Sequence
Studio

Method

How each number is worked out

Masses

Each residue’s formula, plus one water, the end groups and any modification (a disulfide bond, a copper complex, a lipid side chain). Average mass uses standard atomic weights; monoisotopic mass uses each element’s most abundant isotope (¹²C, ¹H, ¹⁴N, ¹⁶O, ³²S, ⁶³Cu).

Charge and pI

Henderson–Hasselbalch with the EMBOSS pKa set. The isoelectric point is the pH where the net charge crosses zero. A peptide with no acidic group, or no basic group, never crosses it, so its pI shows as not defined. A copper complex is read as its free peptide.

Hydropathy

Kyte–Doolittle values per residue; GRAVY is their mean. Non-standard residues take the value of their closest standard residue; a lipid side chain isn’t counted.

Helical wheel

Each residue sits 100° on from the one before, as in an ideal alpha-helix seen end on, and the arrow points to the hydrophobic face, labeled with its moment, μH, from the same Kyte–Doolittle values. A single residue has no face, so no moment. Many short peptides never form a helix, so read it as a picture of the sequence, not of a structure. Reading a helical wheel

ESI ions

[M+H]⁺, [M+2H]²⁺ and so on, from the monoisotopic mass: the four strongest charge states expected from the peptide’s basic sites (free N-terminus, Lys, Arg, His) and its size, between 250 and 2,000 m/z (or [M+H]⁺ alone when lighter), for peptides up to 10 kDa. Larger proteins carry far more charges than this model allows, so none are listed for them. The product pages’ spectra all use the same model.

Extinction coefficient

Pace et al. (1995): tryptophan 5,500, tyrosine 1,490 and each cystine 125 M⁻¹ cm⁻¹ at 280 nm. 2Nal and Dmt absorb there as well but have no Pace value; a sequence with them reads as a lower bound, or as not calculated.