Protein molecular weight calculator

What is protein molecular weight?

Protein molecular weight is the theoretical mass of a protein chain calculated from its amino acid sequence. It is reported in Daltons (Da) or kilodaltons (kDa), where 1 kDa equals 1,000 Da. Researchers use protein molecular weight to estimate SDS-PAGE band positions, plan purification workflows, compare constructs, and interpret intact-protein mass spectrometry data.

This protein molecular weight calculator converts one or more amino acid sequences into Da and kDa values. It accepts FASTA input, raw one-letter protein sequences, and CSV sequence tables. For typical values and examples such as GAPDH, beta-actin, GFP, and Cas9, see the guide to average protein size. For a broader sequence-property report that includes pI, extinction coefficients, instability index, aliphatic index, GRAVY, and atomic composition, use Protein Parameters.

The result is theoretical. Signal peptide cleavage, initiator methionine removal, post-translational modifications, disulfide bonds, cofactors, fusion tags, and glycosylation can all make the measured protein mass differ from the value calculated from the primary sequence alone.

How do you calculate protein molecular weight from an amino acid sequence?

Calculate protein molecular weight from an amino acid sequence by summing its residue masses and adding one terminal water molecule. Residue masses already account for the water lost during peptide-bond formation:

where $m_i$ is the residue mass of each amino acid and $m_{H_2O}$ is the terminal water mass. The default average water mass is 18.01528 Da. The monoisotopic water mass is 18.01056 Da.

For example, the average-mass calculation for Met-Ala-Gly is:

The calculator reports this sequence as 277.339 Da, or 0.277339 kDa.

Mass settings

Default residue masses

The default calculation uses average isotopic residue masses:

How do you use the protein molecular weight calculator?

Paste a FASTA record, a raw one-letter amino acid sequence, or a CSV table with a recognizable sequence column such as sequence, seq, or protein. Uploaded files can use .txt, .csv, .fasta, .fa, or .fas.

FASTA input can contain multiple proteins:

>Protein1
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGE
>Protein2
GIVEQCCTSICSLYQLENYCN

CSV input is useful when sequence IDs and sequences are already in a spreadsheet:

id,sequence
p1,MAG
p2,ACD

Before submitting, choose the mass type and any correction settings that match the protein you want to calculate. Leave disulfide bonds at 0 for reduced proteins or when the oxidation state is unknown. If a sequence contains ambiguous amino acid codes such as B, Z, J, or X, the calculator reports a warning because those residues require averaged or approximate masses.

The result is a deterministic sequence calculation, although it is sometimes called a protein molecular weight prediction. Unknown processing and modifications are the main sources of difference between the calculated mass and an experimentally measured value.

Understanding the results

Each input sequence produces one row in the results table:

Dalton values are displayed to three decimal places. Kilodalton values are displayed to six decimal places so small peptides and protein-size estimates remain readable in the same table.

For gel electrophoresis, kDa is usually the most convenient unit because protein ladders and apparent band sizes are labeled in kDa. For mass spectrometry and stoichiometry calculations, Da or g/mol values are often more direct; numerically, 1 Da per molecule corresponds to 1 g/mol.

Protein molecular weight examples

The examples in the calculator load complete FASTA inputs and the settings shown below. Each example runs locally in the browser and can be edited before recalculation.

Beta-lactoglobulin reference sequence

The beta-lactoglobulin example uses the 162-residue mature bovine chain published with the ExPASy Compute pI/Mw reference output. With Average mass, no initiator Met removal, and no disulfide correction, ProteinIQ returns 18,281.208 Da (18.281208 kDa). The ExPASy example reports 18,281.00 Da; the 0.208 Da difference is approximately 0.0011% and reflects the mass-table precision used by each calculation.

Human ubiquitin

The ubiquitin example contains the canonical 76-residue sequence. With Average mass and no corrections, the calculated molecular weight is 8,564.845 Da (8.564845 kDa). This compact example is useful for checking raw FASTA input and the default residue-mass calculation.

Oxidized insulin A-chain

The insulin example uses the 21-residue human A-chain, selects Monoisotopic mass, and applies one known intrachain disulfide bond. ProteinIQ returns 2,379.984 Da (2.379984 kDa). This is the mass of the isolated A-chain under those assumptions, not intact insulin: the complete hormone also contains the B-chain and two interchain disulfide bonds.

Scientific basis and references

The sequence calculation follows the residue-mass convention used by established protein-property tools: sum the amino acid residue masses, add one terminal water molecule, and subtract the mass of two hydrogen atoms for each specified disulfide bond. ProteinIQ does not infer mature-chain processing, oligomerization, or post-translational modifications.

• Gasteiger et al. describe the protein sequence analysis and molecular-weight calculations used by the ExPASy protein analysis tools.
• Average atomic-mass values are grounded in the IUPAC Commission on Isotopic Abundances and Atomic Weights report, Standard atomic weights of the elements 2021.
• The ExPASy ProtParam documentation provides the reference implementation context and explains important limits, including the absence of automatic post-translational modification and multimer handling.

Limitations and related tools

The molecular weight result represents the sequence and settings provided. It does not automatically add glycosylation, phosphorylation, acetylation, lipidation, heme, metals, fluorescent labels, affinity tags, or other modifications. Add those masses separately when they are known.

Disulfide correction only changes the mass by subtracting two hydrogens per bond. It does not predict which cysteines pair or whether a protein is reduced or oxidized under experimental conditions.

For related calculations, use Protein Parameters for a multi-property sequence report, extinction coefficient for A280-based concentration planning, and peptide mass for protease digestion and peptide mass spectrometry workflows.