calculate molecular weight of protein sequence: Accurate Protein Mass and Composition Calculator
This single-column professional tool lets you calculate molecular weight of protein sequence instantly, review assumptions, copy results, and explore how peptide composition impacts mass for lab-ready reporting.
Protein Molecular Weight Calculator
Enter a protein sequence using one-letter amino acid codes to calculate molecular weight of protein sequence with average masses and realistic terminal modifications.
Only standard amino acids A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y are accepted.
Invalid sequence. Use only standard amino acid letters.
Positive or negative mass shift for N-terminus (e.g., acetylation 42.0106 Da).
Enter a valid number for N-terminus modification.
Positive or negative mass shift for C-terminus (e.g., amidation -0.9840 Da).
Enter a valid number for C-terminus modification.
Average Mass
Monoisotopic Mass
Select average or monoisotopic mass to calculate molecular weight of protein sequence with the appropriate assumption.
Please select a mass type.
Primary Result: Total Molecular Weight
0.000 Da
Real-time
Total Residues:0
Total Residue Mass:0.000 Da
Water Loss (peptide bonds):0.000 Da
Avg Residue Mass:0.000 Da
Modifications Applied:0.000 Da
Formula: Sum of amino acid masses − (number of peptide bonds × 18.01528 Da) + N-terminus modification + C-terminus modification = total mass to calculate molecular weight of protein sequence.
Cumulative mass Per-residue mass
Chart updates live to visualize cumulative progression and per-residue contributions when you calculate molecular weight of protein sequence.
Amino Acid
Count
Mass Contribution (Da)
Composition table shows how each residue drives the total when you calculate molecular weight of protein sequence.
What is {primary_keyword}?
{primary_keyword} is the process of summing amino acid masses, peptide bond water losses, and terminal modifications to express the molecular weight of a protein chain. Scientists, bioinformaticians, and finance teams budgeting reagents use {primary_keyword} to validate sequences before synthesis or ordering peptides.
Labs need {primary_keyword} to check whether mass specs align with theoretical values. Portfolio managers in biotech also rely on {primary_keyword} to estimate reagent costs tied to peptide length. A misconception is that {primary_keyword} is a simple addition; in reality, peptide bonds remove water and terminal chemistry changes totals, so skipping these steps produces errors.
{primary_keyword} Formula and Mathematical Explanation
To {primary_keyword}, add the mass of every amino acid using average or monoisotopic constants, subtract 18.01528 Da for each peptide bond, and add any terminal mass shifts. The count of peptide bonds equals residues minus one. Selecting mass type changes every residue mass used in {primary_keyword}.
Derivation: Total residue mass = Σ(mass of each residue). Peptide bond correction = (residue count − 1) × 18.01528 Da. Total molecular weight = total residue mass − peptide bond correction + N-term mod + C-term mod. This complete sequence-aware arithmetic ensures {primary_keyword} is accurate for synthesis and LC-MS prep.
Variable
Meaning
Unit
Typical Range
ResidueCount
Number of amino acids in sequence used in {primary_keyword}
count
5–2000
ResidueMass
Sum of individual residue masses in {primary_keyword}
Da
500–300000
PeptideBonds
ResidueCount − 1 adjusting {primary_keyword}
count
4–1999
WaterLoss
PeptideBonds × 18.01528 removing mass in {primary_keyword}
Da
72–36000
NTermMod
N-terminus mass shift
Da
-200 to 500
CTermMod
C-terminus mass shift
Da
-200 to 500
Variables central to {primary_keyword} and their typical planning ranges.
Practical Examples (Real-World Use Cases)
Example 1: Short synthetic peptide
Sequence: ACDEFGHIK. Selecting average masses, N-term acetylation 42.0106 Da, C-term amidation -0.9840 Da. {primary_keyword} gives a total near 1070 Da. Output guides procurement quantities and confirms LC-MS reference for quality control. The balanced correction shows how {primary_keyword} prevents under-ordering solvents.
Example 2: Enzyme domain fragment
Sequence: MKTLLILTCLVA. No modifications, monoisotopic masses. {primary_keyword} returns about 1321 Da. This enables bioprocess teams to price isotope-labeled amino acids correctly and maintain accuracy in budgets linked to {primary_keyword} results.
How to Use This {primary_keyword} Calculator
Step 1: Paste your sequence in the Protein Sequence box. Step 2: Enter any terminal mass shifts. Step 3: Choose average or monoisotopic masses. Results update instantly to keep {primary_keyword} transparent. Read the primary result in Da, check intermediate masses, and use Copy Results to move {primary_keyword} outputs into lab notebooks or finance sheets.
Interpretation: If average residue mass is high, {primary_keyword} indicates hydrophobic compositions; plan solvents accordingly. When water loss is large, long chains demand careful desalting to keep {primary_keyword} aligned with mass spectrometry tolerance.
Key Factors That Affect {primary_keyword} Results
1) Mass type choice: Average vs monoisotopic shifts every component within {primary_keyword}. 2) Terminal chemistry: Amidation or acetylation moves totals and budgeting anchored to {primary_keyword}. 3) Sequence length: More peptide bonds amplify water loss in {primary_keyword}. 4) Amino acid mix: Heavy residues like W and Y increase {primary_keyword}; lighter G lowers it. 5) Post-translational modifications: Phosphorylation or glycosylation adds significant Da, altering {primary_keyword} planning for reagents. 6) Sample charge state assumptions: Though not changing mass, charge expectations influence how {primary_keyword} guides MS calibration. 7) Isotopic labeling: 13C or 15N raises residue masses, directly impacting {primary_keyword} economics. 8) Hydration state: Desalting and lyophilization ensure measured mass matches {primary_keyword} predictions.
Frequently Asked Questions (FAQ)
Does {primary_keyword} include disulfide bonds? Only if you keep cysteines unmodified; add -2.0156 Da per bond manually for exact {primary_keyword}.
Should I pick average or monoisotopic? Use monoisotopic for high-res MS; use average for bulk reagent costing tied to {primary_keyword}.
Can I enter non-standard amino acids? Not in this tool; {primary_keyword} supports the 20 canonical residues for accuracy.
What if my sequence is empty? The calculator flags it because {primary_keyword} needs at least one residue.
How are peptide bonds handled? Each bond removes water, so {primary_keyword} subtracts 18.01528 Da per bond.
Do terminal charges change mass? Charge does not change mass, so {primary_keyword} ignores charge but applies terminal modifications.
Is there a limit to sequence length? Very long chains increase computation, but {primary_keyword} scales to thousands of residues for planning.
Why do measured masses differ slightly? Solvent adducts and calibration affect readings; compare to {primary_keyword} with those factors in mind.
Related Tools and Internal Resources
{related_keywords}: Quick access to related peptide budgeting insights supporting {primary_keyword} decisions.
{related_keywords}: Detailed guide on solvent planning grounded in {primary_keyword} outputs.
{related_keywords}: Calibration checklist aligning MS settings with {primary_keyword} expectations.
{related_keywords}: Finance worksheet linking procurement to {primary_keyword} forecasts.