Sequence Molecular Mass Calculator

Sequence Molecular Mass Calculator

Calculating Biopolymer Molecular Mass

The molecular mass (or molecular weight) of a biopolymer like a protein or nucleic acid is the sum of the masses of its constituent monomers (amino acids or nucleotides), adjusted for the chemical bonds formed between them. This value is crucial for various biochemical analyses and techniques, particularly mass spectrometry, where the measured mass helps identify the molecule.

Peptide Mass

For peptides, the mass is calculated by summing the average residue masses of each amino acid in the sequence. The residue mass already accounts for the loss of a water molecule during peptide bond formation. Finally, the mass of a single water molecule (18.015 Da) is added back to account for the free -H on the N-terminus and the free -OH on the C-terminus.

Oligonucleotide Mass (Single-Stranded)

For single-stranded DNA or RNA, the mass is typically calculated by summing the masses of the individual nucleotide monophosphates. A correction factor (-61.96 Da in this calculator, representing a phosphate group difference) is subtracted because the linked nucleotides form a phosphodiester backbone. An additional mass (+159.0 Da, H₃P₂O₆) can be added if the sequence represents, for example, an mRNA molecule with a 5' triphosphate end.

Frequently Asked Questions

What is the difference between average and monoisotopic mass?

• Average Mass: Calculated using the weighted average atomic masses of elements based on their natural isotopic abundance (e.g., Carbon ≈ 12.011 Da). This calculator uses average masses, which is suitable for larger molecules or when comparing to lower-resolution experimental data.
• Monoisotopic Mass: Calculated using the exact mass of the most abundant isotope of each element (e.g., Carbon = 12.000 Da exactly). This value is more relevant for high-resolution mass spectrometry where individual isotopic peaks can be resolved.

How do post-translational modifications (PTMs) affect protein mass?

PTMs are chemical modifications that occur to a protein after it has been synthesized. Common examples include phosphorylation, glycosylation, methylation, and acetylation. These modifications add or remove chemical groups, thereby changing the protein's overall molecular mass. This calculator only considers the mass based on the primary amino acid sequence and does not account for any PTMs.

What are the units Da and g/mol?

Dalton (Da) and grams per mole (g/mol) are essentially interchangeable units for molecular mass. One Dalton is defined as 1/12th the mass of a neutral carbon-12 atom. The numerical value of a substance's mass in Daltons is the same as its molar mass in grams per mole.