Protein Molecular Weight Calculator

Enter your protein's amino acid sequence using single-letter codes to calculate the precise molecular weight in Daltons and kilodaltons (kDa).

Enter protein sequence using single-letter amino acid codes

MW = Σ(amino acid weights) - (n-1) × 18.015, where n = number of amino acids; Water (18.015 Da) is subtracted for each peptide bond formed
For insulin (30 aa): MVHLTPEEKSAVTALWGKVNVDEVGGEALGR; MW = 3495.63 Da = 3.50 kDa; 29 peptide bonds; Most abundant: Leucine (L): 5 (16.7%), Alanine (A): 4 (13.3%)

How is protein molecular weight calculated from amino acid sequence?

Protein molecular weight is calculated by summing the molecular weights of all amino acids in the sequence, then subtracting the weight of water molecules lost during peptide bond formation. Each peptide bond releases one water molecule (18.015 Da), so for a protein with n amino acids, you subtract (n-1) × 18.015 Da. The formula is: MW = Σ(amino acid weights) - (n-1) × 18.015, where n is the number of amino acids.

What are the molecular weights of common amino acids?

Here are the average molecular weights (in Daltons) for the 20 standard amino acids: Alanine (A): 89.09, Arginine (R): 174.20, Asparagine (N): 132.12, Aspartic acid (D): 133.10, Cysteine (C): 121.16, Glutamine (Q): 146.15, Glutamic acid (E): 147.13, Glycine (G): 75.07, Histidine (H): 155.16, Isoleucine (I): 131.17, Leucine (L): 131.17, Lysine (K): 146.19, Methionine (M): 149.21, Phenylalanine (F): 165.19, Proline (P): 115.13, Serine (S): 105.09, Threonine (T): 119.12, Tryptophan (W): 204.23, Tyrosine (Y): 181.19, Valine (V): 117.15.

What is the difference between average and monoisotopic molecular weight?

Average molecular weight uses the weighted average of all naturally occurring isotopes of each element. Monoisotopic weight uses only the most abundant isotope of each element (¹²C, ¹H, ¹⁴N, ¹⁶O, ³²S). For small peptides (< 1000 Da), the difference is small (~0.1-0.5 Da). For large proteins, the difference can be several Daltons. Mass spectrometry typically measures monoisotopic weight, while SDS-PAGE and other methods measure average weight.

Why does my calculated molecular weight differ from SDS-PAGE results?

Several factors can cause discrepancies: Post-translational modifications (glycosylation, phosphorylation) add weight not in the sequence calculation. SDS-PAGE has 5-10% error margin. Disulfide bonds affect migration. Highly charged or hydrophobic proteins migrate anomalously. Membrane proteins often run higher than calculated. Ensure your sequence is complete (including signal peptides if present) and consider if cleavage or modifications occur. For accurate MW, use mass spectrometry.