Peptide Molecular Weight Calculator
Calculate the molecular weight, isoelectric point (pI), and net charge of peptides from amino acid sequence. Supports FASTA format, terminal modifications, and mass-to-molar conversions.
Molecular weight calculations use average isotopic masses and standard pKa values. Results are approximations — always verify with experimental data or manufacturer specifications.
ℹ️ Frequently Asked Questions
How is peptide molecular weight calculated?
The molecular weight is computed by summing the residue masses of each amino acid in the sequence, then adding one water molecule (18.015 Da) to account for the free N- and C-termini.
MW = Σ(residue masses) + H₂O (18.015 Da)
Each residue mass equals the amino acid's molecular weight minus one water molecule lost during peptide bond formation. This calculator uses average isotopic masses, not monoisotopic values.
What is the difference between average and monoisotopic mass?
Average mass uses the weighted average of all naturally occurring isotopes (e.g., C = 12.011 Da). This is what you measure on most lab balances and is appropriate for weighing peptide samples.
Monoisotopic mass uses only the most abundant isotope of each element (e.g., C = 12.000 Da). This is what you see in high-resolution mass spectrometry.
This calculator uses average mass, which is standard for bench-side work such as solution preparation and dilution calculations.
How do N-terminal acetylation and C-terminal amidation affect MW?
N-terminal Acetylation replaces the free amino group (–NH₂) with an acetyl group (CH₃CO–NH–), adding +42.04 Da.
C-terminal Amidation replaces the free carboxyl group (–COOH) with an amide (–CONH₂), resulting in a net change of −0.98 Da (loss of OH, gain of NH₂).
These are among the most common synthetic peptide modifications, often used to improve stability and mimic native protein processing.
What is the isoelectric point (pI)?
The isoelectric point is the pH at which the peptide carries zero net charge. This calculator estimates pI using the Henderson-Hasselbalch equation and a binary search algorithm across pH 0–14.
At pH = pI → net charge ≈ 0
The pI depends on ionizable side chains (D, E, C, Y, H, K, R) as well as the free N- and C-terminal groups. Modifications like acetylation or amidation remove terminal ionizable groups and shift pI.
How do I convert μg to nmol for a peptide?
Use the formula:
nmol = (μg × 1000) / MW
For example, for 10 μg of a peptide with MW = 2,500 Da:
nmol = (10 × 1000) / 2500 = 4.0 nmol
This calculator performs this conversion automatically in the Mass / Mole Conversion section.
What is GRAVY and how is it calculated?
GRAVY (Grand Average of Hydropathy) is the mean hydropathy value of all amino acids in the sequence, using the Kyte-Doolittle scale.
GRAVY = Σ(hydropathy values) / sequence length
Positive GRAVY → hydrophobic peptide (e.g., membrane-spanning regions).
Negative GRAVY → hydrophilic peptide (e.g., soluble proteins).
Scale ranges from −4.5 (Arg, most hydrophilic) to +4.5 (Ile, most hydrophobic).