What is a protein molecular weight calculator?
A protein molecular weight (MW) calculator estimates the mass of a protein or peptide from its amino acid sequence. The result is usually reported in Daltons (Da) or kilodaltons (kDa). This is a standard first step in protein characterization, SDS-PAGE planning, mass spectrometry prep, and recombinant expression workflows.
How this calculator works
The calculator sums residue masses for each amino acid in your sequence, then optionally adds one water molecule to represent the full neutral termini of the peptide chain. If you specify disulfide bonds, the tool subtracts the corresponding hydrogen loss.
Calculation model
- Total MW = sum of residue masses + terminal water (optional) - disulfide correction
- Disulfide correction = number of S-S bonds × mass of 2 hydrogens
- Supports both average and monoisotopic mass tables
Why protein MW is useful
- Estimate where your band should run on SDS-PAGE.
- Check expected mass before LC-MS or MALDI-MS analysis.
- Compare theoretical and observed mass for construct validation.
- Assess effects of mutations, truncations, or tags.
Tips for accurate results
1) Use the mature sequence
If your protein has a signal peptide, pro-peptide, transit peptide, or removable tag, calculate MW for the actual mature form too. Theoretical and experimental masses can differ significantly when processing events are involved.
2) Account for PTMs
Post-translational modifications (phosphorylation, glycosylation, acetylation, ubiquitination, etc.) can shift mass. This calculator gives the sequence-based baseline, not a full PTM-resolved mass profile.
3) Pick the right mass type
Use average mass for many routine biochemical estimates and monoisotopic mass when working with high-resolution mass spectrometry where isotopic composition matters.
Frequently asked questions
Does this include affinity tags like His-tags?
Only if you include those residues in your sequence input. Paste the exact amino acid string for the construct you want to model.
Can I paste FASTA format?
Yes. Header lines and non-sequence characters should be removed for best results, but line breaks and spaces are handled automatically.
What if I have unusual residues?
Standard and several ambiguous one-letter codes are supported. Any unrecognized characters are listed in the output so you can fix the sequence quickly.
Disclaimer: This tool is for educational and planning use. For publication-grade reporting, verify with your experimental method and sequence annotations.