Introduction
This Peptide Mass Calculator helps you find the mass of any peptide or protein sequence. Type in your amino acid sequence, and the tool does the math for you. It calculates both monoisotopic mass and average mass, shows m/z values for common ion modes, and builds a full isotope distribution chart.
You can add modifications like phosphorylation, acetylation, and disulfide bonds. You can also pick an enzyme such as trypsin to digest your sequence into smaller peptide fragments. The tool lists every fragment with its mass, position, and number of missed cleavages. A color-coded map shows you exactly where each modification and cleavage site falls along your sequence.
Every calculation includes a step-by-step solution that breaks down how the final mass is reached. It starts with the sum of residue masses, adds water, applies your chosen modifications, and then converts to your selected ion mode. This makes it easy to check each part of the result and learn how peptide mass calculation works.
The calculator supports FASTA format, multiple sequences at once, N-terminal and C-terminal modifications, cysteine alkylation options, and over 30 built-in post-translational modifications. You can also enter custom mass deltas for any residue. When you are done, export your results as CSV, SVG, or PNG with one click.
How to Use Our Peptide Mass Calculator
Enter your peptide or protein sequence below, choose your settings, and this calculator will give you the molecular mass, m/z values, amino acid composition, digest fragments, and isotope distribution for each sequence.
Peptide / Protein Sequences: Type or paste one or more amino acid sequences into the text box, one per line. Use standard one-letter codes (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y). Add a > before a line to give it a FASTA header name. Type * after S, T, or Y to mark it as phosphorylated.
N-Terminal Modification: Pick a chemical change at the start of your peptide chain. Choose "None" if the N-terminus is free, or select an option like Acetyl, Formyl, or Biotin. Pick "N-PEG" to type in your own custom mass value.
C-Terminal Modification: Pick a chemical change at the end of your peptide chain. Choose "Free acid –OH" for a normal ending or "Amide –NH₂" for an amidated C-terminus.
Cysteine Treatment: Tell the calculator how cysteine residues were treated. Choose "None / Reduced" for free cysteines, or select a reagent like iodoacetamide or iodoacetic acid to add its mass shift to every cysteine.
Methionine Oxidation Toggle: Check this box to add an oxidation mass shift (+15.995 Da) to every methionine in your sequence.
Deamidation Toggle: Check this box to add a deamidation mass shift (+0.984 Da) to every asparagine in your sequence, as if each N changed to D.
Modification Library: Choose a post-translational or chemical modification from the dropdown list, such as phosphorylation, glycosylation, acetylation, or methylation. You can also pick "Custom" to type in your own modification name, mass delta, and target residues. Press "Add Modification" to apply it. All added modifications appear in the tracking table, where you can edit or delete them.
Location (Global or Local): Choose "Global" to apply a modification to every matching residue. Choose "Local" and type specific position numbers (like 3, 7, 22) to apply it only at those spots.
Subunit / Chain: If your protein has more than one chain, type a chain name here to label which chain the modification belongs to. Leave it blank for single-chain inputs.
Enzyme / Cleavage Rule: Pick the enzyme used to digest your protein. Choose "Trypsin" to cut after K and R (not before P), or select another enzyme like Lys C, Asp N, or Chymotrypsin. Choose "None" to skip digestion and see only the full protein mass.
Missed Cleavages: Set how many cut sites the enzyme is allowed to skip. A value of 0 means perfect digestion. Higher numbers show longer peptide fragments that result from incomplete cuts.
Minimum Mass and Maximum Mass: Set a mass range to filter the digest results. Only peptide fragments that fall within this range will appear in the output table.
Mass Type: Choose "Monoisotopic" to use the mass based on the most common isotope of each element. Choose "Average" to use the weighted average mass across all natural isotopes.
Ion Mode (m/z): Pick the ion charge state for your m/z output. Common choices are [M+H]⁺ for singly charged positive ions or [M+2H]²⁺ for doubly charged ions. Choose [M] for the neutral mass.
Results Sort Order: Choose how the fragment table is sorted. You can sort by peptide mass (ascending), by position along the chain, by sequence length, or in alphabetical order.
Instrument Resolution (Advanced): Click "Advanced Instrument Settings" to open this panel. Enter your mass spectrometer's resolution or pick a preset like Quadrupole, Ion Trap, QTOF, Orbitrap, or FT-ICR.
Calculate Button: Press "Calculate" to run the tool. Your results will show the full protein mass, molecular formula, amino acid composition, a step-by-step solution, a digest fragment table, a color-coded sequence map, and an isotope distribution chart. Use the export buttons to copy results, download a CSV file, or save the chart as SVG or PNG.
What Is a Peptide Mass Calculator?
A peptide mass calculator is a tool that finds the molecular weight of a peptide or protein based on its amino acid sequence. Peptides are short chains of amino acids, which are the building blocks of proteins. Each amino acid has a known mass. When amino acids link together, they lose one water molecule per bond. By adding up all the residue masses and accounting for that water loss — a basic stoichiometry calculation — you get the total mass of the peptide.
Why Peptide Mass Matters
Scientists use peptide masses to identify proteins in experiments like mass spectrometry. In mass spectrometry, a machine measures the mass-to-charge ratio (m/z) of molecules. To match what the machine reads to a real protein, researchers need to know the expected mass of each peptide fragment. This is how proteins are identified in biology, medicine, and drug research.
Monoisotopic vs. Average Mass
There are two ways to report a peptide's mass. Monoisotopic mass uses the most common isotope of each element (like carbon-12 and nitrogen-14). This gives the most precise value and is used with high-resolution instruments. Average mass uses the weighted average of all natural isotopes of each element. This is better for lower-resolution instruments or very large proteins.
Enzymatic Digestion
Proteins are often too large to measure directly. Scientists use enzymes like trypsin, which work best within specific pH ranges, to cut proteins into smaller peptide pieces. Trypsin cuts after lysine (K) and arginine (R) residues. Other enzymes cut at different spots. The resulting peptide fragments each have their own mass, and the pattern of these masses acts like a fingerprint to identify the protein.
Post-Translational Modifications
After a protein is made, the cell can attach small chemical groups to certain amino acids. These changes are called post-translational modifications (PTMs). Common examples include phosphorylation, which adds about 80 Da to serine, threonine, or tyrosine, and acetylation, which adds about 42 Da to lysine. Each modification shifts the peptide's mass by a specific amount. A good peptide mass calculator accounts for these shifts so the predicted mass matches what a mass spectrometer actually detects.
Ion Modes and Charge States
Mass spectrometers do not measure neutral mass directly. Instead, they measure charged ions. The most common ion in proteomics is [M+H]⁺, where one proton is added to the peptide. Larger peptides can pick up multiple protons, creating multiply charged ions like [M+2H]²⁺ or [M+3H]³⁺. The measured m/z value depends on both the mass and the number of charges, so choosing the right ion mode is important for accurate results.