 14,139.93 Da (14.14 kDa).
- Monoisotopic mass: 14,130.6520 Da.
- Formula: C626H932N176O183S9.
- pI: 7.38. At pH 7.0 the net charge is +0.68.
- Extinction coefficient: 36,440 M⁻¹ cm⁻¹ with all four cysteines reduced, or 36,690 with them as two cystines. A 1 mg/mL solution reads A280 = 2.577 in a 1 cm cell.
Type 0.5 as the absorbance: the concentration is 0.5 ÷ 36,440 = 13.72 µM, which is 0.194 mg/mL.
FAQ
Why does my pI differ from another tool’s? pKa values for the same amino acid differ between books and programs. The curve near the pI is often shallow, so small changes move it. Treat the pI as a guide to within a few tenths, and check by experiment if it matters.
Why is there no extinction coefficient? A protein with no tryptophan or tyrosine absorbs very little at 280 nm. Use a dye assay such as Bradford or BCA instead.
Does it include modifications? No. Phosphorylation, glycosylation and other changes add mass and change the charge. Signal peptides that are cut off are still counted unless you remove them from the sequence.
Is my sequence uploaded? No. Everything is worked out in your browser and works offline.
Where the numbers come from
- Masses and formula worked out by fibub from each amino acid's chemical formula with IUPAC standard atomic weights and exact isotope masses (general chemistry facts). Checked against Biopython: monoisotopic masses agree to better than 1 part in 100 million; average masses agree to about 1 part in 100,000 (Biopython uses older atomic weights).
- pKa values: fibub's own rounded, approximate values of the kind printed in biochemistry books, not copied from any one table, and editable on the page.
- Extinction coefficients: the conventional per-residue values for Trp, Tyr and cystine at 280 nm used across protein labs (general laboratory facts), editable on the page.
- The example sequence is made up for this tool; it is not a real protein.
Standard scientific values, such as constants, atomic weights and melting points, are facts found in every textbook; we name where ours were checked. If you are an author or publisher and want a value, a credit or a table changed or removed, tell us and we will act quickly.
Last updated 2026-11-09.