Protein Molecular Weight Calculator

Calculate accurate molecular weights for protein sequences with customizable parameters for different applications in biochemistry and mass spectrometry.

Overview

The protein molecular weight calculator determines the exact mass of protein sequences by summing individual amino acid masses and accounting for chemical modifications that occur during protein synthesis and post-translational processing. This tool supports both theoretical calculations for biochemical analysis and precise mass determinations for mass spectrometry applications.

Input Methods

FASTA Sequence Input

Enter protein sequences directly in standard FASTA format or as plain amino acid sequences using single-letter codes (A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V). The calculator automatically processes sequences and ignores formatting characters.

>Example protein
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQ

PDB Structure Input

Fetch protein sequences directly from the Protein Data Bank using PDB IDs. Simply enter a valid PDB identifier (e.g., "1XYZ") and click "Fetch" to automatically retrieve the protein sequence from the structure file. This method ensures accurate sequence data from experimentally determined protein structures.

Calculation Parameters

Mass Type Selection

Average Mass (Default) Uses the weighted average of all naturally occurring isotopes for each element. This calculation method reflects the natural isotopic distribution found in biological samples and is the standard for most biochemical applications, protein purification, and general laboratory work.

Monoisotopic Mass Uses the exact mass of the most abundant isotope for each element (¹²C, ¹H, ¹⁴N, ¹⁶O, ³²S). This precise calculation is essential for mass spectrometry analysis, where isotopic peaks are resolved and the monoisotopic peak is typically measured. Required for accurate peptide identification and quantitative proteomics.

Chemical Modifications

None (Theoretical Mass) Calculates the basic molecular weight using only the standard amino acid residues without any chemical modifications. This represents the theoretical mass of the polypeptide chain.

Reduced Cysteines Assumes all cysteine residues remain in their free sulfhydryl form without disulfide bond formation. This is appropriate for proteins stored under reducing conditions or when disulfide bonds are chemically reduced for analysis.

Carboxymethylated Cysteines (+58 Da per Cys) Adds 58.005 Da to each cysteine residue to account for carboxymethylation, a common chemical modification used to permanently block cysteine residues and prevent disulfide bond formation during protein analysis. This modification is frequently used in proteomics sample preparation.

Phosphorylated (Estimate 10% of S/T/Y) Adds phosphate groups (+79.966 Da) to an estimated 10% of serine, threonine, and tyrosine residues. This provides an approximate molecular weight for proteins with typical phosphorylation patterns, though actual phosphorylation states vary significantly between proteins and conditions.

Peptide Bond Formation

Include Peptide Bond Water Loss (Recommended) Subtracts 18.015 Da (one water molecule) for each peptide bond formed during protein synthesis. A protein with n amino acids contains n-1 peptide bonds, so (n-1) × 18.015 Da is subtracted from the total. This calculation is essential for accurate molecular weight determination since individual amino acids lose water when joined by peptide bonds.

Exclude Water Loss Calculates molecular weight as the simple sum of individual amino acid masses without accounting for peptide bond formation. This method is rarely used for mat