Our peptide calculator is a convenient tool for scientists as a molecular weight peptide calculator, which can be used as an amino acid calculator as well. Additionally, the tool includes a hydrophobicity calculator, a net charge calculator at different pH, isoelectric point calculator and the hydrophilicity ratio.

All peptides possess, at minimum, two ionizable groups – the amino group of the N-terminal residue and the carboxyl group of the C-terminal residue. Additionally, some amino acids comprising the peptide may have ionizable side chain groups.

To calculate the charge on a peptide you must add up the charges from all the positively charged components like the N-terminal amino group, arginine, lysine, and histidine residues, and then subtract the charges from all the negatively charged components like the C-terminal carboxyl group, aspartic acid, glutamic acid, cysteine, and tyrosine residues. The specific charge values depend on the pH and use dissociation constant (pKa) values for each ionizable group.

It’s important to be able to predict the charge carried by a specific peptide in order to understand and control its physicochemical behavior, biological activity, and functional characteristics across various applications. For more guidance on peptide charges and properties, take a read of our peptide guide for beginners.

The overall or net charge on a peptide is simply the sum of the charges of every ionizable group in the peptide. 

The peptide net charge calculator determines the charge of a peptide sequence at a given pH. It utilizes the Henderson-Hasselbalch equation and pKa values of the ionizable groups. The net charge (Z) sums the contributions from positive charges of the N-terminus, arginine, lysine, and histidine residues, and negative charges of the C-terminus, aspartic acid, glutamic acid, cysteine, and tyrosine residues.

Z = ∑Ni/(1+10^(pKai-pH)) – ∑Nj/(1+10^(pH-pKaj))

Ni = Number of positively charged groups

Nj = Number of negatively charged groups

pKai, pKaj = pKa values of the ionizable groups

The calculator employs pKa values from Lehninger’s Principles of Biochemistry for maximum accuracy. View the net charge vs pH plot to analyze the charge behavior over the pH range. This helps predict solubility, folding, binding, and other critical biochemical properties.

The calculator is one of the most useful tool for the peptide chemist to calculate peptide molecular weight and more. With the calculator and its easy use, peptide chemists can have access to a molecular weight peptide calculator and amino acid calculator, the isoelectric point, a peptide net charge calculator at neutral pH, the average hydrophilicity, the percentage of hydrophilic amino acids, the plot of the net charge vs. pH and a hydrophobicity calculator displayed in a plot.

To calculate the different features of the peptide, the calculator will apply the formulas described below:

For the peptide molecular weight calculator and molecular weight amino acid calculator, the following formula is applied:

M: Molecular weight of the amino acid sequence

Mn: Molecular weight of the N-terminus

Mc: Molecular weight of the C-terminus

Ni: Number of the amino acid residues

Mi: Molecular weight of the amino acid residues

For the molecular weight amino acid calculator, you can enter the 1- or 3- letter code of the desired amino acid, and the tool will provide the value the same way it would calculate peptide molecular weight.

The peptide net charge calculator at a given pH is based on the formula below:

Z: Net charge of the peptide sequence

Ni: Number of arginine, lysine, and histidine residues and the N-terminus

pKai, pKa: values of the N-terminus and the arginine, lysine, and histidine residues

Nj: Number of of aspartic acid, glutamic acid, cysteine, and tyrosine residues and the C-terminus

pKaj, pKa: values of the C-terminus and the aspartic acid, glutamic acid, cysteine and tyrosine residues

pH: pH value

The pKa values for cysteine (pKa = 8.33), aspartic acid (pKa = 3.86), glutamic acid (pKa = 4.25), histidine (pKa = 6.0), lysine (pKa = 10.53), arginine (pKa = 12.48), tyrosine (pKa = 10.07), the N-terminal (pKa = 9.69) and C-terminal (pKa = 2.34) are based on the Principles of Biochemistry, Lehninger (1982).

The isoelectric point calculator provides the pH at which the peptide net charge is zero. The isoelectric point is calculated by approximation (accuracy ± 0.01).

The calculation of the average hydrophilicity of a peptide is based on the data from Hopp&Woods. The hydrophilicity value for each amino acid in the peptide sequence is indicated in a bar graph. The ratio of hydrophilic residues to total number of amino acids is reported in %.

For more information on the calculator, please read our details document.

To use our peptide calculator mass properties, enter the sequence or the amino acid using 1-letter or 3-letter amino acid codes and our calculator will provide the following physico-chemical properties of the sequence:

• Molecular weight
• Isoelectric point
• Net charge at neutral pH (7.0)
• Average hydrophilicity
• Ratio of hydrophilic residues to total number of residues
• Net charge vs. pH plot
• Hydrophobicity plot

With the calculator, it’s also possible to add N-terminal and C-terminal modifications to your peptide among Acetyl, Biotynil, pyroglutamic amino acid and amide.

Peptide purity and content are uniquely different quality measurements essential for many research applications. Peptide purity, analyzed via HPLC, represents the percentage of target peptide relative to peptide-based impurities.

Peptide content, however, measured through amino acid analysis or UV spectrophotometry, indicates the total peptide mass fraction versus non-peptide components like salts and moisture. These metrics work together to determine actual peptide quantity. Consider two samples with 95% purity: one with 80% content contains less target peptide than one with 95% content, despite identical purity values. As you can see, this distinction critically impacts the concentration calculation and, in turn, the experimental precision.

Peptide molecular weight is the total mass of a peptide, calculated by summing the molecular weights of its amino acid residues and terminal groups. It is a fundamental parameter in peptide chemistry, influencing the synthesis, purification and characterisation of peptides.

The peptide calculator provides an easy way to calculate molecular weight. By entering the sequence in either 1- or 3-letter codes, the tool applies the formula:

M = Σ(Mi × Ni) + Mn + Mc

Where:

• Mi is the molecular weight of each amino acid
• Ni is the number of residues
• Mn and Mc are the weights of the N- and C-terminal groups

By entering the peptide sequence in 1- or 3-letter codes, the calculator provides precise molecular weight values, streamlining analysis and supporting accurate research outcomes.

The isoelectric point (pI) is the pH at which a peptide or amino acid carries no net charge. This is important in understanding the peptide’s solubility, stability and interaction with other molecules.

The peptide calculator helps determine the isoelectric point by calculating the pH where the net charge of the peptide is zero. The process uses the pKa values of the peptide’s ionisable groups, such as the N- and C-termini and the side chains of specific amino acids (e.g., glutamic acid, histidine, lysine). The result is an approximate value, with a typical accuracy of ± 0.01.

This calculation provides insight into the peptide’s behavior in different pH environments, aiding in its purification and characterization.